Daily Papers

Multimodal large language models (MLLMs) are increasingly being applied to spatial cognition tasks, where they are expected to understand and interact with complex environments. Most existing works improve spatial reasoning by introducing 3D priors or geometric supervision, which enhances performance but incurs substantial data preparation and alignment costs. In contrast, purely 2D approaches often struggle with multi-frame spatial reasoning due to their limited ability to capture cross-frame spatial relationships. To address these limitations, we propose EgoMind, a Chain-of-Thought framework that enables geometry-free spatial reasoning through Role-Play Caption, which jointly constructs a coherent linguistic scene graph across frames, and Progressive Spatial Analysis, which progressively reasons toward task-specific questions. With only 5K auto-generated SFT samples and 20K RL samples, EgoMind achieves competitive results on VSI-Bench, SPAR-Bench, SITE-Bench, and SPBench, demonstrating its effectiveness in strengthening the spatial reasoning capabilities of MLLMs and highlighting the potential of linguistic reasoning for spatial cognition. Code and data are released at https://github.com/Hyggge/EgoMind.

Spatial intelligence (SI) represents a cognitive ability encompassing the visualization, manipulation, and reasoning about spatial relationships, underpinning disciplines from neuroscience to robotics. We introduce SITE, a benchmark dataset towards SI Thorough Evaluation in a standardized format of multi-choice visual question-answering, designed to assess large vision-language models' spatial intelligence across diverse visual modalities (single-image, multi-image, and video) and SI factors (figural to environmental scales, spatial visualization and orientation, intrinsic and extrinsic, static and dynamic). Our approach to curating the benchmark combines a bottom-up survey about 31 existing datasets and a top-down strategy drawing upon three classification systems in cognitive science, which prompt us to design two novel types of tasks about view-taking and dynamic scenes. Extensive experiments reveal that leading models fall behind human experts especially in spatial orientation, a fundamental SI factor. Moreover, we demonstrate a positive correlation between a model's spatial reasoning proficiency and its performance on an embodied AI task.

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolution. Since EXACT'09 pulmonary airway segmentation, limited effort has been directed to quantitative comparison of newly emerged algorithms driven by the maturity of deep learning based approaches and clinical drive for resolving finer details of distal airways for early intervention of pulmonary diseases. Thus far, public annotated datasets are extremely limited, hindering the development of data-driven methods and detailed performance evaluation of new algorithms. To provide a benchmark for the medical imaging community, we organized the Multi-site, Multi-domain Airway Tree Modeling (ATM'22), which was held as an official challenge event during the MICCAI 2022 conference. ATM'22 provides large-scale CT scans with detailed pulmonary airway annotation, including 500 CT scans (300 for training, 50 for validation, and 150 for testing). The dataset was collected from different sites and it further included a portion of noisy COVID-19 CTs with ground-glass opacity and consolidation. Twenty-three teams participated in the entire phase of the challenge and the algorithms for the top ten teams are reviewed in this paper. Quantitative and qualitative results revealed that deep learning models embedded with the topological continuity enhancement achieved superior performance in general. ATM'22 challenge holds as an open-call design, the training data and the gold standard evaluation are available upon successful registration via its homepage.

Mosquito-borne diseases pose a major global health risk, requiring early detection and proactive control of breeding sites to prevent outbreaks. In this paper, we present VisText-Mosquito, a multimodal dataset that integrates visual and textual data to support automated detection, segmentation, and reasoning for mosquito breeding site analysis. The dataset includes 1,828 annotated images for object detection, 142 images for water surface segmentation, and natural language reasoning texts linked to each image. The YOLOv9s model achieves the highest precision of 0.92926 and mAP@50 of 0.92891 for object detection, while YOLOv11n-Seg reaches a segmentation precision of 0.91587 and mAP@50 of 0.79795. For reasoning generation, our fine-tuned BLIP model achieves a final loss of 0.0028, with a BLEU score of 54.7, BERTScore of 0.91, and ROUGE-L of 0.87. This dataset and model framework emphasize the theme "Prevention is Better than Cure", showcasing how AI-based detection can proactively address mosquito-borne disease risks. The dataset and implementation code are publicly available at GitHub: https://github.com/adnanul-islam-jisun/VisText-Mosquito

Surgical site infection (SSI) is one of the most common and costly healthcare-associated infections and and surgical wound care remains a significant clinical challenge in preventing SSIs and improving patient outcomes. While recent studies have explored the use of deep learning for preliminary surgical wound screening, progress has been hindered by concerns over data privacy and the high costs associated with expert annotation. Currently, no publicly available dataset or benchmark encompasses various types of surgical wounds, resulting in the absence of an open-source Surgical-Wound screening tool. To address this gap: (1) we present SurgWound, the first open-source dataset featuring a diverse array of surgical wound types. It contains 697 surgical wound images annotated by 3 professional surgeons with eight fine-grained clinical attributes. (2) Based on SurgWound, we introduce the first benchmark for surgical wound diagnosis, which includes visual question answering (VQA) and report generation tasks to comprehensively evaluate model performance. (3) Furthermore, we propose a three-stage learning framework, WoundQwen, for surgical wound diagnosis. In the first stage, we employ five independent MLLMs to accurately predict specific surgical wound characteristics. In the second stage, these predictions serve as additional knowledge inputs to two MLLMs responsible for diagnosing outcomes, which assess infection risk and guide subsequent interventions. In the third stage, we train a MLLM that integrates the diagnostic results from the previous two stages to produce a comprehensive report. This three-stage framework can analyze detailed surgical wound characteristics and provide subsequent instructions to patients based on surgical images, paving the way for personalized wound care, timely intervention, and improved patient outcomes.

Recent advances in large language models (LLMs), particularly those enhanced through reinforced post-training, have demonstrated impressive reasoning capabilities, as exemplified by models such as OpenAI o1 and DeepSeek-R1. However, these capabilities are predominantly benchmarked on domains like mathematical problem solving and code generation -- leaving open the question of whether such reasoning skills generalize to complex, real-world scenarios. In this paper, we introduce LocationReasoner, a benchmark designed to evaluate LLMs' reasoning abilities in the context of real-world site selection, where models must identify feasible locations by reasoning over diverse and complicated spatial, environmental, and logistical constraints. The benchmark comprises over 300 carefully crafted queries of varying difficulty levels, supported by a sandbox environment with in-house tools for constraint-based location search. Extensive evaluations reveal that state-of-the-art reasoning models offer limited improvement over their non-reasoning predecessors in real-world contexts, with even the latest OpenAI o4 model failing on 30% of site selection tasks. Moreover, agentic strategies such as ReAct and Reflexion often suffer from over-reasoning, leading to worse outcomes than direct code-generation prompting. With key limitations of LLMs in holistic and non-linear reasoning highlighted, we release LocationReasoner to foster the development of LLMs and agents capable of robust, grounded reasoning in real-world decision-making tasks. Codes and data for our benchmark are available at https://github.com/miho-koda/LocationReasoner.

Humans write code in a fundamentally interactive manner and rely on constant execution feedback to correct errors, resolve ambiguities, and decompose tasks. While LLMs have recently exhibited promising coding capabilities, current coding benchmarks mostly consider a static instruction-to-code sequence transduction process, which has the potential for error propagation and a disconnect between the generated code and its final execution environment. To address this gap, we introduce InterCode, a lightweight, flexible, and easy-to-use framework of interactive coding as a standard reinforcement learning (RL) environment, with code as actions and execution feedback as observations. Our framework is language and platform agnostic, uses self-contained Docker environments to provide safe and reproducible execution, and is compatible out-of-the-box with traditional seq2seq coding methods, while enabling the development of new methods for interactive code generation. We use InterCode to create two interactive code environments with Bash and SQL as action spaces, leveraging data from the static Spider and NL2Bash datasets. We demonstrate InterCode's viability as a testbed by evaluating multiple state-of-the-art LLMs configured with different prompting strategies such as ReAct and Plan & Solve. Our results showcase the benefits of interactive code generation and demonstrate that InterCode can serve as a challenging benchmark for advancing code understanding and generation capabilities. InterCode is designed to be easily extensible and can even be used to incorporate new tasks such as Capture the Flag, a popular coding puzzle that is inherently multi-step and involves multiple programming languages. Project site with code and data: https://intercode-benchmark.github.io

Recent advances in large language models and tool-using agents have expanded the range of benchmarked web tasks. Yet an important class of specialized retrieval tasks remains undercharacterized. On many specialized data-retrieval websites, answer-bearing evidence becomes accessible only after establishing the correct site-specific retrieval state through filters, views, hierarchies, or scopes. We term this capability state-gated retrieval (SGR). We introduce SGR-Bench, a benchmark for this setting containing 100 expert-curated tasks spanning six source families and 12 public data ecosystems. Each task requires discovering the appropriate website and configuring its site-specific retrieval state to produce a structured answer. SGR-Bench pairs constraint-guided and goal-oriented formulations of the same underlying problems, enabling controlled comparisons between explicit and implicit guidance for state-gated retrieval. We evaluate eight CLI-based agentic LLM systems and three commercial search-agent products. On SGR-Bench, the strongest system reaches only 66.18% item-level F1, while row-level F1 remains much lower. A manual audit of 156 analyzable failed CLI trajectories shows why: agents often reach a relevant web source, but establish the wrong site-specific retrieval state. Retrieval-scope drift (37.2%) and criterion mismatch (27.6%) dominate, whereas final answer composition accounts for only 10.3%. The dataset and single-case evaluation instructions are available at https://huggingface.co/datasets/PKUAIWeb/SGR-BENCH.

Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary binding prediction and affinity regression. However, these evaluations provide limited evidence of whether models can localize binding sites or identify the non-covalent interactions underlying molecular recognition. To address this gap, we introduce InteractBind, a large-scale protein-ligand dataset comprising approximately 100k protein-ligand pairs, together with a benchmark for fine-grained evaluation. The core fine-grained task is that of binding-site localization, which uses protein-residue and ligand-atom interaction maps spanning six major types of non-covalent interactions to assess whether model-derived interaction maps localize binding sites. InteractBind further includes binding affinity and protein similarity-controlled splits to support realistic generalization assessment. Using InteractBind, we evaluate eight existing sequence-based and interaction-aware models, assessing binary binding prediction and binding-site localization. Results reveal limited binding-site localization despite strong binary binding prediction, with marked variation across non-covalent interaction types. Overall, InteractBind establishes a benchmark paradigm that encourages the development of more interpretable and physically grounded protein-ligand models.

Objective gait assessment in Parkinson's Disease (PD) is limited by the absence of large, diverse, and clinically annotated motion datasets. We introduce CARE-PD, the largest publicly available archive of 3D mesh gait data for PD, and the first multi-site collection spanning 9 cohorts from 8 clinical centers. All recordings (RGB video or motion capture) are converted into anonymized SMPL meshes via a harmonized preprocessing pipeline. CARE-PD supports two key benchmarks: supervised clinical score prediction (estimating Unified Parkinson's Disease Rating Scale, UPDRS, gait scores) and unsupervised motion pretext tasks (2D-to-3D keypoint lifting and full-body 3D reconstruction). Clinical prediction is evaluated under four generalization protocols: within-dataset, cross-dataset, leave-one-dataset-out, and multi-dataset in-domain adaptation. To assess clinical relevance, we compare state-of-the-art motion encoders with a traditional gait-feature baseline, finding that encoders consistently outperform handcrafted features. Pretraining on CARE-PD reduces MPJPE (from 60.8mm to 7.5mm) and boosts PD severity macro-F1 by 17 percentage points, underscoring the value of clinically curated, diverse training data. CARE-PD and all benchmark code are released for non-commercial research at https://neurips2025.care-pd.ca/.

Robotic systems that interact with the physical world must reason about kinematic and dynamic constraints imposed by their own embodiment, their environment, and the task at hand. We introduce KinDER, a benchmark for Kinematic and Dynamic Embodied Reasoning that targets physical reasoning challenges arising in robot learning and planning. KinDER comprises 25 procedurally generated environments, a Gymnasium-compatible Python library with parameterized skills and demonstrations, and a standardized evaluation suite with 13 implemented baselines spanning task and motion planning, imitation learning, reinforcement learning, and foundation-model-based approaches. The environments are designed to isolate five core physical reasoning challenges: basic spatial relations, nonprehensile multi-object manipulation, tool use, combinatorial geometric constraints, and dynamic constraints, disentangled from perception, language understanding, and application-specific complexity. Empirical evaluation shows that existing methods struggle to solve many of the environments, indicating substantial gaps in current approaches to physical reasoning. We additionally include real-to-sim-to-real experiments on a mobile manipulator to assess the correspondence between simulation and real-world physical interaction. KinDER is fully open-sourced and intended to enable systematic comparison across diverse paradigms for advancing physical reasoning in robotics. Website and code: https://prpl-group.com/kinder-site/

Identifying metabolic sites where cytochrome P450 enzymes metabolize small-molecule drugs is essential for drug discovery. Although existing computational approaches have been proposed for site-of-metabolism prediction, they typically ignore cytochrome P450 isoform identity or model isoforms independently, thereby failing to fully capture inherent cross-isoform metabolic patterns. In addition, prior evaluations often rely on top-k metrics, where false positive atoms may be included among the top predictions, underscoring the need for complementary metrics that more directly assess binary atom-level discrimination under severe class imbalance. We propose ATTNSOM, an atom-level site-of-metabolism prediction framework that integrates intrinsic molecular reactivity with cross-isoform relationships. The model combines a shared graph encoder, molecule-conditioned atom representations, and a cross-attention mechanism to capture correlated metabolic patterns across cytochrome P450 isoforms. The model is evaluated on two benchmark datasets annotated with site-of-metabolism labels at atom resolution. Across these benchmarks, the model achieves consistently strong top-k performance across multiple cytochrome P450 isoforms. Relative to ablated variants, the model yields higher Matthews correlation coefficient, indicating improved discrimination of true metabolic sites. These results support the importance of explicitly modeling cross-isoform relationships for site-of-metabolism prediction. The code and datasets are available at https://github.com/dmis-lab/ATTNSOM.

Recent AI-based video editing has enabled users to edit videos through simple text prompts, significantly simplifying the editing process. However, recent zero-shot video editing techniques primarily focus on global or single-object edits, which can lead to unintended changes in other parts of the video. When multiple objects require localized edits, existing methods face challenges, such as unfaithful editing, editing leakage, and lack of suitable evaluation datasets and metrics. To overcome these limitations, we propose a zero-shot Multi-Instance Video Editing framework, called MIVE. MIVE is a general-purpose mask-based framework, not dedicated to specific objects (e.g., people). MIVE introduces two key modules: (i) Disentangled Multi-instance Sampling (DMS) to prevent editing leakage and (ii) Instance-centric Probability Redistribution (IPR) to ensure precise localization and faithful editing. Additionally, we present our new MIVE Dataset featuring diverse video scenarios and introduce the Cross-Instance Accuracy (CIA) Score to evaluate editing leakage in multi-instance video editing tasks. Our extensive qualitative, quantitative, and user study evaluations demonstrate that MIVE significantly outperforms recent state-of-the-art methods in terms of editing faithfulness, accuracy, and leakage prevention, setting a new benchmark for multi-instance video editing. The project page is available at https://kaist-viclab.github.io/mive-site/

Every prediction from a generative medical event model is bounded by how clinical events are tokenized, yet input representation is rarely isolated from other system and architectural choices. We evaluate how representation decisions affect downstream prediction after a shared one-epoch pretraining budget. We train 28 matched transformers on MIMIC-IV and evaluate them on 30 clinical outcomes in three experiments: (1) quantization granularity, reference-range anchoring, and code-value fusion; (2) value encoding (hard bins, soft discretization, code-normalized xVal) crossed with temporal encoding (event order, time tokens, admission-relative RoPE); and (3) native MIMIC laboratory/vital codes versus the Common Longitudinal ICU Format (CLIF)-remapped laboratory/vital codes with compression-preserving perturbation arms. In Experiment 1, fused code-value tokenization improves mortality AUROC from 0.891 to 0.915 (BH-adjusted p < 0.001), hospital length-of-stay AUROC from 0.763 to 0.788 (BH-adjusted p < 0.001), and, for the decile fused-vs-unfused comparison, mean regression Spearman rho across the 13 regression outcomes from 0.414 to 0.494. Across the three temporal encodings, event order only and admission-relative RoPE match or exceed inserting time tokens on average while shortening sequences by 11%. CLIF remapping preserves downstream performance in our single-site setting while yielding a smaller, clinically interpretable token set compatible with multi-site use. Finer-than-decile quantization, reference-range anchoring, and soft discretization help in selective outcomes, while code-normalized xVal remains well below the discrete and soft families, consistent with near-median suppression that persists after the affine variant.

The detection of ligand binding sites for proteins is a fundamental step in Structure-Based Drug Design. Despite notable advances in recent years, existing methods, datasets, and evaluation metrics are confronted with several key challenges: (1) current datasets and methods are centered on individual protein-ligand complexes and neglect that diverse binding sites may exist across multiple complexes of the same protein, introducing significant statistical bias; (2) ligand binding site detection is typically modeled as a discontinuous workflow, employing binary segmentation and subsequent clustering algorithms; (3) traditional evaluation metrics do not adequately reflect the actual performance of different binding site prediction methods. To address these issues, we first introduce UniSite-DS, the first UniProt (Unique Protein)-centric ligand binding site dataset, which contains 4.81 times more multi-site data and 2.08 times more overall data compared to the previously most widely used datasets. We then propose UniSite, the first end-to-end ligand binding site detection framework supervised by set prediction loss with bijective matching. In addition, we introduce Average Precision based on Intersection over Union (IoU) as a more accurate evaluation metric for ligand binding site prediction. Extensive experiments on UniSite-DS and several representative benchmark datasets demonstrate that IoU-based Average Precision provides a more accurate reflection of prediction quality, and that UniSite outperforms current state-of-the-art methods in ligand binding site detection. The dataset and codes will be made publicly available at https://github.com/quanlin-wu/unisite.

Recently, extensive deep learning architectures and pretraining strategies have been explored to support downstream protein applications. Additionally, domain-specific models incorporating biological knowledge have been developed to enhance performance in specialized tasks. In this work, we introduce Protap, a comprehensive benchmark that systematically compares backbone architectures, pretraining strategies, and domain-specific models across diverse and realistic downstream protein applications. Specifically, Protap covers five applications: three general tasks and two novel specialized tasks, i.e., enzyme-catalyzed protein cleavage site prediction and targeted protein degradation, which are industrially relevant yet missing from existing benchmarks. For each application, Protap compares various domain-specific models and general architectures under multiple pretraining settings. Our empirical studies imply that: (i) Though large-scale pretraining encoders achieve great results, they often underperform supervised encoders trained on small downstream training sets. (ii) Incorporating structural information during downstream fine-tuning can match or even outperform protein language models pretrained on large-scale sequence corpora. (iii) Domain-specific biological priors can enhance performance on specialized downstream tasks. Code and datasets are publicly available at https://github.com/Trust-App-AI-Lab/protap.

The rapid advancement of bug-finding techniques has led to the discovery of more vulnerabilities than developers can reasonably fix, creating an urgent need for effective Automated Program Repair (APR) methods. However, the complexity of modern bugs often makes precise root cause analysis difficult and unreliable. To address this challenge, we propose crash-site repair to simplify the repair task while still mitigating the risk of exploitation. In addition, we introduce a template-guided patch generation approach that significantly reduces the token cost of Large Language Models (LLMs) while maintaining both efficiency and effectiveness. We implement our prototype system, WILLIAMT, and evaluate it against state-of-the-art APR tools. Our results show that, when combined with the top-performing agent CodeRover-S, WILLIAMT reduces token cost by 45.9% and increases the bug-fixing rate to 73.5% (+29.6%) on ARVO, a ground-truth open source software vulnerabilities benchmark. Furthermore, we demonstrate that WILLIAMT can function effectively even without access to frontier LLMs: even a local model running on a Mac M4 Mini achieves a reasonable repair rate. These findings highlight the broad applicability and scalability of WILLIAMT.

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in tasks such as abnormality detection and report generation for anatomical modalities, their capability in functional imaging remains largely unexplored. In this work, we identify and quantify a fundamental functional perception gap: the inability of current vision encoders to decode functional tracer biodistribution independent of morphological priors. Identifying Positron Emission Tomography (PET) as the quintessential modality to investigate this disconnect, we introduce PET-Bench, the first large-scale functional imaging benchmark comprising 52,308 hierarchical QA pairs from 9,732 multi-site, multi-tracer PET studies. Extensive evaluation of 19 state-of-the-art MLLMs reveals a critical safety hazard termed the Chain-of-Thought (CoT) hallucination trap. We observe that standard CoT prompting, widely considered to enhance reasoning, paradoxically decouples linguistic generation from visual evidence in PET, producing clinically fluent but factually ungrounded diagnoses. To resolve this, we propose Atomic Visual Alignment (AVA), a simple fine-tuning strategy that enforces the mastery of low-level functional perception prior to high-level diagnostic reasoning. Our results demonstrate that AVA effectively bridges the perception gap, transforming CoT from a source of hallucination into a robust inference tool and improving diagnostic accuracy by up to 14.83%. Code and data are available at https://github.com/yezanting/PET-Bench.

Understanding context is key to understanding human language, an ability which Large Language Models (LLMs) have been increasingly seen to demonstrate to an impressive extent. However, though the evaluation of LLMs encompasses various domains within the realm of Natural Language Processing, limited attention has been paid to probing their linguistic capability of understanding contextual features. This paper introduces a context understanding benchmark by adapting existing datasets to suit the evaluation of generative models. This benchmark comprises of four distinct tasks and nine datasets, all featuring prompts designed to assess the models' ability to understand context. First, we evaluate the performance of LLMs under the in-context learning pretraining scenario. Experimental results indicate that pre-trained dense models struggle with understanding more nuanced contextual features when compared to state-of-the-art fine-tuned models. Second, as LLM compression holds growing significance in both research and real-world applications, we assess the context understanding of quantized models under in-context-learning settings. We find that 3-bit post-training quantization leads to varying degrees of performance reduction on our benchmark. We conduct an extensive analysis of these scenarios to substantiate our experimental results.

Training autonomous web agents is fundamentally limited by the environments they learn from: real-world websites are unsafe to explore, hard to reset, and rarely provide verifiable feedback. We propose VeriEnv, a framework that treats language models as environment creators, automatically cloning real-world websites into fully executable, verifiable synthetic environments. By exposing controlled internal access via a Python SDK, VeriEnv enables agents to self-generate tasks with deterministic, programmatically verifiable rewards, eliminating reliance on heuristic or LLM-based judges. This design decouples agent learning from unsafe real-world interaction while enabling scalable self-evolution through environment expansion. Through experiments on web agent benchmarks, we show that agents trained with VeriEnv generalize to unseen websites, achieve site-specific mastery through self-evolving training, and benefit from scaling the number of training environments. Code and resources will be released at https://github.com/kyle8581/VeriEnv upon acceptance.

Despite remarkable progress, multimodal foundation models still exhibit surprising deficiencies in spatial intelligence. In this work, we explore scaling up multimodal foundation models to cultivate spatial intelligence within the SenseNova-SI family, built upon established multimodal foundations including visual understanding models (i.e., Qwen3-VL and InternVL3) and unified understanding and generation models (i.e., Bagel). We take a principled approach to constructing high-performing and robust spatial intelligence by systematically curating SenseNova-SI-8M: eight million diverse data samples under a rigorous taxonomy of spatial capabilities. SenseNova-SI demonstrates unprecedented performance across a broad range of spatial intelligence benchmarks: 68.7% on VSI-Bench, 43.3% on MMSI, 85.6% on MindCube, 54.6% on ViewSpatial, and 50.1% on SITE, while maintaining strong general multimodal understanding (e.g., 84.9% on MMBench-En). More importantly, we analyze the impact of data scaling, discuss early signs of emergent generalization capabilities enabled by diverse data training, analyze the risk of overfitting and language shortcuts, present a preliminary study on spatial chain-of-thought reasoning, and validate the potential downstream application. SenseNova-SI is an ongoing project, and this report will be updated continuously. All newly trained multimodal foundation models are publicly released to facilitate further research in this direction.

Open community-driven platforms like Chatbot Arena that collect user preference data from site visitors have gained a reputation as one of the most trustworthy publicly available benchmarks for LLM performance. While now standard, it is tricky to implement effective guardrails to collect high-quality annotations from humans. In this paper, we demonstrate that three sources of bad annotations, both malicious and otherwise, can corrupt the reliability of open leaderboard rankings. In particular, we show that only 10\% of poor quality votes by apathetic (site visitors not appropriately incentivized to give correct votes) or adversarial (bad actors seeking to inflate the ranking of a target model) annotators can change the rankings of models by up to 5 places on the leaderboard. Finally, we discuss open challenges in ensuring high-quality human annotations.

Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based tasks. However, pLMs lack structural context. Conversely, graph neural networks (GNNs) designed to leverage 3D structural information have shown promising generalization in protein-related prediction tasks, but their effectiveness is often constrained by the scarcity of labeled structural data. Recognizing that sequence and structural representations are complementary perspectives of the same protein entity, we propose a multimodal bidirectional hierarchical fusion framework to effectively merge these modalities. Our framework employs attention and gating mechanisms to enable effective interaction between pLMs-generated sequential representations and GNN-extracted structural features, improving information exchange and enhancement across layers of the neural network. This bidirectional and hierarchical (Bi-Hierarchical) fusion approach leverages the strengths of both modalities to capture richer and more comprehensive protein representations. Based on the framework, we further introduce local Bi-Hierarchical Fusion with gating and global Bi-Hierarchical Fusion with multihead self-attention approaches. Our method demonstrates consistent improvements over strong baselines and existing fusion techniques in a variety of protein representation learning benchmarks, including enzyme EC classification, model quality assessment, protein-ligand binding affinity prediction, protein-protein binding site prediction, and B cell epitopes prediction. Our method establishes a new state-of-the-art for multimodal protein representation learning, emphasizing the efficacy of Bi-Hierarchical Fusion in bridging sequence and structural modalities.

OpenAI's GPT-Image-2 has effectively erased the visual boundary between authentic and AI-edited document images: a single number on a receipt can be replaced in under a second for a few cents. We release AIForge-Doc v2, a paired dataset of 3,066 GPT-Image-2 document forgeries with pixel-precise masks in DocTamper-compatible format, and benchmark four lines of defence: human inspectors (N=120, n=365 pair-votes via the public 2AFC site CanUSpotAI.com), TruFor (generic forensic), DocTamper (qcf-568, document-specific), and the same GPT-Image-2 model as a zero-shot self-judge -- asked, to avoid the trivial "image is mostly real" reading, whether any region was generated or edited by an AI image model. Human 2AFC accuracy is 0.501, indistinguishable from chance: even side-by-side, inspectors cannot tell GPT-Image-2 receipt forgeries from authentic counterparts. The three computational judges sit only modestly above (TruFor 0.599, DocTamper 0.585, self-judge 0.532). The self-judge fails consistently, not by chance: across five prompt strategies and four policies for handling ambiguous responses, AUC never rises above 0.59. To rule out the possibility that the two forensic detectors are broken on our source domain rather than blind to AI inpainting, we calibrate each on a same-domain traditional-tampering set built for its training distribution: TruFor reaches AUC 0.962 on cross-camera splicing of our dataset, DocTamper reaches 0.852 on cross-document OCR-token splicing with two-pass JPEG re-encoding. Both retain near-published performance on traditional tampering; switching to GPT-Image-2 inpainting drops AUC by 0.27-0.36 (0.962->0.599 TruFor; 0.852->0.585 DocTamper), isolating a detection gap specific to GPT-Image-2 inpainting. We release the dataset, pipeline, four-judge protocol, and calibration sets.