Daily Papers

Traditional molecular string representations, such as SMILES, often pose challenges for AI-driven molecular design due to their non-sequential depiction of molecular substructures. To address this issue, we introduce Sequential Attachment-based Fragment Embedding (SAFE), a novel line notation for chemical structures. SAFE reimagines SMILES strings as an unordered sequence of interconnected fragment blocks while maintaining full compatibility with existing SMILES parsers. It streamlines complex generative tasks, including scaffold decoration, fragment linking, polymer generation, and scaffold hopping, while facilitating autoregressive generation for fragment-constrained design, thereby eliminating the need for intricate decoding or graph-based models. We demonstrate the effectiveness of SAFE by training an 87-million-parameter GPT2-like model on a dataset containing 1.1 billion SAFE representations. Through extensive experimentation, we show that our SAFE-GPT model exhibits versatile and robust optimization performance. SAFE opens up new avenues for the rapid exploration of chemical space under various constraints, promising breakthroughs in AI-driven molecular design.

3D fragment reassembly aims to recover the rigid poses of unordered fragment point clouds or meshes in a common object coordinate system to reconstruct the complete shape. The problem becomes particularly challenging as the number of fragments grows, since the target shape is unknown and fragments provide weak semantic cues. Existing end-to-end approaches are prone to cascading failures due to unreliable contact reasoning, most notably inaccurate fragment adjacencies. To address this, we propose Structure-Aware Reassembly (SARe), a generative framework with SARe-Gen for Euclidean-space assembly generation and SARe-Refine for inference-time refinement, with explicit contact modeling. SARe-Gen jointly predicts fracture-surface token probabilities and an inter-fragment contact graph to localize contact regions and infer candidate adjacencies. It adopts a query-point-based conditioning scheme and extracts aligned local geometric tokens at query locations from a frozen geometry encoder, yielding queryable structural representations without additional structural pretraining. We further introduce an inference-time refinement stage, SARe-Refine. By verifying candidate contact edges with geometric-consistency checks, it selects reliable substructures and resamples the remaining uncertain regions while keeping verified parts fixed, leading to more stable and consistent assemblies in the many-fragment regime. We evaluate SARe across three settings, including synthetic fractures, simulated fractures from scanned real objects, and real physically fractured scans. The results demonstrate state-of-the-art performance, with more graceful degradation and higher success rates as the fragment count increases in challenging large-scale reassembly.

Fragment-based drug discovery has been an effective paradigm in early-stage drug development. An open challenge in this area is designing linkers between disconnected molecular fragments of interest to obtain chemically-relevant candidate drug molecules. In this work, we propose DiffLinker, an E(3)-equivariant 3D-conditional diffusion model for molecular linker design. Given a set of disconnected fragments, our model places missing atoms in between and designs a molecule incorporating all the initial fragments. Unlike previous approaches that are only able to connect pairs of molecular fragments, our method can link an arbitrary number of fragments. Additionally, the model automatically determines the number of atoms in the linker and its attachment points to the input fragments. We demonstrate that DiffLinker outperforms other methods on the standard datasets generating more diverse and synthetically-accessible molecules. Besides, we experimentally test our method in real-world applications, showing that it can successfully generate valid linkers conditioned on target protein pockets.

Pairwise compatibility calculation is at the core of most fragments-reconstruction algorithms, in particular those designed to solve different types of the jigsaw puzzle problem. However, most existing approaches fail, or aren't designed to deal with fragments of realistic geometric properties one encounters in real-life puzzles. And in all other cases, compatibility methods rely strongly on the restricted shapes of the fragments. In this paper, we propose an efficient hybrid (geometric and pictorial) approach for computing the optimal alignment for pairs of fragments, without any assumptions about their shapes, dimensions, or pictorial content. We introduce a new image fragments dataset generated via a novel method for image fragmentation and a formal erosion model that mimics real-world archaeological erosion, along with evaluation metrics for the compatibility task. We then embed our proposed compatibility into an archaeological puzzle-solving framework and demonstrate state-of-the-art neighborhood-level precision and recall on the RePAIR 2D dataset, directly reflecting compatibility performance improvements.

Entity linking (mapping ambiguous mentions in text to entities in a knowledge base) is a foundational step in tasks such as knowledge graph construction, question-answering, and information extraction. Our method, LELA, is a modular coarse-to-fine approach that leverages the capabilities of large language models (LLMs), and works with different target domains, knowledge bases and LLMs, without any fine-tuning phase. Our experiments across various entity linking settings show that LELA is highly competitive with fine-tuned approaches, and substantially outperforms the non-fine-tuned ones.

Recent GraphRAG methods integrate graph structures into text indexing and retrieval, using knowledge graph triples to connect text chunks, thereby improving retrieval coverage and precision. However, we observe that treating text chunks as the basic unit of knowledge representation rigidly groups multiple atomic facts together, limiting the flexibility and adaptability needed to support diverse retrieval scenarios. Additionally, triple-based entity linking is sensitive to relation-extraction errors, which can lead to missing or incorrect reasoning paths and ultimately hurt retrieval accuracy. To address these issues, we propose the Atom-Entity Graph, a more precise and reliable architecture for knowledge representation and indexing. In our approach, knowledge is stored as knowledge atoms, namely individual, self-contained units of factual information, rather than coarse-grained text chunks. This allows knowledge elements to be flexibly reassembled without mutual interference, thereby enabling seamless alignment with diverse query perspectives. Edges between entities simply indicate whether a relationship exists. By combining personalized PageRank with relevance-based filtering, we maintain accurate entity connections and improve the reliability of reasoning. Theoretical analysis and experiments on five public benchmarks show that the proposed AtomicRAG algorithm outperforms strong RAG baselines in retrieval accuracy and reasoning robustness. Code: https://github.com/7HHHHH/AtomicRAG.

We tackle the image reassembly problem with wide space between the fragments, in such a way that the patterns and colors continuity is mostly unusable. The spacing emulates the erosion of which the archaeological fragments suffer. We crop-square the fragments borders to compel our algorithm to learn from the content of the fragments. We also complicate the image reassembly by removing fragments and adding pieces from other sources. We use a two-step method to obtain the reassemblies: 1) a neural network predicts the positions of the fragments despite the gaps between them; 2) a graph that leads to the best reassemblies is made from these predictions. In this paper, we notably investigate the effect of branch-cut in the graph of reassemblies. We also provide a comparison with the literature, solve complex images reassemblies, explore at length the dataset, and propose a new metric that suits its specificities. Keywords: image reassembly, jigsaw puzzle, deep learning, graph, branch-cut, cultural heritage

Event linking connects event mentions in text with relevant nodes in a knowledge base (KB). Prior research in event linking has mainly borrowed methods from entity linking, overlooking the distinct features of events. Compared to the extensively explored entity linking task, events have more complex structures and can be more effectively distinguished by examining their associated arguments. Moreover, the information-rich nature of events leads to the scarcity of event KBs. This emphasizes the need for event linking models to identify and classify event mentions not in the KB as ``out-of-KB,'' an area that has received limited attention. In this work, we tackle these challenges by introducing an argument-aware approach. First, we improve event linking models by augmenting input text with tagged event argument information, facilitating the recognition of key information about event mentions. Subsequently, to help the model handle ``out-of-KB'' scenarios, we synthesize out-of-KB training examples from in-KB instances through controlled manipulation of event arguments. Our experiment across two test datasets showed significant enhancements in both in-KB and out-of-KB scenarios, with a notable 22% improvement in out-of-KB evaluations.

Many applications require grouping instances contained in diverse document datasets into classes. Most widely used methods do not employ deep learning and do not exploit the inherently multimodal nature of documents. Notably, record linkage is typically conceptualized as a string-matching problem. This study develops CLIPPINGS, (Contrastively Linking Pooled Pre-trained Embeddings), a multimodal framework for record linkage. CLIPPINGS employs end-to-end training of symmetric vision and language bi-encoders, aligned through contrastive language-image pre-training, to learn a metric space where the pooled image-text representation for a given instance is close to representations in the same class and distant from representations in different classes. At inference time, instances can be linked by retrieving their nearest neighbor from an offline exemplar embedding index or by clustering their representations. The study examines two challenging applications: constructing comprehensive supply chains for mid-20th century Japan through linking firm level financial records - with each firm name represented by its crop in the document image and the corresponding OCR - and detecting which image-caption pairs in a massive corpus of historical U.S. newspapers came from the same underlying photo wire source. CLIPPINGS outperforms widely used string matching methods by a wide margin and also outperforms unimodal methods. Moreover, a purely self-supervised model trained on only image-OCR pairs also outperforms popular string-matching methods without requiring any labels.

Schema linking -- the process of aligning natural language questions with database schema elements -- is a critical yet underexplored component of Text-to-SQL systems. While recent methods have focused primarily on improving SQL generation, they often neglect the retrieval of relevant schema elements, which can lead to hallucinations and execution failures. In this work, we propose a context-aware bidirectional schema retrieval framework that treats schema linking as a standalone problem. Our approach combines two complementary strategies: table-first retrieval followed by column selection, and column-first retrieval followed by table selection. It is further augmented with techniques such as question decomposition, keyword extraction, and keyphrase extraction. Through comprehensive evaluations on challenging benchmarks such as BIRD and Spider, we demonstrate that our method significantly improves schema recall while reducing false positives. Moreover, SQL generation using our retrieved schema consistently outperforms full-schema baselines and closely approaches oracle performance, all without requiring query refinement. Notably, our method narrows the performance gap between full and perfect schema settings by 50\%. Our findings highlight schema linking as a powerful lever for enhancing Text-to-SQL accuracy and efficiency.

On the WikiSQL benchmark, state-of-the-art text-to-SQL systems typically take a slot-filling approach by building several dedicated models for each type of slots. Such modularized systems are not only complex butalso of limited capacity for capturing inter-dependencies among SQL clauses. To solve these problems, this paper proposes a novel extraction-linking approach, where a unified extractor recognizes all types of slot mentions appearing in the question sentence before a linker maps the recognized columns to the table schema to generate executable SQL queries. Trained with automatically generated annotations, the proposed method achieves the first place on the WikiSQL benchmark.

Schema linking is a critical bottleneck in applying existing Text-to-SQL models to real-world, large-scale, multi-database environments. Through error analysis, we identify two major challenges in schema linking: (1) Database Retrieval: accurately selecting the target database from a large schema pool, while effectively filtering out irrelevant ones; and (2) Schema Item Grounding: precisely identifying the relevant tables and columns within complex and often redundant schemas for SQL generation. Based on these, we introduce LinkAlign, a novel framework tailored for large-scale databases with thousands of fields. LinkAlign comprises three key steps: multi-round semantic enhanced retrieval and irrelevant information isolation for Challenge 1, and schema extraction enhancement for Challenge 2. Each stage supports both Agent and Pipeline execution modes, enabling balancing efficiency and performance via modular design. To enable more realistic evaluation, we construct AmbiDB, a synthetic dataset designed to reflect the ambiguity of real-world schema linking. Experiments on widely-used Text-to-SQL benchmarks demonstrate that LinkAlign consistently outperforms existing baselines on all schema linking metrics. Notably, it improves the overall Text-to-SQL pipeline and achieves a new state-of-the-art score of 33.09% on the Spider 2.0-Lite benchmark using only open-source LLMs, ranking first on the leaderboard at the time of submission. The codes are available at https://github.com/Satissss/LinkAlign

Visual Entity Linking (VEL) is a crucial task for achieving fine-grained visual understanding, matching objects within images (visual mentions) to entities in a knowledge base. Previous VEL tasks rely on textual inputs, but writing queries for complex scenes can be challenging. Visual inputs like clicks or bounding boxes offer a more convenient alternative. Therefore, we propose a new task, Pixel-Level Visual Entity Linking (PL-VEL), which uses pixel masks from visual inputs to refer to objects, supplementing reference methods for VEL. To facilitate research on this task, we have constructed the MaskOVEN-Wiki dataset through an entirely automatic reverse region-entity annotation framework. This dataset contains over 5 million annotations aligning pixel-level regions with entity-level labels, which will advance visual understanding towards fine-grained. Moreover, as pixel masks correspond to semantic regions in an image, we enhance previous patch-interacted attention with region-interacted attention by a visual semantic tokenization approach. Manual evaluation results indicate that the reverse annotation framework achieved a 94.8% annotation success rate. Experimental results show that models trained on this dataset improved accuracy by 18 points compared to zero-shot models. Additionally, the semantic tokenization method achieved a 5-point accuracy improvement over the trained baseline.

Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision (tt KRISS) for biomedical entity linking, by leveraging readily available domain knowledge. In training, it generates self-supervised mention examples on unlabeled text using a domain ontology and trains a contextual encoder using contrastive learning. For inference, it samples self-supervised mentions as prototypes for each entity and conducts linking by mapping the test mention to the most similar prototype. Our approach can easily incorporate entity descriptions and gold mention labels if available. We conducted extensive experiments on seven standard datasets spanning biomedical literature and clinical notes. Without using any labeled information, our method produces tt KRISSBERT, a universal entity linker for four million UMLS entities that attains new state of the art, outperforming prior self-supervised methods by as much as 20 absolute points in accuracy.

CLIP has enabled new and exciting joint vision-language applications, one of which is open-vocabulary segmentation, which can locate any segment given an arbitrary text query. In our research, we ask whether it is possible to discover semantic segments without any user guidance in the form of text queries or predefined classes, and label them using natural language automatically? We propose a novel problem zero-guidance segmentation and the first baseline that leverages two pre-trained generalist models, DINO and CLIP, to solve this problem without any fine-tuning or segmentation dataset. The general idea is to first segment an image into small over-segments, encode them into CLIP's visual-language space, translate them into text labels, and merge semantically similar segments together. The key challenge, however, is how to encode a visual segment into a segment-specific embedding that balances global and local context information, both useful for recognition. Our main contribution is a novel attention-masking technique that balances the two contexts by analyzing the attention layers inside CLIP. We also introduce several metrics for the evaluation of this new task. With CLIP's innate knowledge, our method can precisely locate the Mona Lisa painting among a museum crowd. Project page: https://zero-guide-seg.github.io/.

Schema linking is a crucial step in Text-to-SQL pipelines, which translate natural language queries into SQL. The goal of schema linking is to retrieve relevant tables and columns (signal) while disregarding irrelevant ones (noise). However, imperfect schema linking can often exclude essential columns needed for accurate query generation. In this work, we revisit the need for schema linking when using the latest generation of large language models (LLMs). We find empirically that newer models are adept at identifying relevant schema elements during generation, without the need for explicit schema linking. This allows Text-to-SQL pipelines to bypass schema linking entirely and instead pass the full database schema to the LLM, eliminating the risk of excluding necessary information. Furthermore, as alternatives to schema linking, we propose techniques that improve Text-to-SQL accuracy without compromising on essential schema information. Our approach achieves 71.83\% execution accuracy on the BIRD benchmark, ranking first at the time of submission.

Entity Linking (EL) is an essential and challenging task in natural language processing that seeks to link some text representing an entity within a document or sentence with its corresponding entry in a dictionary or knowledge base. Most existing approaches focus on creating elaborate contextual models that look for clues the words surrounding the entity-text to help solve the linking problem. Although these fine-tuned language models tend to work, they can be unwieldy, difficult to train, and do not transfer well to other domains. Fortunately, Large Language Models (LLMs) like GPT provide a highly-advanced solution to the problems inherent in EL models, but simply naive prompts to LLMs do not work well. In the present work, we define ChatEL, which is a three-step framework to prompt LLMs to return accurate results. Overall the ChatEL framework improves the average F1 performance across 10 datasets by more than 2%. Finally, a thorough error analysis shows many instances with the ground truth labels were actually incorrect, and the labels predicted by ChatEL were actually correct. This indicates that the quantitative results presented in this paper may be a conservative estimate of the actual performance. All data and code are available as an open-source package on GitHub at https://github.com/yifding/In_Context_EL.

Hashtags are semantico-syntactic constructs used across various social networking and microblogging platforms to enable users to start a topic specific discussion or classify a post into a desired category. Segmenting and linking the entities present within the hashtags could therefore help in better understanding and extraction of information shared across the social media. However, due to lack of space delimiters in the hashtags (e.g #nsavssnowden), the segmentation of hashtags into constituent entities ("NSA" and "Edward Snowden" in this case) is not a trivial task. Most of the current state-of-the-art social media analytics systems like Sentiment Analysis and Entity Linking tend to either ignore hashtags, or treat them as a single word. In this paper, we present a context aware approach to segment and link entities in the hashtags to a knowledge base (KB) entry, based on the context within the tweet. Our approach segments and links the entities in hashtags such that the coherence between hashtag semantics and the tweet is maximized. To the best of our knowledge, no existing study addresses the issue of linking entities in hashtags for extracting semantic information. We evaluate our method on two different datasets, and demonstrate the effectiveness of our technique in improving the overall entity linking in tweets via additional semantic information provided by segmenting and linking entities in a hashtag.

We introduce FragAtlas-62M, a specialized foundation model trained on the largest fragment dataset to date. Built on the complete ZINC-22 fragment subset comprising over 62 million molecules, it achieves unprecedented coverage of fragment chemical space. Our GPT-2 based model (42.7M parameters) generates 99.90% chemically valid fragments. Validation across 12 descriptors and three fingerprint methods shows generated fragments closely match the training distribution (all effect sizes < 0.4). The model retains 53.6% of known ZINC fragments while producing 22% novel structures with practical relevance. We release FragAtlas-62M with training code, preprocessed data, documentation, and model weights to accelerate adoption.

The open-vocabulary image segmentation task involves partitioning images into semantically meaningful segments and classifying them with flexible text-defined categories. The recent vision-based foundation models such as the Segment Anything Model (SAM) have shown superior performance in generating class-agnostic image segments. The main challenge in open-vocabulary image segmentation now lies in accurately classifying these segments into text-defined categories. In this paper, we introduce the Universal Segment Embedding (USE) framework to address this challenge. This framework is comprised of two key components: 1) a data pipeline designed to efficiently curate a large amount of segment-text pairs at various granularities, and 2) a universal segment embedding model that enables precise segment classification into a vast range of text-defined categories. The USE model can not only help open-vocabulary image segmentation but also facilitate other downstream tasks (e.g., querying and ranking). Through comprehensive experimental studies on semantic segmentation and part segmentation benchmarks, we demonstrate that the USE framework outperforms state-of-the-art open-vocabulary segmentation methods.

In this paper, we propose a learning-based image fragment pair-searching and -matching approach to solve the challenging restoration problem. Existing works use rule-based methods to match similar contour shapes or textures, which are always difficult to tune hyperparameters for extensive data and computationally time-consuming. Therefore, we propose a neural network that can effectively utilize neighbor textures with contour shape information to fundamentally improve performance. First, we employ a graph-based network to extract the local contour and texture features of fragments. Then, for the pair-searching task, we adopt a linear transformer-based module to integrate these local features and use contrastive loss to encode the global features of each fragment. For the pair-matching task, we design a weighted fusion module to dynamically fuse extracted local contour and texture features, and formulate a similarity matrix for each pair of fragments to calculate the matching score and infer the adjacent segment of contours. To faithfully evaluate our proposed network, we created a new image fragment dataset through an algorithm we designed that tears complete images into irregular fragments. The experimental results show that our proposed network achieves excellent pair-searching accuracy, reduces matching errors, and significantly reduces computational time. Details, sourcecode, and data are available in our supplementary material.

Graph-based Retrieval-Augmented Generation (GraphRAG) mitigates hallucinations in Large Language Models (LLMs) by grounding them in structured knowledge. However, current GraphRAG methods are constrained by a prevailing build-then-reason paradigm, which relies on a static, pre-constructed Knowledge Graph (KG). This paradigm faces two critical challenges. First, the KG's inherent incompleteness often breaks reasoning paths. Second, the graph's low signal-to-noise ratio introduces distractor facts, presenting query-relevant but misleading knowledge that disrupts the reasoning process. To address these challenges, we argue for a reason-and-construct paradigm and propose Relink, a framework that dynamically builds a query-specific evidence graph. To tackle incompleteness, Relink instantiates required facts from a latent relation pool derived from the original text corpus, repairing broken paths on the fly. To handle misleading or distractor facts, Relink employs a unified, query-aware evaluation strategy that jointly considers candidates from both the KG and latent relations, selecting those most useful for answering the query rather than relying on their pre-existence. This empowers Relink to actively discard distractor facts and construct the most faithful and precise evidence path for each query. Extensive experiments on five Open-Domain Question Answering benchmarks show that Relink achieves significant average improvements of 5.4\% in EM and 5.2\% in F1 over leading GraphRAG baselines, demonstrating the superiority of our proposed framework.

Referring segmentation aims to segment the target objects in images or videos based on the textual query. Despite remarkable progress over the past years, existing works always assume that the user-provided queries are already precise and clear. However, this assumption is impractical. In real-world scenarios, it is unrealistic to expect all users to thoroughly review their visual content and carefully ensure their queries are unique and unambiguous. When encountering such cases, existing segmentation models tend to arbitrarily guess the user preferences, often resulting in undesired outcomes. To address this limitation, we propose IC-Seg, a novel agentic framework that proactively clarifies user intent through multi-turn conversation before segmentation. To effectively incentivize this capability, we further introduce Hi-GRPO, a new hierarchical optimization strategy that injects dense and informative supervision signals at the trajectory, turn, and step levels. This strategy encourages efficient intent clarification, effectively eliminating redundant interactions and improving overall dialogue quality. For evaluation, we establish Ambi-RVOS, a referring video object segmentation benchmark with ambiguous user queries. Extensive experiments demonstrate that IC-Seg not only outperforms existing methods by a large margin in resolving ambiguous queries, but also maintains state-of-the-art performance on standard reasoning segmentation benchmarks. Code and data will be released at https://github.com/iSEE-Laboratory/IC-Seg.

Cross-modal entity linking refers to the ability to align entities and their attributes across different modalities. While cross-modal entity linking is a fundamental skill needed for real-world applications such as multimodal code generation, fake news detection, or scene understanding, it has not been thoroughly studied in the literature. In this paper, we introduce a new task and benchmark to address this gap. Our benchmark, MATE, consists of 5.5k evaluation instances featuring visual scenes aligned with their textual representations. To evaluate cross-modal entity linking performance, we design a question-answering task that involves retrieving one attribute of an object in one modality based on a unique attribute of that object in another modality. We evaluate state-of-the-art Vision-Language Models (VLMs) and humans on this task, and find that VLMs struggle significantly compared to humans, particularly as the number of objects in the scene increases. Our analysis also shows that, while chain-of-thought prompting can improve VLM performance, models remain far from achieving human-level proficiency. These findings highlight the need for further research in cross-modal entity linking and show that MATE is a strong benchmark to support that progress.

In Natural Language Processing, entity linking (EL) has centered around Wikipedia, but yet remains underexplored for the job market domain. Disambiguating skill mentions can help us get insight into the current labor market demands. In this work, we are the first to explore EL in this domain, specifically targeting the linkage of occupational skills to the ESCO taxonomy (le Vrang et al., 2014). Previous efforts linked coarse-grained (full) sentences to a corresponding ESCO skill. In this work, we link more fine-grained span-level mentions of skills. We tune two high-performing neural EL models, a bi-encoder (Wu et al., 2020) and an autoregressive model (Cao et al., 2021), on a synthetically generated mention--skill pair dataset and evaluate them on a human-annotated skill-linking benchmark. Our findings reveal that both models are capable of linking implicit mentions of skills to their correct taxonomy counterparts. Empirically, BLINK outperforms GENRE in strict evaluation, but GENRE performs better in loose evaluation (accuracy@k).

Assessing the degree of similarity of code fragments is crucial for ensuring software quality, but it remains challenging due to the need to capture the deeper semantic aspects of code. Traditional syntactic methods often fail to identify these connections. Recent advancements have addressed this challenge, though they frequently sacrifice interpretability. To improve this, we present an approach aiming to improve the transparency of the similarity assessment by using GraphCodeBERT, which enables the identification of semantic relationships between code fragments. This approach identifies similar code fragments and clarifies the reasons behind that identification, helping developers better understand and trust the results. The source code for our implementation is available at https://www.github.com/jorge-martinez-gil/graphcodebert-interpretability.

Entity linking is a prominent thread of research focused on structured data creation by linking spans of text to an ontology or knowledge source. We revisit the use of structured prediction for entity linking which classifies each individual input token as an entity, and aggregates the token predictions. Our system, called SpEL (Structured prediction for Entity Linking) is a state-of-the-art entity linking system that uses some new ideas to apply structured prediction to the task of entity linking including: two refined fine-tuning steps; a context sensitive prediction aggregation strategy; reduction of the size of the model's output vocabulary, and; we address a common problem in entity-linking systems where there is a training vs. inference tokenization mismatch. Our experiments show that we can outperform the state-of-the-art on the commonly used AIDA benchmark dataset for entity linking to Wikipedia. Our method is also very compute efficient in terms of number of parameters and speed of inference.

Knowledge Graph-based Question Answering (KGQA) plays a pivotal role in complex reasoning tasks but remains constrained by two persistent challenges: the structural heterogeneity of Knowledge Graphs(KGs) often leads to semantic mismatch during retrieval, while existing reasoning path retrieval methods lack a global structural perspective. To address these issues, we propose Structure-Tracing Evidence Mining (STEM), a novel framework that reframes multi-hop reasoning as a schema-guided graph search task. First, we design a Semantic-to-Structural Projection pipeline that leverages KG structural priors to decompose queries into atomic relational assertions and construct an adaptive query schema graph. Subsequently, we execute globally-aware node anchoring and subgraph retrieval to obtain the final evidence reasoning graph from KG. To more effectively integrate global structural information during the graph construction process, we design a Triple-Dependent GNN (Triple-GNN) to generate a Global Guidance Subgraph (Guidance Graph) that guides the construction. STEM significantly improves both the accuracy and evidence completeness of multi-hop reasoning graph retrieval, and achieves State-of-the-Art performance on multiple multi-hop benchmarks.

Tasking machines with understanding receipts can have important applications such as enabling detailed analytics on purchases, enforcing expense policies, and inferring patterns of purchase behavior on large collections of receipts. In this paper, we focus on the task of Named Entity Linking (NEL) of scanned receipt line items; specifically, the task entails associating shorthand text from OCR'd receipts with a knowledge base (KB) of grocery products. For example, the scanned item "STO BABY SPINACH" should be linked to the catalog item labeled "Simple Truth Organic Baby Spinach". Experiments that employ a variety of Information Retrieval techniques in combination with statistical phrase detection shows promise for effective understanding of scanned receipt data.

Entity linking aims to link ambiguous mentions to their corresponding entities in a knowledge base. One of the key challenges comes from insufficient labeled data for specific domains. Although dense retrievers have achieved excellent performance on several benchmarks, their performance decreases significantly when only a limited amount of in-domain labeled data is available. In such few-shot setting, we revisit the sparse retrieval method, and propose an ELECTRA-based keyword extractor to denoise the mention context and construct a better query expression. For training the extractor, we propose a distant supervision method to automatically generate training data based on overlapping tokens between mention contexts and entity descriptions. Experimental results on the ZESHEL dataset demonstrate that the proposed method outperforms state-of-the-art models by a significant margin across all test domains, showing the effectiveness of keyword-enhanced sparse retrieval.

Recent advances in Retrieval-Augmented Generation (RAG) have shifted from simple vector similarity to structure-aware approaches like HippoRAG, which leverage Knowledge Graphs (KGs) and Personalized PageRank (PPR) to capture multi-hop dependencies. However, these methods suffer from a "Static Graph Fallacy": they rely on fixed transition probabilities determined during indexing. This rigidity ignores the query-dependent nature of edge relevance, causing semantic drift where random walks are diverted into high-degree "hub" nodes before reaching critical downstream evidence. Consequently, models often achieve high partial recall but fail to retrieve the complete evidence chain required for multi-hop queries. To address this, we propose CatRAG, Context-Aware Traversal for robust RAG, a framework that builds on the HippoRAG 2 architecture and transforms the static KG into a query-adaptive navigation structure. We introduce a multi-faceted framework to steer the random walk: (1) Symbolic Anchoring, which injects weak entity constraints to regularize the random walk; (2) Query-Aware Dynamic Edge Weighting, which dynamically modulates graph structure, to prune irrelevant paths while amplifying those aligned with the query's intent; and (3) Key-Fact Passage Weight Enhancement, a cost-efficient bias that structurally anchors the random walk to likely evidence. Experiments across four multi-hop benchmarks demonstrate that CatRAG consistently outperforms state of the art baselines. Our analysis reveals that while standard Recall metrics show modest gains, CatRAG achieves substantial improvements in reasoning completeness, the capacity to recover the entire evidence path without gaps. These results reveal that our approach effectively bridges the gap between retrieving partial context and enabling fully grounded reasoning. Resources are available at https://github.com/kwunhang/CatRAG.

Retrieving external knowledge and prompting large language models with relevant information is an effective paradigm to enhance the performance of question-answering tasks. Previous research typically handles paragraphs from external documents in isolation, resulting in a lack of context and ambiguous references, particularly in multi-document and complex tasks. To overcome these challenges, we propose a new retrieval framework IIER, that leverages Inter-chunk Interactions to Enhance Retrieval. This framework captures the internal connections between document chunks by considering three types of interactions: structural, keyword, and semantic. We then construct a unified Chunk-Interaction Graph to represent all external documents comprehensively. Additionally, we design a graph-based evidence chain retriever that utilizes previous paths and chunk interactions to guide the retrieval process. It identifies multiple seed nodes based on the target question and iteratively searches for relevant chunks to gather supporting evidence. This retrieval process refines the context and reasoning chain, aiding the large language model in reasoning and answer generation. Extensive experiments demonstrate that IIER outperforms strong baselines across four datasets, highlighting its effectiveness in improving retrieval and reasoning capabilities.

When completing knowledge-intensive tasks, humans sometimes need not just an answer but also a corresponding reference passage for auxiliary reading. Previous methods required obtaining pre-segmented article chunks through additional retrieval models. This paper explores leveraging the parameterized knowledge stored during the pre-training phase of large language models (LLMs) to independently recall reference passage from any starting position. We propose a two-stage framework that simulates the scenario of humans recalling easily forgotten references. Initially, the LLM is prompted to recall document title identifiers to obtain a coarse-grained document set. Then, based on the acquired coarse-grained document set, it recalls fine-grained passage. In the two-stage recall process, we use constrained decoding to ensure that content outside of the stored documents is not generated. To increase speed, we only recall a short prefix in the second stage, then locate its position to retrieve a complete passage. Experiments on KILT knowledge-sensitive tasks have verified that LLMs can independently recall reference passage location in various task forms, and the obtained reference significantly assist downstream tasks.

Semi-structured documents integrate diverse interleaved data elements (e.g., tables, charts, hierarchical paragraphs) arranged in various and often irregular layouts. These documents are widely observed across domains and account for a large portion of real-world data. However, existing methods struggle to support natural language question answering over these documents due to three main technical challenges: (1) The elements extracted by techniques like OCR are often fragmented and stripped of their original semantic context, making them inadequate for analysis. (2) Existing approaches lack effective representations to capture hierarchical structures within documents (e.g., associating tables with nested chapter titles) and to preserve layout-specific distinctions (e.g., differentiating sidebars from main content). (3) Answering questions often requires retrieving and aligning relevant information scattered across multiple regions or pages, such as linking a descriptive paragraph to table cells located elsewhere in the document. To address these issues, we propose MoDora, an LLM-powered system for semi-structured document analysis. First, we adopt a local-alignment aggregation strategy to convert OCR-parsed elements into layout-aware components, and conduct type-specific information extraction for components with hierarchical titles or non-text elements. Second, we design the Component-Correlation Tree (CCTree) to hierarchically organize components, explicitly modeling inter-component relations and layout distinctions through a bottom-up cascade summarization process. Finally, we propose a question-type-aware retrieval strategy that supports (1) layout-based grid partitioning for location-based retrieval and (2) LLM-guided pruning for semantic-based retrieval. Experiments show MoDora outperforms baselines by 5.97%-61.07% in accuracy. The code is at https://github.com/weAIDB/MoDora.

Some Question Answering (QA) systems rely on knowledge bases (KBs) to provide accurate answers. Entity Linking (EL) plays a critical role in linking natural language mentions to KB entries. However, most existing EL methods are designed for long contexts and do not perform well on short, ambiguous user questions in QA tasks. We propose an entity linking agent for QA, based on a Large Language Model that simulates human cognitive workflows. The agent actively identifies entity mentions, retrieves candidate entities, and makes decision. To verify the effectiveness of our agent, we conduct two experiments: tool-based entity linking and QA task evaluation. The results confirm the robustness and effectiveness of our agent.

Tracing connections between historical texts is an important part of intertextual research, enabling scholars to reconstruct the virtual library of a writer and identify the sources influencing their creative process. These intertextual links manifest in diverse forms, ranging from direct verbatim quotations to subtle allusions and paraphrases disguised by morphological variation. Language models offer a promising path forward due to their capability of capturing semantic similarity beyond lexical overlap. However, the development of new methods for this task is held back by the scarcity of standardized benchmarks and easy-to-use datasets. We address this gap by introducing Loci Similes, a benchmark for Latin intertextuality detection comprising of a curated dataset of ~172k text segments containing 545 expert-verified parallels linking Late Antique authors to a corpus of classical authors. Using this data, we establish baselines for retrieval and classification of intertextualities with state-of-the-art LLMs.

Information Retrieval (IR) methods aim to identify relevant documents in response to a given query, which have gained remarkable attention due to their successful application in various natural language tasks. However, existing approaches typically consider only the textual information within the documents, which overlooks the fact that documents can contain multiple modalities, including texts, images, and tables. Further, they often segment each long document into multiple discrete passages for embedding, preventing them from capturing the overall document context and interactions between paragraphs. We argue that these two limitations lead to suboptimal document representations for retrieval. In this work, to address them, we aim to produce more comprehensive and nuanced document representations by holistically embedding documents interleaved with different modalities. Specifically, we achieve this by leveraging the capability of recent vision-language models that enable the processing and integration of text, images, and tables into a unified format and representation. Moreover, to mitigate the information loss from segmenting documents into passages, instead of representing and retrieving passages individually, we further merge the representations of segmented passages into one single document representation, while we additionally introduce a reranking strategy to decouple and identify the relevant passage within the document if necessary. Then, through extensive experiments on diverse information retrieval scenarios considering both the textual and multimodal queries, we show that our approach substantially outperforms relevant baselines, thanks to the consideration of the multimodal information interleaved within the documents in a unified way.

Recent advances in zero-shot referring image segmentation (RIS), driven by models such as the Segment Anything Model (SAM) and CLIP, have made substantial progress in aligning visual and textual information. Despite these successes, the extraction of precise and high-quality mask region representations remains a critical challenge, limiting the full potential of RIS tasks. In this paper, we introduce a training-free, hybrid global-local feature extraction approach that integrates detailed mask-specific features with contextual information from the surrounding area, enhancing mask region representation. To further strengthen alignment between mask regions and referring expressions, we propose a spatial guidance augmentation strategy that improves spatial coherence, which is essential for accurately localizing described areas. By incorporating multiple spatial cues, this approach facilitates more robust and precise referring segmentation. Extensive experiments on standard RIS benchmarks demonstrate that our method significantly outperforms existing zero-shot RIS models, achieving substantial performance gains. We believe our approach advances RIS tasks and establishes a versatile framework for region-text alignment, offering broader implications for cross-modal understanding and interaction. Code is available at https://github.com/fhgyuanshen/HybridGL .

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

Scientific artifacts such as models and datasets are foundations for research. With the rapid growth of platforms like HuggingFace, researchers now have access to a large number of artifacts. Yet, a key challenge remains: how can we automatically discover the state-of-the-art (SOTA) model for a given dataset by fully leveraging existing artifacts? We formalize this task as automatic SOTA discovery by modeling HuggingFace as an artifact graph, where nodes are models/datasets and edges represent evaluations. We propose ArtifactLinker, a two-stage framework: (1) ranking promising unobserved model--dataset links using Graph Neural Networks (GNNs) or graph-augmented Large Language Models (LLMs), and (2) verifying top-ranked links via coding experiments with LLM-based agents. We further introduce a benchmark named ArtifactBench with 14,053 artifacts and 51,337 relations to evaluate the performance of both stages. Results show that (1) graph structures between existing artifacts are effective for missing link prediction; (2) end-to-end ranking and verification with ArtifactLinker help discover potential SOTA results and research insights.

The contour estimation of transparent fragments is very important for autonomous reassembly, especially in the fields of precision optical instrument repair, cultural relic restoration, and identification of other precious device broken accidents. Different from general intact transparent objects, the contour estimation of transparent fragments face greater challenges due to strict optical properties, irregular shapes and edges. To address this issue, a general transparent fragments contour estimation framework based on visual-tactile fusion is proposed in this paper. First, we construct the transparent fragment dataset named TransFrag27K, which includes a multiscene synthetic data of broken fragments from multiple types of transparent objects, and a scalable synthetic data generation pipeline. Secondly, we propose a visual grasping position detection network named TransFragNet to identify, locate and segment the sampling grasping position. And, we use a two-finger gripper with Gelsight Mini sensors to obtain reconstructed tactile information of the lateral edge of the fragments. By fusing this tactile information with visual cues, a visual-tactile fusion material classifier is proposed. Inspired by the way humans estimate a fragment's contour combining vision and touch, we introduce a general transparent fragment contour estimation framework based on visual-tactile fusion, demonstrates strong performance in real-world validation. Finally, a multi-dimensional similarity metrics based contour matching and reassembly algorithm is proposed, providing a reproducible benchmark for evaluating visual-tactile contour estimation and fragment reassembly. The experimental results demonstrate the validity of the proposed framework. The dataset and codes are available at https://github.com/Keithllin/Transparent-Fragments-Contour-Estimation.

Zero-shot entity linking (EL) aims at aligning entity mentions to unseen entities to challenge the generalization ability. Previous methods largely focus on the candidate retrieval stage and ignore the essential candidate ranking stage, which disambiguates among entities and makes the final linking prediction. In this paper, we propose a read-and-select (ReS) framework by modeling the main components of entity disambiguation, i.e., mention-entity matching and cross-entity comparison. First, for each candidate, the reading module leverages mention context to output mention-aware entity representations, enabling mention-entity matching. Then, in the selecting module, we frame the choice of candidates as a sequence labeling problem, and all candidate representations are fused together to enable cross-entity comparison. Our method achieves the state-of-the-art performance on the established zero-shot EL dataset ZESHEL with a 2.55% micro-average accuracy gain, with no need for laborious multi-phase pre-training used in most of the previous work, showing the effectiveness of both mention-entity and cross-entity interaction.

Entity Linking (EL) models are well-trained at mapping mentions to their corresponding entities according to a given context. However, EL models struggle to disambiguate long-tail entities due to their limited training data. Meanwhile, large language models (LLMs) are more robust at interpreting uncommon mentions. Yet, due to a lack of specialized training, LLMs suffer at generating correct entity IDs. Furthermore, training an LLM to perform EL is cost-intensive. Building upon these insights, we introduce LLM-Augmented Entity Linking LLMAEL, a plug-and-play approach to enhance entity linking through LLM data augmentation. We leverage LLMs as knowledgeable context augmenters, generating mention-centered descriptions as additional input, while preserving traditional EL models for task specific processing. Experiments on 6 standard datasets show that the vanilla LLMAEL outperforms baseline EL models in most cases, while the fine-tuned LLMAEL set the new state-of-the-art results across all 6 benchmarks.

While Contrastive Language-Image Pre-training (CLIP) has advanced open-vocabulary predictions, its performance on semantic segmentation remains suboptimal. This shortfall primarily stems from its spatial-invariant semantic features and constrained resolution. While previous adaptations addressed spatial invariance semantic by modifying the self-attention in CLIP's image encoder, the issue of limited resolution remains unexplored. Different from previous segment-then-splice methods that segment sub-images via a sliding window and splice the results, we introduce a splice-then-segment paradigm that incorporates Segment-Anything Model (SAM) to tackle the resolution issue since SAM excels at extracting fine-grained semantic correlations from high-resolution images. Specifically, we introduce Trident, a training-free framework that first splices features extracted by CLIP and DINO from sub-images, then leverages SAM's encoder to create a correlation matrix for global aggregation, enabling a broadened receptive field for effective segmentation. Besides, we propose a refinement strategy for CLIP's coarse segmentation outputs by transforming them into prompts for SAM, further enhancing the segmentation performance. Trident achieves a significant improvement in the mIoU across eight benchmarks compared with the current SOTA, increasing from 44.4 to 48.6.Code is available at https://github.com/YuHengsss/Trident.

Entity linking (EL) aligns textual mentions with their corresponding entities in a knowledge base, facilitating various applications such as semantic search and question answering. Recent advances in multimodal entity linking (MEL) have shown that combining text and images can reduce ambiguity and improve alignment accuracy. However, most existing MEL methods overlook the rich structural information available in the form of knowledge-graph (KG) triples. In this paper, we propose KGMEL, a novel framework that leverages KG triples to enhance MEL. Specifically, it operates in three stages: (1) Generation: Produces high-quality triples for each mention by employing vision-language models based on its text and images. (2) Retrieval: Learns joint mention-entity representations, via contrastive learning, that integrate text, images, and (generated or KG) triples to retrieve candidate entities for each mention. (3) Reranking: Refines the KG triples of the candidate entities and employs large language models to identify the best-matching entity for the mention. Extensive experiments on benchmark datasets demonstrate that KGMEL outperforms existing methods. Our code and datasets are available at: https://github.com/juyeonnn/KGMEL.

Multimodal entity linking (MEL) aims to link ambiguous mentions within multimodal contexts to corresponding entities in a multimodal knowledge base. Most existing approaches to MEL are based on representation learning or vision-and-language pre-training mechanisms for exploring the complementary effect among multiple modalities. However, these methods suffer from two limitations. On the one hand, they overlook the possibility of considering negative samples from the same modality. On the other hand, they lack mechanisms to capture bidirectional cross-modal interaction. To address these issues, we propose a Multi-level Matching network for Multimodal Entity Linking (M3EL). Specifically, M3EL is composed of three different modules: (i) a Multimodal Feature Extraction module, which extracts modality-specific representations with a multimodal encoder and introduces an intra-modal contrastive learning sub-module to obtain better discriminative embeddings based on uni-modal differences; (ii) an Intra-modal Matching Network module, which contains two levels of matching granularity: Coarse-grained Global-to-Global and Fine-grained Global-to-Local, to achieve local and global level intra-modal interaction; (iii) a Cross-modal Matching Network module, which applies bidirectional strategies, Textual-to-Visual and Visual-to-Textual matching, to implement bidirectional cross-modal interaction. Extensive experiments conducted on WikiMEL, RichpediaMEL, and WikiDiverse datasets demonstrate the outstanding performance of M3EL when compared to the state-of-the-art baselines.

Mathematical symbols and descriptions appear in various forms across document section boundaries without explicit markup. In this paper, we present a new large-scale dataset that emphasizes extracting symbols and descriptions in scientific documents. Symlink annotates scientific papers of 5 different domains (i.e., computer science, biology, physics, mathematics, and economics). Our experiments on Symlink demonstrate the challenges of the symbol-description linking task for existing models and call for further research effort in this area. We will publicly release Symlink to facilitate future research.

Tool-use capability is a fundamental component of LLM agents, enabling them to interact with external systems through structured function calls. However, existing research exhibits inconsistent interaction representations, largely overlooks the structural distribution of tool-use trajectories, and relies on incompatible evaluation benchmarks. We present UniToolCall, a unified framework for tool learning that standardizes the entire pipeline from toolset construction and dataset generation to evaluation. The framework curates a large tool pool of 22k+ tools and constructs a hybrid training corpus of 390k+ instances by combining 10 standardized public datasets with structurally controlled synthetic trajectories. It explicitly models diverse interaction patterns, including single-hop vs. multi-hop and single-turn vs. multi-turn, while capturing both serial and parallel execution structures. To support coherent multi-turn reasoning, we further introduce an Anchor Linkage mechanism that enforces cross-turn dependencies. Furthermore, we convert 7 public benchmarks into a unified Query--Action--Observation--Answer (QAOA) representation with fine-grained evaluation at the function-call, turn, and conversation levels. Experiments show that fine-tuning Qwen3-8B on our dataset substantially improves tool-use performance. Under the distractor-heavy Hybrid-20 setting, achieves 93.0% single-turn Strict Precision, outperforming commercial models including GPT, Gemini, and Claude.

Referring 3D Segmentation is a visual-language task that segments all points of the specified object from a 3D point cloud described by a sentence of query. Previous works perform a two-stage paradigm, first conducting language-agnostic instance segmentation then matching with given text query. However, the semantic concepts from text query and visual cues are separately interacted during the training, and both instance and semantic labels for each object are required, which is time consuming and human-labor intensive. To mitigate these issues, we propose a novel Referring 3D Segmentation pipeline, Label-Efficient and Single-Stage, dubbed LESS, which is only under the supervision of efficient binary mask. Specifically, we design a Point-Word Cross-Modal Alignment module for aligning the fine-grained features of points and textual embedding. Query Mask Predictor module and Query-Sentence Alignment module are introduced for coarse-grained alignment between masks and query. Furthermore, we propose an area regularization loss, which coarsely reduces irrelevant background predictions on a large scale. Besides, a point-to-point contrastive loss is proposed concentrating on distinguishing points with subtly similar features. Through extensive experiments, we achieve state-of-the-art performance on ScanRefer dataset by surpassing the previous methods about 3.7% mIoU using only binary labels. Code is available at https://github.com/mellody11/LESS.

Relation linking is essential to enable question answering over knowledge bases. Although there are various efforts to improve relation linking performance, the current state-of-the-art methods do not achieve optimal results, therefore, negatively impacting the overall end-to-end question answering performance. In this work, we propose a novel approach for relation linking framing it as a generative problem facilitating the use of pre-trained sequence-to-sequence models. We extend such sequence-to-sequence models with the idea of infusing structured data from the target knowledge base, primarily to enable these models to handle the nuances of the knowledge base. Moreover, we train the model with the aim to generate a structured output consisting of a list of argument-relation pairs, enabling a knowledge validation step. We compared our method against the existing relation linking systems on four different datasets derived from DBpedia and Wikidata. Our method reports large improvements over the state-of-the-art while using a much simpler model that can be easily adapted to different knowledge bases.

Linking information across sources is fundamental to a variety of analyses in social science, business, and government. While large language models (LLMs) offer enormous promise for improving record linkage in noisy datasets, in many domains approximate string matching packages in popular softwares such as R and Stata remain predominant. These packages have clean, simple interfaces and can be easily extended to a diversity of languages. Our open-source package LinkTransformer aims to extend the familiarity and ease-of-use of popular string matching methods to deep learning. It is a general purpose package for record linkage with transformer LLMs that treats record linkage as a text retrieval problem. At its core is an off-the-shelf toolkit for applying transformer models to record linkage with four lines of code. LinkTransformer contains a rich repository of pre-trained transformer semantic similarity models for multiple languages and supports easy integration of any transformer language model from Hugging Face or OpenAI. It supports standard functionality such as blocking and linking on multiple noisy fields. LinkTransformer APIs also perform other common text data processing tasks, e.g., aggregation, noisy de-duplication, and translation-free cross-lingual linkage. Importantly, LinkTransformer also contains comprehensive tools for efficient model tuning, to facilitate different levels of customization when off-the-shelf models do not provide the required accuracy. Finally, to promote reusability, reproducibility, and extensibility, LinkTransformer makes it easy for users to contribute their custom-trained models to its model hub. By combining transformer language models with intuitive APIs that will be familiar to many users of popular string matching packages, LinkTransformer aims to democratize the benefits of LLMs among those who may be less familiar with deep learning frameworks.

Text-to-SQL systems powered by Large Language Models have excelled on academic benchmarks but struggle in complex enterprise environments. The primary limitation lies in their reliance on static schema representations, which fails to resolve semantic ambiguity and scale effectively to large, complex databases. To address this, we propose APEX-SQL, an Agentic Text-to-SQL Framework that shifts the paradigm from passive translation to agentic exploration. Our framework employs a hypothesis-verification loop to ground model reasoning in real data. In the schema linking phase, we use logical planning to verbalize hypotheses, dual-pathway pruning to reduce the search space, and parallel data profiling to validate column roles against real data, followed by global synthesis to ensure topological connectivity. For SQL generation, we introduce a deterministic mechanism to retrieve exploration directives, allowing the agent to effectively explore data distributions, refine hypotheses, and generate semantically accurate SQLs. Experiments on BIRD (70.65% execution accuracy) and Spider 2.0-Snow (51.01% execution accuracy) demonstrate that APEX-SQL outperforms competitive baselines with reduced token consumption. Further analysis reveals that agentic exploration acts as a performance multiplier, unlocking the latent reasoning potential of foundation models in enterprise settings. Ablation studies confirm the critical contributions of each component in ensuring robust and accurate data analysis.

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

Large language model (LLM)-enhanced recommendation models inject LLM representations into backbone recommenders to exploit rich item text without inference-time LLM cost. However, we find that existing LLM-enhanced methods significantly hinder the optimization of backbone models, resulting in high training losses that are difficult to reduce. To address it, we establish a comprehensive theoretical analysis of local optimization curvature and identify two key causes: 1) large norm disparity and 2) semantic-collaboration misaligned angular clustering of LLM representations. Guided by these insights, we propose Training-Friendly LLM-Enhanced Recommender (TF-LLMER), a lightweight framework with two key components. First, we highlight the necessity of item embedding normalization to eliminate norm-driven instability and achieve provable control over optimization conditioning. Second, we introduce Rec-PCA, a recommendation-aware dimensionality reduction method that injects collaborative structure into the representation transformation to resolve semantic-collaboration misaligned angular clustering. It jointly optimizes semantic information retention and alignment with an item-item co-occurrence graph constructed from interaction histories. The graph captures collaborative structure, and alignment is promoted by penalizing total variation over the graph. Both theory and extensive experiments demonstrate that TF-LLMER significantly outperforms state-of-the-art methods. Our code is available at https://github.com/woriazzc/TF-LLMER.

A conventional approach to entity linking is to first find mentions in a given document and then infer their underlying entities in the knowledge base. A well-known limitation of this approach is that it requires finding mentions without knowing their entities, which is unnatural and difficult. We present a new model that does not suffer from this limitation called EntQA, which stands for Entity linking as Question Answering. EntQA first proposes candidate entities with a fast retrieval module, and then scrutinizes the document to find mentions of each candidate with a powerful reader module. Our approach combines progress in entity linking with that in open-domain question answering and capitalizes on pretrained models for dense entity retrieval and reading comprehension. Unlike in previous works, we do not rely on a mention-candidates dictionary or large-scale weak supervision. EntQA achieves strong results on the GERBIL benchmarking platform.

Multimodal entity linking plays a crucial role in a wide range of applications. Recent advances in large language model-based methods have become the dominant paradigm for this task, effectively leveraging both textual and visual modalities to enhance performance. Despite their success, these methods still face two challenges, including unnecessary incorporation of image data in certain scenarios and the reliance only on a one-time extraction of visual features, which can undermine their effectiveness and accuracy. To address these challenges, we propose a novel LLM-based framework for the multimodal entity linking task, called Intra- and Inter-modal Collaborative Reflections. This framework prioritizes leveraging text information to address the task. When text alone is insufficient to link the correct entity through intra- and inter-modality evaluations, it employs a multi-round iterative strategy that integrates key visual clues from various aspects of the image to support reasoning and enhance matching accuracy. Extensive experiments on three widely used public datasets demonstrate that our framework consistently outperforms current state-of-the-art methods in the task, achieving improvements of 3.2%, 5.1%, and 1.6%, respectively. Our code is available at https://github.com/ziyan-xiaoyu/I2CR/.

Automated assembly of 3D fractures is essential in orthopedics, archaeology, and our daily life. This paper presents Jigsaw, a novel framework for assembling physically broken 3D objects from multiple pieces. Our approach leverages hierarchical features of global and local geometry to match and align the fracture surfaces. Our framework consists of four components: (1) front-end point feature extractor with attention layers, (2) surface segmentation to separate fracture and original parts, (3) multi-parts matching to find correspondences among fracture surface points, and (4) robust global alignment to recover the global poses of the pieces. We show how to jointly learn segmentation and matching and seamlessly integrate feature matching and rigidity constraints. We evaluate Jigsaw on the Breaking Bad dataset and achieve superior performance compared to state-of-the-art methods. Our method also generalizes well to diverse fracture modes, objects, and unseen instances. To the best of our knowledge, this is the first learning-based method designed specifically for 3D fracture assembly over multiple pieces. Our code is available at https://jiaxin-lu.github.io/Jigsaw/.

Large language model (LLM) contexts are typically constructed using retrieval-augmented generation (RAG), which involves ranking and selecting the top-k passages. The approach causes fragmentation in information graphs in document structures, over-retrieval, and duplication of content alongside insufficient query context, including 2nd and 3rd order facets. In this paper, a structure-informed and diversity-constrained context bubble construction framework is proposed that assembles coherent, citable bundles of spans under a strict token budget. The method preserves and exploits inherent document structure by organising multi-granular spans (e.g., sections and rows) and using task-conditioned structural priors to guide retrieval. Starting from high-relevance anchor spans, a context bubble is constructed through constrained selection that balances query relevance, marginal coverage, and redundancy penalties. It will explicitly constrain diversity and budget, producing compact and informative context sets, unlike top-k retrieval. Moreover, a full retrieval is emitted that traces the scoring and selection choices of the records, thus providing auditability and deterministic tuning. Experiments on enterprise documents demonstrate the efficiency of context bubble as it significantly reduces redundant context, is better able to cover secondary facets and has a better answer quality and citation faithfulness within a limited context window. Ablation studies demonstrate that both structural priors as well as diversity constraint selection are necessary; removing either component results in a decline in coverage and an increase in redundant or incomplete context.

Segment matching is an important intermediate task in computer vision that establishes correspondences between semantically or geometrically coherent regions across images. Unlike keypoint matching, which focuses on localized features, segment matching captures structured regions, offering greater robustness to occlusions, lighting variations, and viewpoint changes. In this paper, we leverage the spatial understanding of 3D foundation models to tackle wide-baseline segment matching, a challenging setting involving extreme viewpoint shifts. We propose an architecture that uses the inductive bias of these 3D foundation models to match segments across image pairs with up to 180 degree view-point change rotation. Extensive experiments show that our approach outperforms state-of-the-art methods, including the SAM2 video propagator and local feature matching methods, by up to 30% on the AUPRC metric, on ScanNet++ and Replica datasets. We further demonstrate benefits of the proposed model on relevant downstream tasks, including 3D instance mapping and object-relative navigation. Project Page: https://segmast3r.github.io/

Drug discovery is a complex process that involves multiple scenarios and stages, such as fragment-constrained molecule generation, hit generation and lead optimization. However, existing molecular generative models can only tackle one or two of these scenarios and lack the flexibility to address various aspects of the drug discovery pipeline. In this paper, we present Generalist Molecular generative model (GenMol), a versatile framework that addresses these limitations by applying discrete diffusion to the Sequential Attachment-based Fragment Embedding (SAFE) molecular representation. GenMol generates SAFE sequences through non-autoregressive bidirectional parallel decoding, thereby allowing utilization of a molecular context that does not rely on the specific token ordering and enhanced computational efficiency. Moreover, under the discrete diffusion framework, we introduce fragment remasking, a strategy that optimizes molecules by replacing fragments with masked tokens and regenerating them, enabling effective exploration of chemical space. GenMol significantly outperforms the previous GPT-based model trained on SAFE representations in de novo generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These experimental results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design.

The reasoning segmentation task, which demands a nuanced comprehension of intricate queries to accurately pinpoint object regions, is attracting increasing attention. However, Multi-modal Large Language Models (MLLM) often find it difficult to accurately localize the objects described in complex reasoning contexts. We believe that the act of reasoning segmentation should mirror the cognitive stages of human visual search, where each step is a progressive refinement of thought toward the final object. Thus we introduce the Chains of Reasoning and Segmenting (CoReS) and find this top-down visual hierarchy indeed enhances the visual search process. Specifically, we propose a dual-chain structure that generates multi-modal, chain-like outputs to aid the segmentation process. Furthermore, to steer the MLLM's outputs into this intended hierarchy, we incorporate in-context inputs as guidance. Extensive experiments demonstrate the superior performance of our CoReS, which surpasses the state-of-the-art method by 6.5\% on the ReasonSeg dataset. Project: https://chain-of-reasoning-and-segmentation.github.io/.

Molecular optimization seeks to improve a molecule through small structural edits while preserving similarity to the starting compound. Recent language-model approaches typically treat this task as prompt-conditioned sequence generation. However, relying on natural language introduces an inherent data-scaling bottleneck, often leads to chemical hallucinations, and ignores the strong context dependence of fragment effects. We present FORGE, a two-stage framework that reformulates molecular optimization as context-aware local editing. By utilizing automatically mined, verified low-to-high edit pairs instead of expensive human text annotations, Stage 1 ranks candidate fragments by their property contribution under the full molecular context to inject chemical prior, and Stage 2 generates explicit fragment replacements. Built on a compact 0.6B language model, FORGE further adapts to unseen black-box objectives through in-context demonstrations. Across Prompt-MolOpt, PMO-1k and ChemCoTBench, FORGE consistently outperforms prior methods, including substantially larger language models and graph methods. These results highlight the value of explicit fragment-level supervision as a more easily obtainable, scalable, and hallucination-less alternative to natural language training.

Retrieval-Augmented Generation (RAG) systems rely on retrieving relevant evidence from a corpus to support downstream generation. The common practice of splitting a long document into multiple shorter passages enables finer-grained and targeted information retrieval. However, it also introduces challenges when a correct retrieval would require inference across passages, such as resolving coreference, disambiguating entities, and aggregating evidence scattered across multiple sources. Many state-of-the-art (SOTA) reranking methods, despite utilizing powerful large pretrained language models with potentially high inference costs, still neglect the aforementioned challenges. Therefore, we propose Embedding-Based Context-Aware Reranker (EBCAR), a lightweight reranking framework operating directly on embeddings of retrieved passages with enhanced cross-passage understandings through the structural information of the passages and a hybrid attention mechanism, which captures both high-level interactions across documents and low-level relationships within each document. We evaluate EBCAR against SOTA rerankers on the ConTEB benchmark, demonstrating its effectiveness for information retrieval requiring cross-passage inference and its advantages in both accuracy and efficiency.

Open Information Extraction (OIE) methods extract facts from natural language text in the form of ("subject"; "relation"; "object") triples. These facts are, however, merely surface forms, the ambiguity of which impedes their downstream usage; e.g., the surface phrase "Michael Jordan" may refer to either the former basketball player or the university professor. Knowledge Graphs (KGs), on the other hand, contain facts in a canonical (i.e., unambiguous) form, but their coverage is limited by a static schema (i.e., a fixed set of entities and predicates). To bridge this gap, we need the best of both worlds: (i) high coverage of free-text OIEs, and (ii) semantic precision (i.e., monosemy) of KGs. In order to achieve this goal, we propose a new benchmark with novel evaluation protocols that can, for example, measure fact linking performance on a granular triple slot level, while also measuring if a system has the ability to recognize that a surface form has no match in the existing KG. Our extensive evaluation of several baselines show that detection of out-of-KG entities and predicates is more difficult than accurate linking to existing ones, thus calling for more research efforts on this difficult task. We publicly release all resources (data, benchmark and code) on https://github.com/nec-research/fact-linking.

We present the zero-shot entity linking task, where mentions must be linked to unseen entities without in-domain labeled data. The goal is to enable robust transfer to highly specialized domains, and so no metadata or alias tables are assumed. In this setting, entities are only identified by text descriptions, and models must rely strictly on language understanding to resolve the new entities. First, we show that strong reading comprehension models pre-trained on large unlabeled data can be used to generalize to unseen entities. Second, we propose a simple and effective adaptive pre-training strategy, which we term domain-adaptive pre-training (DAP), to address the domain shift problem associated with linking unseen entities in a new domain. We present experiments on a new dataset that we construct for this task and show that DAP improves over strong pre-training baselines, including BERT. The data and code are available at https://github.com/lajanugen/zeshel.

Large language models (LLMs) have become the cornerstone of modern AI. However, the existing paradigm of next-token prediction fundamentally limits their ability to form coherent, high-level concepts, making it a critical barrier to human-like understanding and reasoning. Take the phrase "ribonucleic acid" as an example: an LLM will first decompose it into tokens, i.e., artificial text fragments ("rib", "on", ...), then learn each token sequentially, rather than grasping the phrase as a unified, coherent semantic entity. This fragmented representation hinders deeper conceptual understanding and, ultimately, the development of truly intelligent systems. In response, we introduce Concept-Aware Fine-Tuning (CAFT), a novel multi-token training method that redefines how LLMs are fine-tuned. By enabling the learning of sequences that span multiple tokens, this method fosters stronger concept-aware learning. Our experiments demonstrate significant improvements compared to conventional next-token finetuning methods across diverse tasks, including traditional applications like text summarization and domain-specific ones like de novo protein design. Multi-token prediction was previously only possible in the prohibitively expensive pretraining phase; CAFT, to our knowledge, is the first to bring the multi-token setting to the post-training phase, thus effectively democratizing its benefits for the broader community of practitioners and researchers. Finally, the unexpected effectiveness of our proposed method suggests wider implications for the machine learning research community. All code and data are available at https://github.com/michaelchen-lab/caft-llm

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

Recent advances in vision language models (VLM) have been driven by contrastive models such as CLIP, which learn to associate visual information with their corresponding text descriptions. However, these models have limitations in understanding complex compositional scenes involving multiple objects and their spatial relationships. To address these challenges, we propose a novel approach that diverges from commonly used strategies, which rely on the design of hard-negative augmentations. Instead, our work focuses on integrating inductive biases into pre-trained CLIP-like models to improve their compositional understanding without using any additional hard-negatives. To that end, we introduce a binding module that connects a scene graph, derived from a text description, with a slot-structured image representation, facilitating a structured similarity assessment between the two modalities. We also leverage relationships as text-conditioned visual constraints, thereby capturing the intricate interactions between objects and their contextual relationships more effectively. Our resulting model not only enhances the performance of CLIP-based models in multi-object compositional understanding but also paves the way towards more accurate and sample-efficient image-text matching of complex scenes.

Contrastive Language-Image Pre-training (CLIP) has accomplished extraordinary success for semantic understanding but inherently struggles to perceive geometric structure. Existing methods attempt to bridge this gap by querying CLIP with textual prompts, a process that is often indirect and inefficient. This paper introduces a fundamentally different approach using a dual-pathway decoder. We present SPACE-CLIP, an architecture that unlocks and interprets latent geometric knowledge directly from a frozen CLIP vision encoder, completely bypassing the text encoder and its associated textual prompts. A semantic pathway interprets high-level features, dynamically conditioned on global context using feature-wise linear modulation (FiLM). In addition, a structural pathway extracts fine-grained spatial details from early layers. These complementary streams are hierarchically fused, enabling a robust synthesis of semantic context and precise geometry. Extensive experiments on the KITTI benchmark show that SPACE-CLIP dramatically outperforms previous CLIP-based methods. Our ablation studies validate that the synergistic fusion of our dual pathways is critical to this success. SPACE-CLIP offers a new, efficient, and architecturally elegant blueprint for repurposing large-scale vision models. The proposed method is not just a standalone depth estimator, but a readily integrable spatial perception module for the next generation of embodied AI systems, such as vision-language-action (VLA) models. Our model is available at https://github.com/taewan2002/space-clip

Visually linking matching cues is a crucial ability in daily life, such as identifying the same person in multiple photos based on their cues, even without knowing who they are. Despite the extensive knowledge that vision-language models (VLMs) possess, it remains largely unexplored whether they are capable of performing this fundamental task. To address this, we introduce VLM^2-Bench, a benchmark designed to assess whether VLMs can Visually Link Matching cues, with 9 subtasks and over 3,000 test cases. Comprehensive evaluation across eight open-source VLMs and GPT-4o, along with further analysis of various language-side and vision-side prompting methods, leads to a total of eight key findings. We identify critical challenges in models' ability to link visual cues, highlighting a significant performance gap where even GPT-4o lags 34.80% behind humans. Based on these insights, we advocate for (i) enhancing core visual capabilities to improve adaptability and reduce reliance on prior knowledge, (ii) establishing clearer principles for integrating language-based reasoning in vision-centric tasks to prevent unnecessary biases, and (iii) shifting vision-text training paradigms toward fostering models' ability to independently structure and infer relationships among visual cues.

Generating molecules that satisfy precise numeric constraints over multiple physicochemical properties is critical and challenging. Although large language models (LLMs) are expressive, they struggle with precise multi-objective control and numeric reasoning without external structure and feedback. We introduce M olGen, a fragment-level, retrieval-augmented, two-stage framework for molecule generation under multi-property constraints. Stage I : Prototype generation: a multi-agent reasoner performs retrieval-anchored, fragment-level edits to produce a candidate near the feasible region. Stage II : RL-based fine-grained optimization: a fragment-level optimizer trained with Group Relative Policy Optimization (GRPO) applies one- or multi-hop refinements to explicitly minimize the property errors toward our target while regulating edit complexity and deviation from the prototype. A large, automatically curated dataset with reasoning chains of fragment edits and measured property deltas underpins both stages, enabling deterministic, reproducible supervision and controllable multi-hop reasoning. Unlike prior work, our framework better reasons about molecules by leveraging fragments and supports controllable refinement toward numeric targets. Experiments on generation under two sets of property constraints (QED, LogP, Molecular Weight and HOMO, LUMO) show consistent gains in validity and precise satisfaction of multi-property targets, outperforming strong LLMs and graph-based algorithms.

We propose AV-Link, a unified framework for Video-to-Audio and Audio-to-Video generation that leverages the activations of frozen video and audio diffusion models for temporally-aligned cross-modal conditioning. The key to our framework is a Fusion Block that enables bidirectional information exchange between our backbone video and audio diffusion models through a temporally-aligned self attention operation. Unlike prior work that uses feature extractors pretrained for other tasks for the conditioning signal, AV-Link can directly leverage features obtained by the complementary modality in a single framework i.e. video features to generate audio, or audio features to generate video. We extensively evaluate our design choices and demonstrate the ability of our method to achieve synchronized and high-quality audiovisual content, showcasing its potential for applications in immersive media generation. Project Page: snap-research.github.io/AVLink/

Referring Remote Sensing Image Segmentation provides a flexible and fine-grained framework for remote sensing scene analysis via vision-language collaborative interpretation. Current approaches predominantly utilize a three-stage pipeline encompassing dual-modal encoding, cross-modal interaction, and pixel decoding. These methods demonstrate significant limitations in managing complex semantic relationships and achieving precise cross-modal alignment, largely due to their coupled processing mechanism that conflates target localization with boundary delineation. This architectural coupling amplifies error propagation under semantic ambiguity while restricting model generalizability and interpretability. To address these issues, we propose RSRefSeg 2, a decoupling paradigm that reformulates the conventional workflow into a collaborative dual-stage framework: coarse localization followed by fine segmentation. RSRefSeg 2 integrates CLIP's cross-modal alignment strength with SAM's segmentation generalizability through strategic foundation model collaboration. Specifically, CLIP is employed as the dual-modal encoder to activate target features within its pre-aligned semantic space and generate localization prompts. To mitigate CLIP's misactivation challenges in multi-entity scenarios described by referring texts, a cascaded second-order prompter is devised, which enhances precision through implicit reasoning via decomposition of text embeddings into complementary semantic subspaces. These optimized semantic prompts subsequently direct the SAM to generate pixel-level refined masks, thereby completing the semantic transmission pipeline. Extensive experiments (RefSegRS, RRSIS-D, and RISBench) demonstrate that RSRefSeg 2 surpasses contemporary methods in segmentation accuracy (+~3% gIoU) and complex semantic interpretation. Code is available at: https://github.com/KyanChen/RSRefSeg2.

Diffusion models have demonstrated remarkable performance in the domain of text-to-image generation. However, most widely used models still employ CLIP as their text encoder, which constrains their ability to comprehend dense prompts, encompassing multiple objects, detailed attributes, complex relationships, long-text alignment, etc. In this paper, we introduce an Efficient Large Language Model Adapter, termed ELLA, which equips text-to-image diffusion models with powerful Large Language Models (LLM) to enhance text alignment without training of either U-Net or LLM. To seamlessly bridge two pre-trained models, we investigate a range of semantic alignment connector designs and propose a novel module, the Timestep-Aware Semantic Connector (TSC), which dynamically extracts timestep-dependent conditions from LLM. Our approach adapts semantic features at different stages of the denoising process, assisting diffusion models in interpreting lengthy and intricate prompts over sampling timesteps. Additionally, ELLA can be readily incorporated with community models and tools to improve their prompt-following capabilities. To assess text-to-image models in dense prompt following, we introduce Dense Prompt Graph Benchmark (DPG-Bench), a challenging benchmark consisting of 1K dense prompts. Extensive experiments demonstrate the superiority of ELLA in dense prompt following compared to state-of-the-art methods, particularly in multiple object compositions involving diverse attributes and relationships.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

We consider the task of linking social media accounts that belong to the same author in an automated fashion on the basis of the content and metadata of their corresponding document streams. We focus on learning an embedding that maps variable-sized samples of user activity -- ranging from single posts to entire months of activity -- to a vector space, where samples by the same author map to nearby points. The approach does not require human-annotated data for training purposes, which allows us to leverage large amounts of social media content. The proposed model outperforms several competitive baselines under a novel evaluation framework modeled after established recognition benchmarks in other domains. Our method achieves high linking accuracy, even with small samples from accounts not seen at training time, a prerequisite for practical applications of the proposed linking framework.

Referring image segmentation aims to segment specific targets based on a natural text expression. Recently, parameter-efficient tuning (PET) has emerged as a promising paradigm. However, existing PET-based methods often suffer from the fact that visual features can't emphasize the text-referred target instance but activate co-category yet unrelated objects. We analyze and quantify this problem, terming it the `non-target activation' (NTA) issue. To address this, we propose a novel framework, TALENT, which utilizes target-aware efficient tuning for PET-based RIS. Specifically, we first propose a Rectified Cost Aggregator (RCA) to efficiently aggregate text-referred features. Then, to calibrate `NTA' into accurate target activation, we adopt a Target-aware Learning Mechanism (TLM), including contextual pairwise consistency learning and target-centric contrastive learning. The former uses the sentence-level text feature to achieve a holistic understanding of the referent and constructs a text-referred affinity map to optimize the semantic association of visual features. The latter further enhances target localization to discover the distinct instance while suppressing associations with other unrelated ones. The two objectives work in concert and address `NTA' effectively. Extensive evaluations show that TALENT outperforms existing methods across various metrics (e.g., 2.5\% mIoU gains on G-Ref val set). Our codes will be released at: https://github.com/Kimsure/TALENT.

We introduce ReFinED, an efficient end-to-end entity linking model which uses fine-grained entity types and entity descriptions to perform linking. The model performs mention detection, fine-grained entity typing, and entity disambiguation for all mentions within a document in a single forward pass, making it more than 60 times faster than competitive existing approaches. ReFinED also surpasses state-of-the-art performance on standard entity linking datasets by an average of 3.7 F1. The model is capable of generalising to large-scale knowledge bases such as Wikidata (which has 15 times more entities than Wikipedia) and of zero-shot entity linking. The combination of speed, accuracy and scale makes ReFinED an effective and cost-efficient system for extracting entities from web-scale datasets, for which the model has been successfully deployed. Our code and pre-trained models are available at https://github.com/alexa/ReFinED

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

This report presents a framework called Segment And Track Anything (SAMTrack) that allows users to precisely and effectively segment and track any object in a video. Additionally, SAM-Track employs multimodal interaction methods that enable users to select multiple objects in videos for tracking, corresponding to their specific requirements. These interaction methods comprise click, stroke, and text, each possessing unique benefits and capable of being employed in combination. As a result, SAM-Track can be used across an array of fields, ranging from drone technology, autonomous driving, medical imaging, augmented reality, to biological analysis. SAM-Track amalgamates Segment Anything Model (SAM), an interactive key-frame segmentation model, with our proposed AOT-based tracking model (DeAOT), which secured 1st place in four tracks of the VOT 2022 challenge, to facilitate object tracking in video. In addition, SAM-Track incorporates Grounding-DINO, which enables the framework to support text-based interaction. We have demonstrated the remarkable capabilities of SAM-Track on DAVIS-2016 Val (92.0%), DAVIS-2017 Test (79.2%)and its practicability in diverse applications. The project page is available at: https://github.com/z-x-yang/Segment-and-Track-Anything.

This paper focuses on the Referring Image Segmentation (RIS) task, which aims to segment objects from an image based on a given language description. The critical problem of RIS is achieving fine-grained alignment between different modalities to recognize and segment the target object. Recent advances using the attention mechanism for cross-modal interaction have achieved excellent progress. However, current methods tend to lack explicit principles of interaction design as guidelines, leading to inadequate cross-modal comprehension. Additionally, most previous works use a single-modal mask decoder for prediction, losing the advantage of full cross-modal alignment. To address these challenges, we present a Fully Aligned Network (FAN) that follows four cross-modal interaction principles. Under the guidance of reasonable rules, our FAN achieves state-of-the-art performance on the prevalent RIS benchmarks (RefCOCO, RefCOCO+, G-Ref) with a simple architecture.

We present a geometric framework for filtered approximate nearest neighbor (ANN) search. Filtering a proximity graph by a metadata predicate produces a subgraph, a fiber, whose connectivity and geometry can differ sharply from the full graph. Using local signals, we propose a two-phase search algorithm that combines full-graph exploration with filtered-neighbor descent when the local geometry is favorable. These signals also classify search failures into three regimes: topological cuts, geometric folds, and genuine basins. A key observation is that all three share a common resolution: restarting the search in a fiber-present cluster near the query. To support this, we introduce a lightweight anchor structure that identifies such regions and restarts the search accordingly. We show empirically that the method outperforms FAISS HNSW on filtered search and the three failure regimes separate cleanly and shift predictably with filter selectivity.

Scientific paper retrieval, particularly framed as document-to-document retrieval, aims to identify relevant papers in response to a long-form query paper, rather than a short query string. Previous approaches to this task have focused on abstracts, embedding them into dense vectors as surrogates for full documents and calculating similarity across them, although abstracts provide only sparse and high-level summaries. To address this, we propose PRISM, a novel document-to-document retrieval method that introduces multiple, fine-grained representations for both the query and candidate papers. In particular, each query paper is decomposed into multiple aspect-specific views and individually embedded, which are then matched against candidate papers similarity segmented to consider their multifaceted dimensions. Moreover, we present SciFullBench, a novel benchmark in which the complete and segmented context of full papers for both queries and candidates is available. Then, experimental results show that PRISM improves performance by an average of 4.3% over existing retrieval baselines.

Text-rich Graph Knowledge Bases (TG-KBs) have become increasingly crucial for answering queries by providing textual and structural knowledge. However, current retrieval methods often retrieve these two types of knowledge in isolation without considering their mutual reinforcement and some hybrid methods even bypass structural retrieval entirely after neighboring aggregation. To fill in this gap, we propose a Mixture of Structural-and-Textual Retrieval (MoR) to retrieve these two types of knowledge via a Planning-Reasoning-Organizing framework. In the Planning stage, MoR generates textual planning graphs delineating the logic for answering queries. Following planning graphs, in the Reasoning stage, MoR interweaves structural traversal and textual matching to obtain candidates from TG-KBs. In the Organizing stage, MoR further reranks fetched candidates based on their structural trajectory. Extensive experiments demonstrate the superiority of MoR in harmonizing structural and textual retrieval with insights, including uneven retrieving performance across different query logics and the benefits of integrating structural trajectories for candidate reranking. Our code is available at https://github.com/Yoega/MoR.

Multimodal Large Language Models (MLLMs) have achieved remarkable performance in Visually Rich Document Understanding (VRDU) tasks, but their capabilities are mainly evaluated on pristine, well-structured document images. We consider content restoration from shredded fragments, a challenging VRDU setting that requires integrating visual pattern recognition with semantic reasoning under significant content discontinuities. To facilitate systematic evaluation of complex VRDU tasks, we introduce ShredBench, a benchmark supported by an automated generation pipeline that renders fragmented documents directly from Markdown. The proposed pipeline ensures evaluation validity by allowing the flexible integration of latest or unseen textual sources to prevent training data contamination. ShredBench assesses four scenarios (English, Chinese, Code, Table) with three fragmentation granularities (8, 12, 16 pieces). Empirical evaluations on state-of-the-art MLLMs reveal a significant performance gap: The method is effective on intact documents; however, once the document is shredded, restoration becomes a significant challenge, with NED dropping sharply as fragmentation increases. Our findings highlight that current MLLMs lack the fine-grained cross-modal reasoning required to bridge visual discontinuities, identifying a critical gap in robust VRDU research.

Jigsaw puzzle solving has been an increasingly popular task in the computer vision research community. Recent works have utilized cutting-edge architectures and computational approaches to reassemble groups of pieces into a coherent image, while achieving increasingly good results on well established datasets. However, most of these approaches share a common, restricting setting: operating solely on strictly square puzzle pieces. In this work, we introduce GAP, a set of novel jigsaw puzzles datasets containing synthetic, heavily eroded pieces of unrestricted shapes, generated by a learned distribution of real-world archaeological fragments. We also introduce PuzzleFlow, a novel ViT and Flow-Matching based framework for jigsaw puzzle solving, capable of handling complex puzzle pieces and demonstrating superior performance on GAP when compared to both classic and recent prominent works in this domain.

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale, building protein structures de novo from cryo-EM maps becomes possible. Recently, recognition-based de novo building methods have shown the potential to streamline this process. However, it cannot build a complete structure due to the low signal-to-noise ratio (SNR) problem. At the same time, AlphaFold has led to a great breakthrough in predicting protein structures. This has inspired us to combine fragment recognition and structure prediction methods to build a complete structure. In this paper, we propose a new method named FFF that bridges protein structure prediction and protein structure recognition with flexible fitting. First, a multi-level recognition network is used to capture various structural features from the input 3D cryo-EM map. Next, protein structural fragments are generated using pseudo peptide vectors and a protein sequence alignment method based on these extracted features. Finally, a complete structural model is constructed using the predicted protein fragments via flexible fitting. Based on our benchmark tests, FFF outperforms the baseline methods for building complete protein structures.

The interactive segmentation task consists in the creation of object segmentation masks based on user interactions. The most common way to guide a model towards producing a correct segmentation consists in clicks on the object and background. The recently published Segment Anything Model (SAM) supports a generalized version of the interactive segmentation problem and has been trained on an object segmentation dataset which contains 1.1B masks. Though being trained extensively and with the explicit purpose of serving as a foundation model, we show significant limitations of SAM when being applied for interactive segmentation on novel domains or object types. On the used datasets, SAM displays a failure rate FR_{30}@90 of up to 72.6 %. Since we still want such foundation models to be immediately applicable, we present a framework that can adapt SAM during immediate usage. For this we will leverage the user interactions and masks, which are constructed during the interactive segmentation process. We use this information to generate pseudo-labels, which we use to compute a loss function and optimize a part of the SAM model. The presented method causes a relative reduction of up to 48.1 % in the FR_{20}@85 and 46.6 % in the FR_{30}@90 metrics.

Online encyclopedias, such as Wikipedia, have been well-developed and researched in the last two decades. One can find any attributes or other information of a wiki item on a wiki page edited by a community of volunteers. However, the traditional text, images and tables can hardly express some aspects of an wiki item. For example, when we talk about ``Shiba Inu'', one may care more about ``How to feed it'' or ``How to train it not to protect its food''. Currently, short-video platforms have become a hallmark in the online world. Whether you're on TikTok, Instagram, Kuaishou, or YouTube Shorts, short-video apps have changed how we consume and create content today. Except for producing short videos for entertainment, we can find more and more authors sharing insightful knowledge widely across all walks of life. These short videos, which we call knowledge videos, can easily express any aspects (e.g. hair or how-to-feed) consumers want to know about an item (e.g. Shiba Inu), and they can be systematically analyzed and organized like an online encyclopedia. In this paper, we propose Kuaipedia, a large-scale multi-modal encyclopedia consisting of items, aspects, and short videos lined to them, which was extracted from billions of videos of Kuaishou (Kwai), a well-known short-video platform in China. We first collected items from multiple sources and mined user-centered aspects from millions of users' queries to build an item-aspect tree. Then we propose a new task called ``multi-modal item-aspect linking'' as an expansion of ``entity linking'' to link short videos into item-aspect pairs and build the whole short-video encyclopedia. Intrinsic evaluations show that our encyclopedia is of large scale and highly accurate. We also conduct sufficient extrinsic experiments to show how Kuaipedia can help fundamental applications such as entity typing and entity linking.

Retrieval Augmented Generation (RAG) has become the standard approach for equipping Large Language Models (LLMs) with up-to-date knowledge. However, standard RAG, relying on independent passage retrieval, often fails to capture the interconnected nature of information required for complex, multi-hop reasoning. While structured RAG methods attempt to address this using knowledge graphs built from triples, we argue that the inherent context loss of triples (context collapse) limits the fidelity of the knowledge representation. We introduce PropRAG, a novel RAG framework that shifts from triples to context-rich propositions and introduces an efficient, LLM-free online beam search over proposition paths to discover multi-step reasoning chains. By coupling a higher-fidelity knowledge representation with explicit path discovery, PropRAG achieves state-of-the-art zero-shot Recall@5 and F1 scores on 2Wiki, HotpotQA, and MuSiQue, advancing non-parametric knowledge integration by improving evidence retrieval through richer representation and efficient reasoning path discovery.

Breaking long documents into smaller segments is a fundamental challenge in information retrieval. Whether for search engines, question-answering systems, or retrieval-augmented generation (RAG), effective segmentation determines how well systems can locate and return relevant information. However, traditional methods, such as fixed-length or coherence-based segmentation, ignore user intent, leading to chunks that split answers or contain irrelevant noise. We introduce Intent-Driven Dynamic Chunking (IDC), a novel approach that uses predicted user queries to guide document segmentation. IDC leverages a Large Language Model to generate likely user intents for a document and then employs a dynamic programming algorithm to find the globally optimal chunk boundaries. This represents a novel application of DP to intent-aware segmentation that avoids greedy pitfalls. We evaluated IDC on six diverse question-answering datasets, including news articles, Wikipedia, academic papers, and technical documentation. IDC outperformed traditional chunking strategies on five datasets, improving top-1 retrieval accuracy by 5% to 67%, and matched the best baseline on the sixth. Additionally, IDC produced 40-60% fewer chunks than baseline methods while achieving 93-100% answer coverage. These results demonstrate that aligning document structure with anticipated information needs significantly boosts retrieval performance, particularly for long and heterogeneous documents.

Cross-domain scientific synthesis requires connecting mechanistic explanations across fragmented literature, a capability that remains challenging for both retrieval-based systems and unconstrained language models. While recent work has applied large language models to scientific summarization and question answering, these approaches provide limited control over reasoning depth and structural grounding. We frame mechanistic synthesis as a graph-constrained multi-hop reasoning problem over literature-derived concept graphs. Given a scientific query and a compact, query-local corpus, SciNets constructs a directed concept graph and synthesizes mechanistic explanations by identifying multi-hop reasoning paths that connect concepts that rarely co-occur within individual papers. We systematically compare shortest-path reasoning, k-shortest paths with diversity constraints, stochastic random walks, and a retrieval-augmented language model baseline. Rather than evaluating correctness, which is often indeterminate when synthesizing connections across distributed sources, we introduce a behavioral framework that measures symbolic reasoning depth, mechanistic diversity, and grounding stability. Across machine learning, biology, and climate science tasks, explicit graph constraints enable controllable multi-hop reasoning while revealing a consistent trade-off: deeper and more diverse symbolic reasoning increases grounding instability, whereas shortest-path reasoning remains highly stable but structurally conservative. These findings provide a systematic behavioral characterization of the limits and capabilities of current graph-LLM integration for scientific synthesis.

3D referring expression comprehension (3DREC) and segmentation (3DRES) have overlapping objectives, indicating their potential for collaboration. However, existing collaborative approaches predominantly depend on the results of one task to make predictions for the other, limiting effective collaboration. We argue that employing separate branches for 3DREC and 3DRES tasks enhances the model's capacity to learn specific information for each task, enabling them to acquire complementary knowledge. Thus, we propose the MCLN framework, which includes independent branches for 3DREC and 3DRES tasks. This enables dedicated exploration of each task and effective coordination between the branches. Furthermore, to facilitate mutual reinforcement between these branches, we introduce a Relative Superpoint Aggregation (RSA) module and an Adaptive Soft Alignment (ASA) module. These modules significantly contribute to the precise alignment of prediction results from the two branches, directing the module to allocate increased attention to key positions. Comprehensive experimental evaluation demonstrates that our proposed method achieves state-of-the-art performance on both the 3DREC and 3DRES tasks, with an increase of 2.05% in Acc@0.5 for 3DREC and 3.96% in mIoU for 3DRES.

Query rewriting aims to generate a new query that can complement the original query to improve the information retrieval system. Recent studies on query rewriting, such as query2doc (Q2D), query2expand (Q2E) and querey2cot (Q2C), rely on the internal knowledge of Large Language Models (LLMs) to generate a relevant passage to add information to the query. Nevertheless, the efficacy of these methodologies may markedly decline in instances where the requisite knowledge is not encapsulated within the model's intrinsic parameters. In this paper, we propose a novel structured query rewriting method called Crafting the Path tailored for retrieval systems. Crafting the Path involves a three-step process that crafts query-related information necessary for finding the passages to be searched in each step. Specifically, the Crafting the Path begins with Query Concept Comprehension, proceeds to Query Type Identification, and finally conducts Expected Answer Extraction. Experimental results show that our method outperforms previous rewriting methods, especially in less familiar domains for LLMs. We demonstrate that our method is less dependent on the internal parameter knowledge of the model and generates queries with fewer factual inaccuracies. Furthermore, we observe that Crafting the Path has less latency compared to the baselines.

Segment Anything Model (SAM) is a foundation model for interactive segmentation, and it has catalyzed major advances in generative AI, computational photography, and medical imaging. This model takes in an arbitrary user input and provides segmentation masks of the corresponding objects. It is our goal to develop a version of SAM that is appropriate for use in a photography app. The original SAM model has a few challenges in this setting. First, original SAM a 600 million parameter based on ViT-H, and its high computational cost and large model size that are not suitable for todays mobile hardware. We address this by proposing the SqueezeSAM model architecture, which is 50x faster and 100x smaller than SAM. Next, when a user takes a photo on their phone, it might not occur to them to click on the image and get a mask. Our solution is to use salient object detection to generate the first few clicks. This produces an initial segmentation mask that the user can interactively edit. Finally, when a user clicks on an object, they typically expect all related pieces of the object to be segmented. For instance, if a user clicks on a person t-shirt in a photo, they expect the whole person to be segmented, but SAM typically segments just the t-shirt. We address this with a new data augmentation scheme, and the end result is that if the user clicks on a person holding a basketball, the person and the basketball are all segmented together.

Conventional representation learning algorithms for knowledge graphs (KG) map each entity to a unique embedding vector. Such a shallow lookup results in a linear growth of memory consumption for storing the embedding matrix and incurs high computational costs when working with real-world KGs. Drawing parallels with subword tokenization commonly used in NLP, we explore the landscape of more parameter-efficient node embedding strategies with possibly sublinear memory requirements. To this end, we propose NodePiece, an anchor-based approach to learn a fixed-size entity vocabulary. In NodePiece, a vocabulary of subword/sub-entity units is constructed from anchor nodes in a graph with known relation types. Given such a fixed-size vocabulary, it is possible to bootstrap an encoding and embedding for any entity, including those unseen during training. Experiments show that NodePiece performs competitively in node classification, link prediction, and relation prediction tasks while retaining less than 10% of explicit nodes in a graph as anchors and often having 10x fewer parameters. To this end, we show that a NodePiece-enabled model outperforms existing shallow models on a large OGB WikiKG 2 graph having 70x fewer parameters.

Referring Image Segmentation is a comprehensive task to segment an object referred by a textual query from an image. In nature, the level of difficulty in this task is affected by the existence of similar objects and the complexity of the referring expression. Recent RIS models still show a significant performance gap between easy and hard scenarios. We pose that the bottleneck exists in the data, and propose a simple but powerful data augmentation method, Negative-mined Mosaic Augmentation (NeMo). This method augments a training image into a mosaic with three other negative images carefully curated by a pretrained multimodal alignment model, e.g., CLIP, to make the sample more challenging. We discover that it is critical to properly adjust the difficulty level, neither too ambiguous nor too trivial. The augmented training data encourages the RIS model to recognize subtle differences and relationships between similar visual entities and to concretely understand the whole expression to locate the right target better. Our approach shows consistent improvements on various datasets and models, verified by extensive experiments.

Reverse Chain-of-Thought Generation (RCG) synthesizes reasoning traces from query-answer pairs, but runs the risk of producing post-hoc rationalizations: when models can see the answer during generation, the answer serves as a cognitive anchor that shapes the entire explanation. We formalize this phenomenon through a three-level measurement hierarchy: lexical, entropic, and probabilistic anchoring, each captures surface artifacts, entropy dynamics, and latent answer dependence, respectively. We analyze semantic suppression, the intuitive mitigation strategy that instructs models to ignore the answer, to find out its counterproduction: while it reduces lexical overlap, it paradoxically increases entropic and probabilistic anchoring. Drawing on Ironic Process Theory from cognitive psychology, we attribute this failure to active monitoring of the forbidden answer, which inadvertently deepens dependence on it. To break this cycle, we propose Structural Skeleton-guided Reasoning (SSR), a two-phase approach that first generates an answer-invariant functional skeleton structure, then uses this skeleton to guide full trace generation. By redirecting the information flow to structural planning rather than answer monitoring, SSR consistently reduces anchoring across all three levels. We further introduce Distilled SSR (SSR-D), which fine-tunes models on teacher-generated SSR traces to ensure reliable structural adherence. Experiments across open-ended reasoning benchmarks demonstrate that SSR-D achieves up to 10% improvement over suppression baselines while preserving out-of-distribution (OOD) generalization.

The adoption of Large Language Models (LLMs) in scientific writing promises efficiency but risks introducing informational entropy. While "hallucinated papers" are a known artifact, the systematic degradation of valid citation chains remains unquantified. We conducted a forensic audit of 50 recent survey papers in Artificial Intelligence (N=5,514 citations) published between September 2024 and January 2026. We utilized a hybrid verification pipeline combining DOI resolution, Crossref metadata analysis, Semantic Scholar queries, and fuzzy text matching to distinguish between formatting errors ("Sloppiness") and verifiable non-existence ("Phantoms). We detect a persistent 17.0% Phantom Rate -- citations that cannot be resolved to any digital object despite aggressive forensic recovery. Diagnostic categorization reveals three distinct failure modes: pure hallucinations (5.1%), hallucinated identifiers with valid titles (16.4%), and parsing-induced matching failures (78.5%). Longitudinal analysis reveals a flat trend (+0.07 pp/month), suggesting that high-entropy citation practices have stabilized as an endemic feature of the field. The scientific citation graph in AI survey literature exhibits "link rot" at scale. This suggests a mechanism where AI tools act as "lazy research assistants," retrieving correct titles but hallucinating metadata, thereby severing the digital chain of custody required for reproducible science.

Accurately recognizing a revisited place is crucial for embodied agents to localize and navigate. This requires visual representations to be distinct, despite strong variations in camera viewpoint and scene appearance. Existing visual place recognition pipelines encode the "whole" image and search for matches. This poses a fundamental challenge in matching two images of the same place captured from different camera viewpoints: "the similarity of what overlaps can be dominated by the dissimilarity of what does not overlap". We address this by encoding and searching for "image segments" instead of the whole images. We propose to use open-set image segmentation to decompose an image into `meaningful' entities (i.e., things and stuff). This enables us to create a novel image representation as a collection of multiple overlapping subgraphs connecting a segment with its neighboring segments, dubbed SuperSegment. Furthermore, to efficiently encode these SuperSegments into compact vector representations, we propose a novel factorized representation of feature aggregation. We show that retrieving these partial representations leads to significantly higher recognition recall than the typical whole image based retrieval. Our segments-based approach, dubbed SegVLAD, sets a new state-of-the-art in place recognition on a diverse selection of benchmark datasets, while being applicable to both generic and task-specialized image encoders. Finally, we demonstrate the potential of our method to ``revisit anything'' by evaluating our method on an object instance retrieval task, which bridges the two disparate areas of research: visual place recognition and object-goal navigation, through their common aim of recognizing goal objects specific to a place. Source code: https://github.com/AnyLoc/Revisit-Anything.

Line segments are powerful features complementary to points. They offer structural cues, robust to drastic viewpoint and illumination changes, and can be present even in texture-less areas. However, describing and matching them is more challenging compared to points due to partial occlusions, lack of texture, or repetitiveness. This paper introduces a new matching paradigm, where points, lines, and their descriptors are unified into a single wireframe structure. We propose GlueStick, a deep matching Graph Neural Network (GNN) that takes two wireframes from different images and leverages the connectivity information between nodes to better glue them together. In addition to the increased efficiency brought by the joint matching, we also demonstrate a large boost of performance when leveraging the complementary nature of these two features in a single architecture. We show that our matching strategy outperforms the state-of-the-art approaches independently matching line segments and points for a wide variety of datasets and tasks. The code is available at https://github.com/cvg/GlueStick.

Scholarly data are largely fragmented across siloed databases with divergent metadata and missing linkages among them. We present the Science Data Lake, a locally-deployable infrastructure built on DuckDB and simple Parquet files that unifies eight open sources - Semantic Scholar, OpenAlex, SciSciNet, Papers with Code, Retraction Watch, Reliance on Science, a preprint-to-published mapping, and Crossref - via DOI normalization while preserving source-level schemas. The resource comprises approximately 960GB of Parquet files spanning ~293 million uniquely identifiable papers across ~22 schemas and ~153 SQL views. An embedding-based ontology alignment using BGE-large sentence embeddings maps 4,516 OpenAlex topics to 13 scientific ontologies (~1.3 million terms), yielding 16,150 mappings covering 99.8% of topics (geq 0.65 threshold) with F1 = 0.77 at the recommended geq 0.85 operating point, outperforming TF-IDF, BM25, and Jaro-Winkler baselines on a 300-pair gold-standard evaluation. We validate through 10 automated checks, cross-source citation agreement analysis (pairwise Pearson r = 0.76 - 0.87), and stratified manual annotation. Four vignettes demonstrate cross-source analyses infeasible with any single database. The resource is open source, deployable on a single drive or queryable remotely via HuggingFace, and includes structured documentation suitable for large language model (LLM) based research agents.

LLMs have fundamentally transformed dense retrieval, upgrading backbones from discriminative encoders to generative architectures. However, a critical disconnect remains: while LLMs possess strong reasoning capabilities, current retrievers predominantly utilize them as static encoders, leaving their potential for complex reasoning unexplored. To address this, existing approaches typically adopt rewrite-then-retrieve pipelines to generate explicit CoT rationales before retrieval. However, this incurs prohibitive latency. In this paper, we propose LaSER, a novel self-distillation framework that internalizes explicit reasoning into the latent space of dense retrievers. Operating on a shared LLM backbone, LaSER introduces a dual-view training mechanism: an Explicit view that explicitly encodes ground-truth reasoning paths, and a Latent view that performs implicit latent thinking. To bridge the gap between these views, we design a multi-grained alignment strategy. Beyond standard output alignment, we introduce a trajectory alignment mechanism that synchronizes the intermediate latent states of the latent path with the semantic progression of the explicit reasoning segments. This allows the retriever to think silently and effectively without autoregressive text generation. Extensive experiments on both in-domain and out-of-domain reasoning-intensive benchmarks demonstrate that LaSER significantly outperforms state-of-the-art baselines. Furthermore, analyses across diverse backbones and model scales validate the robustness of our approach, confirming that our unified learning framework is essential for eliciting effective latent thinking. Our method successfully combines the reasoning depth of explicit CoT pipelines with the inference efficiency of standard dense retrievers.

Few-shot segmentation aims to segment unseen object categories from just a handful of annotated examples. This requires mechanisms that can both identify semantically related objects across images and accurately produce segmentation masks. We note that Segment Anything 2 (SAM2), with its prompt-and-propagate mechanism, offers both strong segmentation capabilities and a built-in feature matching process. However, we show that its representations are entangled with task-specific cues optimized for object tracking, which impairs its use for tasks requiring higher level semantic understanding. Our key insight is that, despite its class-agnostic pretraining, SAM2 already encodes rich semantic structure in its features. We propose SANSA (Semantically AligNed Segment Anything 2), a framework that makes this latent structure explicit, and repurposes SAM2 for few-shot segmentation through minimal task-specific modifications. SANSA achieves state-of-the-art performance on few-shot segmentation benchmarks specifically designed to assess generalization, outperforms generalist methods in the popular in-context setting, supports various prompts flexible interaction via points, boxes, or scribbles, and remains significantly faster and more compact than prior approaches. Code is available at https://github.com/ClaudiaCuttano/SANSA.

Multi-document grounded dialogue systems (DGDS) belong to a class of conversational agents that answer users' requests by finding supporting knowledge from a collection of documents. Most previous studies aim to improve the knowledge retrieval model or propose more effective ways to incorporate external knowledge into a parametric generation model. These methods, however, focus on retrieving knowledge from mono-granularity language units (e.g. passages, sentences, or spans in documents), which is not enough to effectively and efficiently capture precise knowledge in long documents. This paper proposes Re3G, which aims to optimize both coarse-grained knowledge retrieval and fine-grained knowledge extraction in a unified framework. Specifically, the former efficiently finds relevant passages in a retrieval-and-reranking process, whereas the latter effectively extracts finer-grain spans within those passages to incorporate into a parametric answer generation model (BART, T5). Experiments on DialDoc Shared Task demonstrate the effectiveness of our method.

Corruption studies, the primary tool for evaluating chain-of-thought (CoT) faithfulness, identify which chain positions are "computationally important" by measuring accuracy when steps are replaced with errors. We identify a systematic confound: for chains with explicit terminal answer statements, the dominant format in standard benchmarks, corruption studies detect where the answer text appears, not where computation occurs. A within-dataset format ablation provides the key evidence: on standard GSM8K chains ending with "the answer is X," removing only the answer statement, preserving all reasoning, collapses suffix sensitivity ~19x at 3B (N=300, p=0.022). Conflicting-answer experiments quantify the causal mechanism: at 7B, CC accuracy drops to near-zero (<=0.02) across five architecture families; the followed-wrong rate spans 0.63-1.00 at 3B-7B and attenuates at larger scales (0.300 at Phi-4-14B, ~0.01 at 32B). A within-stable 7B replication (9.3x attenuation, N=76, p=7.8e-3; Qwen3-8B N=299, p=0.004) provides converging evidence, and the pattern replicates on MATH (DeepSeek-R1-7B: 10.9x suffix-survival recovery). On chains without answer suffixes the same protocol identifies the prefix as load-bearing (Delta=-0.77, p<10^-12). Generation-time probes confirm a dissociation: the answer is not early-determined during generation (early commitment <5%), yet at consumption time model outputs systematically follow the explicit answer text. The format-determination effect persists through 14B (8.5x ratio, p=0.001) and converges toward zero at 32B. We propose a three-prerequisite protocol (question-only control, format characterization, all-position sweep) as a minimum standard for corruption-based faithfulness studies.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Large language models (LLMs), while exhibiting exceptional performance, suffer from hallucinations, especially on knowledge-intensive tasks. Existing works propose to augment LLMs with individual text units retrieved from external knowledge corpora to alleviate the issue. However, in many domains, texts are interconnected (e.g., academic papers in a bibliographic graph are linked by citations and co-authorships) which form a (text-attributed) graph. The knowledge in such graphs is encoded not only in single texts/nodes but also in their associated connections. To facilitate the research of augmenting LLMs with graphs, we manually construct a Graph Reasoning Benchmark dataset called GRBench, containing 1,740 questions that can be answered with the knowledge from 10 domain graphs. Then, we propose a simple and effective framework called Graph Chain-of-thought (Graph-CoT) to augment LLMs with graphs by encouraging LLMs to reason on the graph iteratively. Each Graph-CoT iteration consists of three sub-steps: LLM reasoning, LLM-graph interaction, and graph execution. We conduct systematic experiments with three LLM backbones on GRBench, where Graph-CoT outperforms the baselines consistently. The code is available at https://github.com/PeterGriffinJin/Graph-CoT.

We present SegLLM, a novel multi-round interactive reasoning segmentation model that enhances LLM-based segmentation by exploiting conversational memory of both visual and textual outputs. By leveraging a mask-aware multimodal LLM, SegLLM re-integrates previous segmentation results into its input stream, enabling it to reason about complex user intentions and segment objects in relation to previously identified entities, including positional, interactional, and hierarchical relationships, across multiple interactions. This capability allows SegLLM to respond to visual and text queries in a chat-like manner. Evaluated on the newly curated MRSeg benchmark, SegLLM outperforms existing methods in multi-round interactive reasoning segmentation by over 20%. Additionally, we observed that training on multi-round reasoning segmentation data enhances performance on standard single-round referring segmentation and localization tasks, resulting in a 5.5% increase in cIoU for referring expression segmentation and a 4.5% improvement in Acc@0.5 for referring expression localization.

Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for entity-level tasks such as entity linking where the ability to model entity relations (especially synonymy) is pivotal. To address this challenge, we propose SapBERT, a pretraining scheme that self-aligns the representation space of biomedical entities. We design a scalable metric learning framework that can leverage UMLS, a massive collection of biomedical ontologies with 4M+ concepts. In contrast with previous pipeline-based hybrid systems, SapBERT offers an elegant one-model-for-all solution to the problem of medical entity linking (MEL), achieving a new state-of-the-art (SOTA) on six MEL benchmarking datasets. In the scientific domain, we achieve SOTA even without task-specific supervision. With substantial improvement over various domain-specific pretrained MLMs such as BioBERT, SciBERTand and PubMedBERT, our pretraining scheme proves to be both effective and robust.

Large language models (LLMs) have recently shown strong progress on scientific reasoning, yet two major bottlenecks remain. First, explicit retrieval fragments reasoning, imposing a hidden "tool tax" of extra tokens and steps. Second, multi-agent pipelines often dilute strong solutions by averaging across all candidates. We address these challenges with a unified framework that combines implicit retrieval and structured collaboration. At its foundation, a Monitor-based retrieval module operates at the token level, integrating external knowledge with minimal disruption to reasoning. On top of this substrate, Hierarchical Solution Refinement (HSR) iteratively designates each candidate as an anchor to be repaired by its peers, while Quality-Aware Iterative Reasoning (QAIR) adapts refinement to solution quality. On Humanity's Last Exam (HLE) Bio/Chem Gold, our framework achieves 48.3\% accuracy -- the highest reported to date, surpassing the strongest agent baseline by 13.4 points and leading frontier LLMs by up to 18.1 points, while simultaneously reducing token usage by 53.5\% and agent steps by 43.7\%. Results on SuperGPQA and TRQA confirm robustness across domains. Error analysis shows that reasoning failures and knowledge gaps co-occur in over 85\% of cases, while diversity analysis reveals a clear dichotomy: retrieval tasks benefit from solution variety, whereas reasoning tasks favor consensus. Together, these findings demonstrate how implicit augmentation and structured refinement overcome the inefficiencies of explicit tool use and uniform aggregation. Code is available at: https://github.com/tangxiangru/Eigen-1.

The accessibility of documents within a collection holds a pivotal role in Information Retrieval, signifying the ease of locating specific content in a collection of documents. This accessibility can be achieved via two distinct avenues. The first is through some retrieval model using a keyword or other feature-based search, and the other is where a document can be navigated using links associated with them, if available. Metrics such as PageRank, Hub, and Authority illuminate the pathways through which documents can be discovered within the network of content while the concept of Retrievability is used to quantify the ease with which a document can be found by a retrieval model. In this paper, we compare these two perspectives, PageRank and retrievability, as they quantify the importance and discoverability of content in a corpus. Through empirical experimentation on benchmark datasets, we demonstrate a subtle similarity between retrievability and PageRank particularly distinguishable for larger datasets.

Retrieval-Augmented Generation (RAG) plays a crucial role in grounding Large Language Models by leveraging external knowledge, whereas the effectiveness is often compromised by the retrieval of contextually flawed or incomplete information. To address this, knowledge graph-based RAG methods have evolved towards hierarchical structures, organizing knowledge into multi-level summaries. However, these approaches still suffer from two critical, unaddressed challenges: high-level conceptual summaries exist as disconnected ``semantic islands'', lacking the explicit relations needed for cross-community reasoning; and the retrieval process itself remains structurally unaware, often degenerating into an inefficient flat search that fails to exploit the graph's rich topology. To overcome these limitations, we introduce LeanRAG, a framework that features a deeply collaborative design combining knowledge aggregation and retrieval strategies. LeanRAG first employs a novel semantic aggregation algorithm that forms entity clusters and constructs new explicit relations among aggregation-level summaries, creating a fully navigable semantic network. Then, a bottom-up, structure-guided retrieval strategy anchors queries to the most relevant fine-grained entities and then systematically traverses the graph's semantic pathways to gather concise yet contextually comprehensive evidence sets. The LeanRAG can mitigate the substantial overhead associated with path retrieval on graphs and minimizes redundant information retrieval. Extensive experiments on four challenging QA benchmarks with different domains demonstrate that LeanRAG significantly outperforming existing methods in response quality while reducing 46\% retrieval redundancy. Code is available at: https://github.com/RaZzzyz/LeanRAG

Referring video object segmentation (RVOS) aims at segmenting an object in a video following human instruction. Current state-of-the-art methods fall into an offline pattern, in which each clip independently interacts with text embedding for cross-modal understanding. They usually present that the offline pattern is necessary for RVOS, yet model limited temporal association within each clip. In this work, we break up the previous offline belief and propose a simple yet effective online model using explicit query propagation, named OnlineRefer. Specifically, our approach leverages target cues that gather semantic information and position prior to improve the accuracy and ease of referring predictions for the current frame. Furthermore, we generalize our online model into a semi-online framework to be compatible with video-based backbones. To show the effectiveness of our method, we evaluate it on four benchmarks, \ie, Refer-Youtube-VOS, Refer-DAVIS17, A2D-Sentences, and JHMDB-Sentences. Without bells and whistles, our OnlineRefer with a Swin-L backbone achieves 63.5 J&F and 64.8 J&F on Refer-Youtube-VOS and Refer-DAVIS17, outperforming all other offline methods.

Image-text matching remains a challenging task due to heterogeneous semantic diversity across modalities and insufficient distance separability within triplets. Different from previous approaches focusing on enhancing multi-modal representations or exploiting cross-modal correspondence for more accurate retrieval, in this paper we aim to leverage the knowledge transfer between peer branches in a boosting manner to seek a more powerful matching model. Specifically, we propose a brand-new Deep Boosting Learning (DBL) algorithm, where an anchor branch is first trained to provide insights into the data properties, with a target branch gaining more advanced knowledge to develop optimal features and distance metrics. Concretely, an anchor branch initially learns the absolute or relative distance between positive and negative pairs, providing a foundational understanding of the particular network and data distribution. Building upon this knowledge, a target branch is concurrently tasked with more adaptive margin constraints to further enlarge the relative distance between matched and unmatched samples. Extensive experiments validate that our DBL can achieve impressive and consistent improvements based on various recent state-of-the-art models in the image-text matching field, and outperform related popular cooperative strategies, e.g., Conventional Distillation, Mutual Learning, and Contrastive Learning. Beyond the above, we confirm that DBL can be seamlessly integrated into their training scenarios and achieve superior performance under the same computational costs, demonstrating the flexibility and broad applicability of our proposed method. Our code is publicly available at: https://github.com/Paranioar/DBL.

Vector search and retrieval-augmented generation (RAG) rest on the assumption that cosine similarity between text embeddings reflects conceptual relatedness. We measure where this assumption breaks. We build an augmented citation graph over 3.58M scientific papers and partition it via Leiden CPM at two granularities: sub-field (L1) and research-agenda (L2, hierarchical inside each L1). Four state-of-the-art embeddings (Gemini, Qwen3-8B, Qwen3-0.6B, SPECTER2) clear the L1 bar reasonably (45-52% top-10 same-rate) but stop working at L2: only 15-21% of top-10 neighbors share the query's research agenda. In absolute terms, 8 of every 10 retrieved papers are off-agenda. The failure is universal across eight scientific domains and all four models; SPECTER2, despite its citation-based contrastive training, is the weakest. As a diagnostic probe, we test whether the same augmented graph also functions as a retrieval signal: a deliberately simple citation-count rerank reaches 57.7% top-1 L2 on top of LLM-expanded Boolean retrieval and 59.6% on top of plain BM25, on 80 curated agenda queries -- about 9 points above the best cosine retriever (Gemini, 50.6%) and 20 points above BM25 alone (39.3%). The probe isolates a slice of the agenda-matching signal the graph carries but the embeddings miss, connecting recent theoretical limits on single-vector retrieval to a concrete failure mode of scientific RAG.

Establishing precise traceability between embedded systems datasheets and their corresponding code implementations remains a fundamental challenge in systems engineering, particularly for low-level software where manual mapping between specification documents and large code repositories is infeasible. Existing Traceability Link Recovery approaches primarily rely on lexical similarity and information retrieval techniques, which struggle to capture the semantic, structural, and symbol level relationships prevalent in embedded systems software. We present a hierarchical datasheet-to-code mapping methodology that employs large language models for semantic analysis while explicitly structuring the traceability process across multiple abstraction levels. Rather than performing direct specification-to-code matching, the proposed approach progressively narrows the search space through repository-level structure inference, file-level relevance estimation, and fine-grained symbollevel alignment. The method extends beyond function-centric mapping by explicitly covering macros, structs, constants, configuration parameters, and register definitions commonly found in systems-level C/C++ codebases. We evaluate the approach on multiple open-source embedded systems repositories using manually curated datasheet-to-code ground truth. Experimental results show substantial improvements over traditional information-retrieval-based baselines, achieving up to 73.3% file mapping accuracy. We significantly reduce computational overhead, lowering total LLM token consumption by 84% and end-to-end runtime by approximately 80%. This methodology supports automated analysis of large embedded software systems and enables downstream applications such as training data generation for systems-aware machine learning models, standards compliance verification, and large-scale specification coverage analysis.

Information retrieval based knowledge base question answering (KBQA) first retrieves a subgraph to reduce search space, then reasons on the subgraph to select answer entities. Existing approaches have three issues that impede the retrieval of such subgraphs. Firstly, there is no off-the-shelf toolkit for semantic-relevant subgraph retrieval. Secondly, existing methods are knowledge-graph-dependent, resulting in outdated knowledge graphs used even in recent studies. Thirdly, previous solutions fail to incorporate the best available techniques for entity linking or path expansion. In this paper, we present SRTK, a user-friendly toolkit for semantic-relevant subgraph retrieval from large-scale knowledge graphs. SRTK is the first toolkit that streamlines the entire lifecycle of subgraph retrieval across multiple knowledge graphs. Additionally, it comes with state-of-the-art subgraph retrieval algorithms, guaranteeing an up-to-date solution set out of the box.

Attention mechanisms are critical to the success of large language models (LLMs), driving significant advancements in multiple fields. However, for graph-structured data, which requires emphasis on topological connections, they fall short compared to message-passing mechanisms on fixed links, such as those employed by Graph Neural Networks (GNNs). This raises a question: ``Does attention fail for graphs in natural language settings?'' Motivated by these observations, we embarked on an empirical study from the perspective of attention mechanisms to explore how LLMs process graph-structured data. The goal is to gain deeper insights into the attention behavior of LLMs over graph structures. We uncovered unique phenomena regarding how LLMs apply attention to graph-structured data and analyzed these findings to improve the modeling of such data by LLMs. The primary findings of our research are: 1) While LLMs can recognize graph data and capture text-node interactions, they struggle to model inter-node relationships within graph structures due to inherent architectural constraints. 2) The attention distribution of LLMs across graph nodes does not align with ideal structural patterns, indicating a failure to adapt to graph topology nuances. 3) Neither fully connected attention nor fixed connectivity is optimal; each has specific limitations in its application scenarios. Instead, intermediate-state attention windows improve LLM training performance and seamlessly transition to fully connected windows during inference. Source code: https://github.com/millioniron/LLM_exploration{LLM4Exploration}