Daily Papers

Video generators build long videos by composing shorter parts, either by generating segments one after another or by autoregressively extending chunks. Each new part usually depends on memories of historical observations, such as recent frames, selected key frames, memory banks, or cached features. These memories preserve visible evidence from the past, but current generators do not reliably turn such evidence into a world-state interface: what holds in the video world after previous actions and how it should change under the next prompt. A past frame remains valid history, but it may not describe the state needed by the next segment; some states must instead be inferred from occluded or implicit changes rather than copied from a directly observed frame. This creates a simple but overlooked question for video continuation: given a previous video, its prompt, and a new prompt, can a model generate a continuation that reflects the state determined by both the historical video and the new prompt? To answer this question, we introduce Statebench, a benchmark that targets this gap by testing continuations over three state categories: past-visible states, occluded-process states, and complex-transition states. We further propose Stateagent, which explicitly maintains an entity-state representation, updates it under the new prompt, grounds the predicted post-action state as a future end frame, and renders the next video. Experiments show that our method improves controlled video continuation by raising the all-case state score (SCS-All) from 45.2 to 69.3, and also benefits story generation at the one-minute scale. Code is avaliable at https://github.com/AMAP-ML/StateAgent.

Transition state (TS) structures define the critical geometries and energy barriers underlying chemical reactivity, yet their fleeting nature renders them experimentally elusive and drives the reliance on costly, high-throughput density functional theory (DFT) calculations. Here, we introduce TS-GEN, a conditional flow-matching generative model that maps samples from a simple Gaussian prior directly to transition-state saddle-point geometries in a single, deterministic pass. By embedding both reactant and product conformations as conditioning information, TS-GEN learns to transport latent noise to true TS structures via an optimal-transport path, effectively replacing the iterative optimization common in nudged-elastic band or string-method algorithms. TS-GEN delivers unprecedented accuracy, achieving a root-mean-square deviation of 0.004 mathring{A} (vs. 0.103 mathring{A} for prior state-of-the-art) and a mean barrier-height error of 1.019 {rm kcal/mol} (vs. 2.864 {rm kcal/mol}), while requiring only 0.06 {rm s} GPU time per inference. Over 87% of generated TSs meet chemical-accuracy criteria (<1.58 {rm kcal/mol} error), substantially outpacing existing methods. TS-GEN also exhibits strong transferability to out-of-distribution reactions from a larger database. By uniting sub-angstrom precision, sub-second speed, and broad applicability, TS-GEN will be highly useful for high-throughput exploration of complex reaction networks, paving the way to the exploration of novel chemical reaction mechanisms.

Despite the variety of available computational approaches, state-of-the-art methods for calculating excitation energies such as time-dependent density functional theory (TDDFT), are computationally demanding and thus limited to moderate system sizes. Here, we introduce a new variation of constrained DFT (CDFT), wherein the constraint corresponds to a particular transition (T), or combination of transitions, between occupied and virtual orbitals, rather than a region of the simulation space as in traditional CDFT. We compare T-CDFT with TDDFT and DeltaSCF results for the low lying excited states (S_{1} and T_{1}) of a set of gas phase acene molecules and OLED emitters, as well as with reference results from the literature. At the PBE level of theory, T-CDFT outperforms DeltaSCF for both classes of molecules, while also proving to be more robust. For the local excitations seen in the acenes, T-CDFT and TDDFT perform equally well. For the charge-transfer (CT)-like excitations seen in the OLED molecules, T-CDFT also performs well, in contrast to the severe energy underestimation seen with TDDFT. In other words, T-CDFT is equally applicable to both local excitations and CT states, providing more reliable excitation energies at a much lower computational cost than TDDFT. T-CDFT is designed for large systems and has been implemented in the linear scaling BigDFT code. It is therefore ideally suited for exploring the effects of explicit environments on excitation energies, paving the way for future simulations of excited states in complex realistic morphologies, such as those which occur in OLED materials.

While Long Chain-of-Thought (CoT) reasoning significantly improves Large Language Models (LLMs) performance on complex reasoning tasks, the substantial computational and memory costs of generating long CoT sequences limit their efficiency and practicality. Existing studies usually enhance the reasoning efficiency of LLMs by compressing CoT sequences. However, this approach conflicts with test-time scaling, limiting the reasoning capacity of LLMs. In this paper, we propose an efficient reasoning framework that models the reasoning process of LLMs as a state-transition process. Specifically, we first apply a linear attention mechanism to estimate the LLM's reasoning state, which records the historical reasoning information from previous reasoning steps. Then, based on the query prompt and the reasoning state, the LLM can efficiently perform the current reasoning step and update the state. With the linear attention, each token in the current reasoning step can directly retrieve relevant historical reasoning information from the reasoning state, without explicitly attending to tokens in previous reasoning steps. In this way, the computational complexity of attention is reduced from quadratic to linear, significantly improving the reasoning efficiency of LLMs. In addition, we propose a state-based reasoning strategy to mitigate the over-thinking issue caused by noisy reasoning steps. Extensive experiments across multiple datasets and model sizes demonstrate that our framework not only improves the reasoning efficiency of LLMs but also enhances their reasoning performance.

Chain-of-thought (CoT) reasoning enables large language models (LLMs) to break down complex problems into interpretable intermediate steps, significantly enhancing model transparency and performance in reasoning tasks. However, conventional CoT methods rely on heuristic sampling without structured modeling of reasoning transitions, constraining their ability to systematically explore and discover diverse and effective reasoning trajectories. In this work, we introduce CTRLS, a framework that formulates CoT reasoning as a Markov decision process (MDP) with latent state transitions, enabling principled and state-aware exploration via distributional reinforcement learning. By modelling reasoning actions as explicit probability distributions in latent space, our approach explicitly models epistemic uncertainty, facilitating robust exploration of the reasoning space. As part of our framework, we introduce an on-policy reinforcement learning strategy incorporating epsilon-greedy exploration and entropy-based regularization to iteratively refine latent state transitions without requiring additional fine-tuning of the underlying LLM. Theoretical analyses provide evidence lower bounds (ELBO), theoretically grounding our transition-aware modeling of latent reasoning dynamics. Further experiments demonstrate improvements in reasoning accuracy, diversity, and exploration efficiency across benchmark reasoning tasks.

Solving complex planning problems requires Large Language Models (LLMs) to explicitly model the state transition to avoid rule violations, comply with constraints, and ensure optimality-a task hindered by the inherent ambiguity of natural language. To overcome such ambiguity, Planning Domain Definition Language (PDDL) is leveraged as a planning abstraction that enables precise and formal state descriptions. With PDDL, we can generate a symbolic world model where classic searching algorithms, such as A*, can be seamlessly applied to find optimal plans. However, directly generating PDDL domains with current LLMs remains an open challenge due to the lack of PDDL training data. To address this challenge, we propose to scale up the test-time computation of LLMs to enhance their PDDL reasoning capabilities, thereby enabling the generation of high-quality PDDL domains. Specifically, we introduce a simple yet effective algorithm, which first employs a Best-of-N sampling approach to improve the quality of the initial solution and then refines the solution in a fine-grained manner with verbalized machine learning. Our method outperforms o1-mini by a considerable margin in the generation of PDDL domain, achieving over 50% success rate on two tasks (i.e., generating PDDL domains from natural language description or PDDL problems). This is done without requiring additional training. By taking advantage of PDDL as state abstraction, our method is able to outperform current state-of-the-art methods on almost all competition-level planning tasks.

Understanding the temporal dynamics of Earth's surface is a mission of multi-temporal remote sensing image analysis, significantly promoted by deep vision models with its fuel -- labeled multi-temporal images. However, collecting, preprocessing, and annotating multi-temporal remote sensing images at scale is non-trivial since it is expensive and knowledge-intensive. In this paper, we present a scalable multi-temporal remote sensing change data generator via generative modeling, which is cheap and automatic, alleviating these problems. Our main idea is to simulate a stochastic change process over time. We consider the stochastic change process as a probabilistic semantic state transition, namely generative probabilistic change model (GPCM), which decouples the complex simulation problem into two more trackable sub-problems, \ie, change event simulation and semantic change synthesis. To solve these two problems, we present the change generator (Changen), a GAN-based GPCM, enabling controllable object change data generation, including customizable object property, and change event. The extensive experiments suggest that our Changen has superior generation capability, and the change detectors with Changen pre-training exhibit excellent transferability to real-world change datasets.

The evolution of Large Language Models (LLMs) from static instruction-followers to autonomous agents necessitates operating within complex, stateful environments to achieve precise state-transition objectives. However, this paradigm is bottlenecked by data scarcity, as existing tool-centric reverse-synthesis pipelines fail to capture the rigorous logic of real-world applications. We introduce LOGIGEN, a logic-driven framework that synthesizes verifiable training data based on three core pillars: Hard-Compiled Policy Grounding, Logic-Driven Forward Synthesis, and Deterministic State Verification. Specifically, a Triple-Agent Orchestration is employed: the Architect compiles natural-language policy into database constraints to enforce hard rules; the Set Designer initializes boundary-adjacent states to trigger critical policy conflicts; and the Explorer searches this environment to discover causal solution paths. This framework yields a dataset of 20,000 complex tasks across 8 domains, where validity is strictly guaranteed by checking exact state equivalence. Furthermore, we propose a verification-based training protocol where Supervised Fine-Tuning (SFT) on verifiable trajectories establishes compliance with hard-compiled policy, while Reinforcement Learning (RL) guided by dense state-rewards refines long-horizon goal achievement. On τ^2-Bench, LOGIGEN-32B(RL) achieves a 79.5\% success rate, substantially outperforming the base model (40.7\%). These results demonstrate that logic-driven synthesis combined with verification-based training effectively constructs the causally valid trajectories needed for next-generation agents.

Intelligent robots need to interact with diverse objects across various environments. The appearance and state of objects frequently undergo complex transformations depending on the object properties, e.g., phase transitions. However, in the vision community, segmenting dynamic objects with phase transitions is overlooked. In light of this, we introduce the concept of phase in segmentation, which categorizes real-world objects based on their visual characteristics and potential morphological and appearance changes. Then, we present a new benchmark, Multi-Phase, Multi-Transition, and Multi-Scenery Video Object Segmentation (M^3-VOS), to verify the ability of models to understand object phases, which consists of 479 high-resolution videos spanning over 10 distinct everyday scenarios. It provides dense instance mask annotations that capture both object phases and their transitions. We evaluate state-of-the-art methods on M^3-VOS, yielding several key insights. Notably, current appearance-based approaches show significant room for improvement when handling objects with phase transitions. The inherent changes in disorder suggest that the predictive performance of the forward entropy-increasing process can be improved through a reverse entropy-reducing process. These findings lead us to propose ReVOS, a new plug-andplay model that improves its performance by reversal refinement. Our data and code will be publicly available at https://zixuan-chen.github.io/M-cube-VOS.github.io/.

Code agents are advancing rapidly, but debugging them is becoming increasingly difficult. As frameworks orchestrate parallel tool calls and multi-stage workflows over complex tasks, making the agent's state transitions and error propagation hard to observe. In these runs, an early misstep can trap the agent in unproductive loops or even cascade into fundamental errors, forming hidden error chains that make it hard to tell when the agent goes off track and why. Existing agent tracing analyses either focus on simple interaction or rely on small-scale manual inspection, which limits their scalability and usefulness for real coding workflows. We present CodeTracer, a tracing architecture that parses heterogeneous run artifacts through evolving extractors, reconstructs the full state transition history as a hierarchical trace tree with persistent memory, and performs failure onset localization to pinpoint the failure origin and its downstream chain. To enable systematic evaluation, we construct CodeTraceBench from a large collection of executed trajectories generated by four widely used code agent frameworks on diverse code tasks (e.g., bug fixing, refactoring, and terminal interaction), with supervision at both the stage and step levels for failure localization. Experiments show that CodeTracer substantially outperforms direct prompting and lightweight baselines, and that replaying its diagnostic signals consistently recovers originally failed runs under matched budgets. Our code and data are publicly available.

Knowledge graph embedding (KGE) aims to learn continuous vectors of relations and entities in knowledge graph. Recently, transition-based KGE methods have achieved promising performance, where the single relation vector learns to translate head entity to tail entity. However, this scoring pattern is not suitable for complex scenarios where the same entity pair has different relations. Previous models usually focus on the improvement of entity representation for 1-to-N, N-to-1 and N-to-N relations, but ignore the single relation vector. In this paper, we propose a novel transition-based method, TranS, for knowledge graph embedding. The single relation vector in traditional scoring patterns is replaced with synthetic relation representation, which can solve these issues effectively and efficiently. Experiments on a large knowledge graph dataset, ogbl-wikikg2, show that our model achieves state-of-the-art results.

Graphs are an essential part of many machine learning problems such as analysis of parse trees, social networks, knowledge graphs, transportation systems, and molecular structures. Applying machine learning in these areas typically involves learning the graph structure and the relationship between the nodes of the graph. However, learning the graph structure is often complex, particularly when the graph is cyclic, and the transitions from one node to another are conditioned such as graphs used to represent a finite state machine. To solve this problem, we propose to extend the memory based Neural Turing Machine (NTM) with two novel additions. We allow for transitions between nodes to be influenced by information received from external environments, and we let the NTM learn the context of those transitions. We refer to this extension as the Conditional Neural Turing Machine (CNTM). We show that the CNTM can infer conditional transition graphs by empirically verifiying the model on two data sets: a large set of randomly generated graphs, and a graph modeling the information retrieval process during certain crisis situations. The results show that the CNTM is able to reproduce the paths inside the graph with accuracy ranging from 82,12% for 10 nodes graphs to 65,25% for 100 nodes graphs.

We introduce CrossWKV, a novel cross-attention mechanism for the state-based RWKV-7 model, designed to enhance the expressive power of text-to-image generation. Leveraging RWKV-7's linear-complexity Weighted Key-Value (WKV) architecture, CrossWKV integrates text and image modalities in a single pass, utilizing a generalized delta rule with vector-valued gating and low-rank adaptations (LoRA) to achieve superior cross-modal alignment. Unlike Transformer-based models, CrossWKV's non-diagonal, input-dependent transition matrix enables it to represent complex functions beyond the TC^0 complexity class, including all regular languages, as demonstrated by its ability to perform state-tracking tasks like S_5 permutation modeling. Evaluated within the Diffusion in RWKV-7 (DIR-7) on datasets such as LAION-5B and ImageNet, CrossWKV achieves a Frechet Inception Distance (FID) of 2.88 and a CLIP score of 0.33 on ImageNet 256x256, matching state-of-the-art performance while offering robust generalization across diverse prompts. The model's enhanced expressivity, combined with constant memory usage and linear scaling, positions it as a powerful solution for advanced cross-modal tasks, with potential applications in high-resolution generation and dynamic state manipulation.Code at https://github.com/TorchRWKV/flash-linear-attention

Instruction-based image editing has achieved remarkable success in semantic alignment, yet state-of-the-art models frequently fail to render physically plausible results when editing involves complex causal dynamics, such as refraction or material deformation. We attribute this limitation to the dominant paradigm that treats editing as a discrete mapping between image pairs, which provides only boundary conditions and leaves transition dynamics underspecified. To address this, we reformulate physics-aware editing as predictive physical state transitions and introduce PhysicTran38K, a large-scale video-based dataset comprising 38K transition trajectories across five physical domains, constructed via a two-stage filtering and constraint-aware annotation pipeline. Building on this supervision, we propose PhysicEdit, an end-to-end framework equipped with a textual-visual dual-thinking mechanism. It combines a frozen Qwen2.5-VL for physically grounded reasoning with learnable transition queries that provide timestep-adaptive visual guidance to a diffusion backbone. Experiments show that PhysicEdit improves over Qwen-Image-Edit by 5.9% in physical realism and 10.1% in knowledge-grounded editing, setting a new state-of-the-art for open-source methods, while remaining competitive with leading proprietary models.

We investigate BZT shocks and the QCD phase transition in the dense core of a cold quark star in beta equilibrium subject to the multicomponent van der Waals (MvdW) equation of state (EoS) as a model of internal structure. When this system is expressed in terms of multiple components, it can be used to explore the impact of a phase transition from a hadronic state to a quark plasma state with a complex clustering structure. The clustering can take the form of colored diquarks or triquarks and bound colorless meson, baryon, or hyperon states at the phase transition boundary. The resulting multicomponent EoS system is nonconvex, which can give rise to Bethe-Zel'dovich-Thompson (BZT) phase changing shock waves. Using the BZT shock wave condition we find constraints on the quark density and examine how this changes the tidal deformability of the compact core. These results are then combined with the TOV equations to find the resulting mass and radius relationship. These state are compared to recent astrophysical high-mass neutron star systems, which may provide evidence for a core that has undergone a quark gluon phase transition such as PSR 0943+10 or GW 190814.

Visual counting is a fundamental pillar of multimodal intelligence, requiring a seamless integration of fine-grained grounding and spatial reasoning. While Multimodal Large Language Models (MLLMs) have achieved remarkable success in qualitative scene understanding, their quantitative precision remains a significant bottleneck, often characterized by persistent numerical hallucinations. Existing counting benchmarks primarily focus on basic perception in simplified contexts, failing to capture the complex failure modes that emerge under logical constraints or adversarial conditions. To address these limitations, we introduce HoloCount, a holistic and diagnostically rich benchmark structured around a three-level hierarchical taxonomy. HoloCount evaluates MLLMs across: (1) Semantic Counting, focusing on atomic and property-based enumeration; (2) Analytical Counting, assessing logical composition through spatial and set-based reasoning; and (3) Robustness Testing, probing model integrity against adverse scenarios and grounded counter-priors, such as high-density scenes and linguistic biases. Through an exhaustive evaluation of over 20 state-of-the-art MLLMs, we reveal a critical performance gap: even top-tier models degrade significantly as tasks transition from perception to complex analytical reasoning and adverse scenarios. Our findings provide a systematic landscape of current MLLM counting capabilities and offer a roadmap for developing more grounded and reliable multimodal systems. The dataset is available at https://mm-mvr.github.io/HoloCount/.

Unsupervised pre-training strategies have proven to be highly effective in natural language processing and computer vision. Likewise, unsupervised reinforcement learning (RL) holds the promise of discovering a variety of potentially useful behaviors that can accelerate the learning of a wide array of downstream tasks. Previous unsupervised RL approaches have mainly focused on pure exploration and mutual information skill learning. However, despite the previous attempts, making unsupervised RL truly scalable still remains a major open challenge: pure exploration approaches might struggle in complex environments with large state spaces, where covering every possible transition is infeasible, and mutual information skill learning approaches might completely fail to explore the environment due to the lack of incentives. To make unsupervised RL scalable to complex, high-dimensional environments, we propose a novel unsupervised RL objective, which we call Metric-Aware Abstraction (METRA). Our main idea is, instead of directly covering the entire state space, to only cover a compact latent space Z that is metrically connected to the state space S by temporal distances. By learning to move in every direction in the latent space, METRA obtains a tractable set of diverse behaviors that approximately cover the state space, being scalable to high-dimensional environments. Through our experiments in five locomotion and manipulation environments, we demonstrate that METRA can discover a variety of useful behaviors even in complex, pixel-based environments, being the first unsupervised RL method that discovers diverse locomotion behaviors in pixel-based Quadruped and Humanoid. Our code and videos are available at https://seohong.me/projects/metra/

The adaptation of large-scale Vision-Language Models (VLMs) like CLIP to downstream tasks with extremely limited data -- specifically in the one-shot regime -- is often hindered by a significant "Stability-Plasticity" dilemma. While efficient caching mechanisms have been introduced by training-free methods such as Tip-Adapter, these approaches often function as local Nadaraya-Watson estimators. Such estimators are characterized by inherent boundary bias and a lack of global structural regularization. In this paper, ReHARK (Refined Hybrid Adaptive RBF Kernels) is proposed as a synergistic training-free framework that reinterprets few-shot adaptation through global proximal regularization in a Reproducing Kernel Hilbert Space (RKHS). A multistage refinement pipeline is introduced, consisting of: (1) Hybrid Prior Construction, where zero-shot textual knowledge from CLIP and GPT-3 is fused with visual class prototypes to form a robust semantic-visual anchor; (2) Support Set Augmentation (Bridging), where intermediate samples are generated to smooth the transition between visual and textual modalities; (3) Adaptive Distribution Rectification, where test feature statistics are aligned with the augmented support set to mitigate domain shifts; and (4) Multi-Scale RBF Kernels, where an ensemble of kernels is employed to capture complex feature geometries across diverse scales. Superior stability and accuracy are demonstrated through extensive experiments on 11 diverse benchmarks. A new state-of-the-art for one-shot adaptation is established by ReHARK, which achieves an average accuracy of 65.83%, significantly outperforming existing baselines. Code is available at https://github.com/Jahid12012021/ReHARK.

Identifying transition states (TSs) on potential energy surfaces is a central computational bottleneck in mechanistic studies of catalytic materials. A TS search is not a single calculation but a long-horizon, multi-step workflow of atomistic simulations with delayed, asynchronous feedback and heterogeneous failure modes that require a joint multimodal analysis of scalar convergence diagnostics and atomic geometries along the reaction path. To address this challenge, we propose TSAgent, an agentic workflow that automates TS search directly at the density functional theory (DFT) level of quantum chemical accuracy. TSAgent operates through a persistent plan-execute-analyze-replan loop, continuously adapting its strategy based on convergence diagnostics and geometric feedback without human intervention. We evaluate TSAgent on a diverse 100-example subset of the OC20NEB heterogeneous catalysis benchmark, where it successfully locates TSs with 83% accuracy. In a direct comparison against expert DFT practitioners on 10 held-out examples, TSAgent achieves a 70% success rate compared to a human-expert average of 73 +/- 12%. Finally, TSAgent independently reproduces Bronsted-Evans-Polanyi scaling relationships for NH3 dissociation on metal and single-atom alloy surfaces from a published heterogeneous catalysis study, demonstrating that its utility extends beyond curated benchmarks to real scientific investigations.

The Model Context Protocol (MCP) has unified the interface between Large Language Models (LLMs) and external tools, yet a fundamental gap remains in how agents conceptualize the environments within which they operate. Current paradigms are bifurcated: Task-level planning often ignores execution-time dynamics, while reactive execution lacks long-horizon foresight. We present MCP-Cosmos, a framework that infuses generative World Models (WM) into the MCP ecosystem to enable predictive task automation. By unifying three disparate technologies, namely MCP, World Model, and Agent, we demonstrate that a "Bring Your Own World Model" (BYOWM) strategy allows agents to simulate state transitions and refine plans in a latent space before execution. We conducted experiments using two strategies, namely ReAct and SPIRAL with 2 planning models and 3 representative world models over 20+ MCP-Bench tasks. We observed improvements in Agent's environment interaction KPI such as tool success rate and tool parameter accuracy. The framework also offers new metrics such as Execution Quality to generate new insights about the effectiveness of world models compared to baseline.

In real-world scenarios, the application of reinforcement learning is significantly challenged by complex non-stationarity. Most existing methods attempt to model changes in the environment explicitly, often requiring impractical prior knowledge of environments. In this paper, we propose a new perspective, positing that non-stationarity can propagate and accumulate through complex causal relationships during state transitions, thereby compounding its sophistication and affecting policy learning. We believe that this challenge can be more effectively addressed by implicitly tracing the causal origin of non-stationarity. To this end, we introduce the Causal-Origin REPresentation (COREP) algorithm. COREP primarily employs a guided updating mechanism to learn a stable graph representation for the state, termed as causal-origin representation. By leveraging this representation, the learned policy exhibits impressive resilience to non-stationarity. We supplement our approach with a theoretical analysis grounded in the causal interpretation for non-stationary reinforcement learning, advocating for the validity of the causal-origin representation. Experimental results further demonstrate the superior performance of COREP over existing methods in tackling non-stationarity problems.

Accurate determination of transition states is central to an understanding of reaction kinetics. Double-endpoint methods where both initial and final states are specified, such as the climbing image nudged elastic band (CI-NEB), identify the minimum energy path between the two and thereby the saddle point on the energy surface that is relevant for the given transition, thus providing an estimate of the transition state within the harmonic approximation of transition state theory. Such calculations can, however, incur high computational costs and may suffer stagnation on exceptionally flat or rough energy surfaces. Conversely, methods that only require specification of an initial set of atomic coordinates, such as the minimum mode following (MMF) method, offer efficiency but can converge on saddle points that are not relevant for transition of interest. Here, we present an adaptive hybrid algorithm that integrates the CI-NEB with the MMF method so as to get faster convergence to the relevant saddle point. The method is benchmarked for the Baker-Chan (BC) saddle point test set using the PET-MAD machine-learned potential as well as 59 transitions of a heptamer island on Pt(111) from the OptBench benchmark set. A Bayesian analysis of the performance shows a reduction in energy and force calculations of 57% [95% CrI: -64%, -50%] relative to CI-NEB for the BC set, while a 31% mean reduction is found for the transitions of the heptamer island. These results establish this hybrid method as a highly effective tool for high-throughput automated chemical discovery of atomic rearrangements.

Under the conditions of superfluid-Mott-insulator criticality in two dimensions, the trapping centers--i.e., local potential wells and bumps--are generically characterized by an integer charge corresponding to the number of trapped particles (if positive) or holes (if negative). Varying the strength of the center leads to a transition between two competing ground states with charges differing by pm 1. The hallmark of the transition scenario is a splitting of the number density distortion, δn(r), into a half-integer core and a large halo carrying the complementary charge of pm 1/2. The sign of the halo changes across the transition and the radius of the halo, r_0, diverges on the approach to the critical strength of the center, V = V_c, by the law r_0 propto |V-V_c|^{-tildeν}, with tildeν approx 2.33(5).

Medical care follows complex clinical pathways that extend beyond isolated physician-patient encounters, emphasizing decision-making and transitions between different stages. Current benchmarks focusing on static exams or isolated dialogues inadequately evaluate large language models (LLMs) in dynamic clinical scenarios. We introduce CP-Env, a controllable agentic hospital environment designed to evaluate LLMs across end-to-end clinical pathways. CP-Env simulates a hospital ecosystem with patient and physician agents, constructing scenarios ranging from triage and specialist consultation to diagnostic testing and multidisciplinary team meetings for agent interaction. Following real hospital adaptive flow of healthcare, it enables branching, long-horizon task execution. We propose a three-tiered evaluation framework encompassing Clinical Efficacy, Process Competency, and Professional Ethics. Results reveal that most models struggle with pathway complexity, exhibiting hallucinations and losing critical diagnostic details. Interestingly, excessive reasoning steps can sometimes prove counterproductive, while top models tend to exhibit reduced tool dependency through internalized knowledge. CP-Env advances medical AI agents development through comprehensive end-to-end clinical evaluation. We provide the benchmark and evaluation tools for further research and development at https://github.com/SPIRAL-MED/CP_ENV.

Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of the high energy barriers that separate these states. Although recent machine learning techniques are proposed to sample rare events, they are often limited to simple systems and rely on collective variables (CVs) derived from costly domain expertise. In this paper, we introduce a novel approach that trains diffusion path samplers (DPS) to address the transition path sampling (TPS) problem without requiring CVs. We reformulate the problem as an amortized sampling from the transition path distribution by minimizing the log-variance divergence between the path distribution induced by DPS and the transition path distribution. Based on the log-variance divergence, we propose learnable control variates to reduce the variance of gradient estimators and the off-policy training objective with replay buffers and simulated annealing techniques to improve sample efficiency and diversity. We also propose a scale-based equivariant parameterization of the bias forces to ensure scalability for large systems. We extensively evaluate our approach, termed TPS-DPS, on a synthetic system, small peptide, and challenging fast-folding proteins, demonstrating that it produces more realistic and diverse transition pathways than existing baselines.

Transformer-based architectures have dominated sequence modeling, largely due to the expressive power of attention mechanisms. However, for a class of deterministic state tracking tasks---such as parity checking, modular counting, and parenthesis matching---attention may be overkill. In this paper, we show that state propagation alone is sufficient. We propose the Complex State Propagator (CSP), a minimalistic recurrent architecture that only propagates hidden states across layers without output projections at intermediate steps. The state is represented as a complex-valued vector, updated via input-dependent rotations in the complex domain. To enable deep propagation without gradient vanishing or degradation, we introduce a block-level skip connection alongside element-wise complex normalization and SiLU activation at sequence boundaries. Applied with Focal Loss, CSP achieves 100\% accuracy with perfect F1 scores across canonical tasks.

Direct speech-to-speech translation (S2ST) translates speech from one language into another using a single model. However, due to the presence of linguistic and acoustic diversity, the target speech follows a complex multimodal distribution, posing challenges to achieving both high-quality translations and fast decoding speeds for S2ST models. In this paper, we propose DASpeech, a non-autoregressive direct S2ST model which realizes both fast and high-quality S2ST. To better capture the complex distribution of the target speech, DASpeech adopts the two-pass architecture to decompose the generation process into two steps, where a linguistic decoder first generates the target text, and an acoustic decoder then generates the target speech based on the hidden states of the linguistic decoder. Specifically, we use the decoder of DA-Transformer as the linguistic decoder, and use FastSpeech 2 as the acoustic decoder. DA-Transformer models translations with a directed acyclic graph (DAG). To consider all potential paths in the DAG during training, we calculate the expected hidden states for each target token via dynamic programming, and feed them into the acoustic decoder to predict the target mel-spectrogram. During inference, we select the most probable path and take hidden states on that path as input to the acoustic decoder. Experiments on the CVSS Fr-En benchmark demonstrate that DASpeech can achieve comparable or even better performance than the state-of-the-art S2ST model Translatotron 2, while preserving up to 18.53x speedup compared to the autoregressive baseline. Compared with the previous non-autoregressive S2ST model, DASpeech does not rely on knowledge distillation and iterative decoding, achieving significant improvements in both translation quality and decoding speed. Furthermore, DASpeech shows the ability to preserve the speaker's voice of the source speech during translation.

Coupling together distinct correlated and topologically non-trivial electronic phases of matter can potentially induce novel electronic orders and phase transitions among them. Transition metal dichalcogenide compounds serve as a bedrock for exploration of such hybrid systems. They host a variety of exotic electronic phases and their Van der Waals nature enables to admix them, either by exfoliation and stacking or by stoichiometric growth, and thereby induce novel correlated complexes. Here we investigate the compound 4Hb-TaS_2 that interleaves the Mott-insulating state of 1T-TaS_2 and the putative spin liquid it hosts together with the metallic state of 2H-TaS_2 and the low temperature superconducting phase it harbors. We reveal a thermodynamic phase diagram that hosts a first order quantum phase transition between a correlated Kondo cluster state and a flat band state in which the Kondo cluster becomes depleted. We demonstrate that this intrinsic transition can be induced by an electric field and temperature as well as by manipulation of the interlayer coupling with the probe tip, hence allowing to reversibly toggle between the Kondo cluster and the flat band states. The phase transition is manifested by a discontinuous change of the complete electronic spectrum accompanied by hysteresis and low frequency noise. We find that the shape of the transition line in the phase diagram is determined by the local compressibility and the entropy of the two electronic states. Our findings set such heterogeneous structures as an exciting platform for systematic investigation and manipulation of Mott-metal transitions and strongly correlated phases and quantum phase transitions therein.

We point out that there are two different chiral spin liquid states on the triangular lattice and discuss the conducting states that are expected on doping them. These states labeled CS1 and CS2 are associated with two distinct topological orders with different edge states, although they both spontaneously break time reversal symmetry and exhibit the same quantized spin Hall conductance. While CSL1 is related to the Kalmeyer-Laughlin state, CSL2 is the ν=4 member of Kitaev's 16 fold way classification. Both states are described within the Abrikosov fermion representation of spins, and the effect of doping can be accessed by introducing charged holons. On doping CSL2, condensation of charged holons leads to a topological d+id superconductor. However on doping CSL1 , in sharp contrast , two different scenarios can arise: first, if holons condense, a chiral metal with doubled unit cell and finite Hall conductivity is obtained. However, in a second novel scenario, the internal magnetic flux adjusts with doping and holons form a bosonic integer quantum Hall (BIQH) state. Remarkably, the latter phase is identical to a d+id superconductor. In this case the Mott insulator to superconductor transition is associated with a bosonic variant of the integer quantum Hall plateau transition for the holon. We connect the above two scenarios to two recent numerical studies of doped chiral spin liquids on triangular lattice. Our work clarifies the complex relation between topological superconductors, chiral spin liquids and quantum criticality .

The principle of detailed balance states that in equilibrium each elementary process is equilibrated by its reverse process. For many real physico-chemical complex systems (e.g. homogeneous combustion, heterogeneous catalytic oxidation, most enzyme reactions etc), detailed mechanisms include both reversible and irreversible reactions. In this case, the principle of detailed balance cannot be applied directly. We represent irreversible reactions as limits of reversible steps and obtain the principle of detailed balance for complex mechanisms with some irreversible elementary processes. We proved two consequences of the detailed balance for these mechanisms: the structural condition and the algebraic condition that form together the extended form of detailed balance. The algebraic condition is the principle of detailed balance for the reversible part. The structural condition is: the convex hull of the stoichiometric vectors of the irreversible reactions has empty intersection with the linear span of the stoichiometric vectors of the reversible reaction. Physically, this means that the irreversible reactions cannot be included in oriented pathways. The systems with the extended form of detailed balance are also the limits of the reversible systems with detailed balance when some of the equilibrium concentrations (or activities) tend to zero. Surprisingly, the structure of the limit reaction mechanism crucially depends on the relative speeds of this tendency to zero.

The many-body nature of nuclear physics problems poses significant computational challenges. These challenges become even more pronounced when studying the resonance states of nuclear systems, which are governed by the non-Hermitian Hamiltonian. Quantum computing, particularly for quantum many-body systems, offers a promising alternative, especially within the constraints of current noisy intermediate-scale quantum (NISQ) devices. This work aims to simulate nuclear resonances using quantum algorithms by developing a variational framework compatible with non-Hermitian Hamiltonians and implementing it fully on a quantum simulator. We employ the complex scaling technique to extract resonance positions classically and adapt it for quantum simulations using a two-step algorithm. First, we transform the non-Hermitian Hamiltonian into a Hermitian form by using the energy variance as a cost function within a variational framework. Second, we perform theta-trajectory calculations to determine optimal resonance positions in the complex energy plane. To address resource constraints on NISQ devices, we utilize Gray Code (GC) encoding to reduce qubit requirements. We first validate our approach using a schematic potential model that mimics a nuclear potential, successfully reproducing known resonance energies with high fidelity. We then extend the method to a more realistic alpha-alpha nuclear potential and compute the resonance energies with a basis size of 16, using only four qubits. This study demonstrates, for the first time, that the complete theta-trajectory method can be implemented on a quantum computer without relying on any classical input beyond the Hamiltonian. The results establish a scalable and efficient quantum framework for simulating resonance phenomena in nuclear systems. This work represents a significant step toward quantum simulations of open quantum systems.

We introduce the framework of model space into quantum imaginary time evolution (QITE) to enable stable estimation of ground and excited states using a quantum computer. Model-space QITE (MSQITE) propagates a model space to the exact one by retaining its orthogonality, and hence is able to describe multiple states simultaneously. The quantum Lanczos (QLanczos) algorithm is extended to MSQITE to accelerate the convergence. The present scheme is found to outperform both the standard QLanczos and the recently proposed folded-spectrum QITE in simulating excited states. Moreover, we demonstrate that spin contamination can be effectively removed by shifting the imaginary time propagator, and thus excited states with a particular spin quantum number are efficiently captured without falling into the different spin states that have lower energies. We also investigate how different levels of the unitary approximation employed in MSQITE can affect the results. The effectiveness of the algorithm over QITE is demonstrated by noise simulations for the H4 model system.

I introduce a novel mathematical framework integrating topological dynamics, operator algebras, and ergodic geometry to study lattices of asynchronous metric dynamical systems. Each node in the lattice carries an internal flow represented by a one-parameter family of operators, evolving on its own time scale. I formalize stratified state spaces capturing multiple levels of synchronized behavior, define an asynchronous evolution metric that quantifies phase-offset distances between subsystems, and characterize emergent coherent topologies arising when subsystems synchronize. Within this framework, I develop formal operators for the evolution of each subsystem and give precise conditions under which phase-aligned synchronization occurs across the lattice. The main results include: (1) the existence and uniqueness of coherent (synchronized) states under a contractive coupling condition, (2) stability of these coherent states and criteria for their emergence as a collective phase transition in a continuous operator topology, and (3) the influence of symmetries, with group-invariant coupling leading to flow-invariant synchrony subspaces and structured cluster dynamics. Proofs are given for each theorem, demonstrating full mathematical rigor. In a final section, I discuss hypothetical applications of this framework to symbolic lattice systems (e.g. subshifts), to invariant group actions on dynamical lattices, and to operator fields over stratified manifolds in the spirit of noncommutative geometry. Throughout, I write in the first person to emphasize the exploratory nature of this work. The paper avoids any reference to cosmology or observers, focusing instead on clean, formal mathematics suitable for a broad array of dynamical systems.

The realization that complex systems such as ecological communities can collapse or shift regimes suddenly and without rapid external forcing poses a serious challenge to our understanding and management of the natural world. The potential to identify early warning signals that would allow researchers and managers to predict such events before they happen has therefore been an invaluable discovery that offers a way forward in spite of such seemingly unpredictable behavior. Research into early warning signals has demonstrated that it is possible to define and detect such early warning signals in advance of a transition in certain contexts. Here we describe the pattern emerging as research continues to explore just how far we can generalize these results. A core of examples emerges that shares three properties: the phenomenon of rapid regime shifts, a pattern of 'critical slowing down' that can be used to detect the approaching shift, and a mechanism of bifurcation driving the sudden change. As research has expanded beyond these core examples, it is becoming clear that not all systems that show regime shifts exhibit critical slowing down, or vice versa. Even when systems exhibit critical slowing down, statistical detection is a challenge. We review the literature that explores these edge cases and highlight the need for (a) new early warning behaviors that can be used in cases where rapid shifts do not exhibit critical slowing down, (b) the development of methods to identify which behavior might be an appropriate signal when encountering a novel system; bearing in mind that a positive indication for some systems is a negative indication in others, and (c) statistical methods that can distinguish between signatures of early warning behaviors and noise.

The paper sets forth comprehensive basics of Discrete Thermodynamics of Chemical Equilibria (DTD), developed by the author during the last decade and spread over series of publications. Based on the linear equations of irreversible thermodynamics, De Donder's definition of the thermodynamic force, and the Le Chatelier principle, DTD brings forward a notion of chemical equilibrium as a balance of internal and external thermodynamic forces, acting against a chemical system. The basic expression of DTD is a logistic map that ties together energetic characteristics of the chemical transformation in the system, its deviation from true thermodynamic equilibrium, and the sum of thermodynamic forces, causing that deviation. System deviation from thermodynamic equilibrium is the major variable of the theory. Solutions to the basic map define the chemical system domain of states comprising bifurcation diagrams with four areas, from true thermodynamic equilibrium to chaos, having specific distinctive meaning for chemical systems. The theory is derived from the currently recognized ideas of chemical thermodynamics and binds classical and contemporary thermodynamics of chemical equilibria into a unique concept. DTD opens new opportunities in understanding and analysis of equilibria in chemical systems. Some new results, included in the paper, have never been published before.

Large-amplitude molecular motions which occur during isomerization can cause significant changes in electronic structure. These variations in electronic properties can be used to identify vibrationally-excited eigenstates which are localized along the potential energy surface. This work demonstrates that nuclear quadrupole hyperfine interactions can be used as a diagnostic marker of progress along the isomerization path in both the HC14N/H14NC and DC15N/D15NC chemical systems. Ab initio calculations at the CCSD(T)/cc-pCVQZ level indicate that the hyperfine interaction is extremely sensitive to the chemical bonding of the quadrupolar 14N nucleus and can therefore be used to determine in which potential well the vibrational wavefunction is localized. A natural bonding orbital analysis along the isomerization path further demonstrates that hyperfine interactions arise from the asphericity of the electron density at the quadrupolar nucleus. Using the CCSD(T) potential surface, the quadrupole coupling constants of highly-excited vibrational states are computed from a one-dimensional internal coordinate path Hamiltonian. The excellent agreement between ab initio calculations and recent measurements demonstrates that nuclear quadrupole hyperfine structure can be used as a diagnostic tool for characterizing localized HCN and HNC vibrational states.

Let L denote the Laplacian matrix of a graph G. We study continuous quantum walks on G defined by the transition matrix U(t)=expleft(itLright). The initial state is of the pair state form, e_a-e_b with a,b being any two vertices of G. We provide two ways to construct infinite families of graphs that have perfect pair transfer. We study a "transitivity" phenomenon which cannot occur in vertex state transfer. We characterize perfect pair state transfer on paths and cycles. We also study the case when quantum walks are generated by the unsigned Laplacians of underlying graphs and the initial states are of the plus state form, e_a+e_b. When the underlying graphs are bipartite, plus state transfer is equivalent to pair state transfer.

A recent study shows that if the power spectra (PS) of accreting compact objects consist of a combination of Lorentzian functions that are coherent in different energy bands but incoherent with each other, the same is true for the Real and Imaginary parts of the cross spectrum (CS). Using this idea, we discovered imaginary quasi-periodic oscillations (QPOs) in NICER observations of the black hole candidate MAXI J1820+070. The imaginary QPOs appear as narrow features with a small Real and large Imaginary part in the CS but are not significantly detected in the PS when they overlap in frequency with other variability components. The coherence function drops and the phase lags increase abruptly at the frequency of the imaginary QPO. We show that the multi-Lorentzian model that fits the PS and CS of the source in two energy bands correctly reproduces the lags and the coherence, and that the narrow drop of the coherence is caused by the interaction of the imaginary QPO with other variability components. The imaginary QPO appears only in the decay of the outburst, during the transition from the high-soft to the low-hard state of MAXI J1820+070, and its frequency decreases from approximately 5 Hz to around 1 Hz as the source spectrum hardens. We also analysed the earlier observations of the transition, where no narrow features were seen, and we identified a QPO in the PS that appears to evolve into the imaginary QPO as the source hardens. As for the type-B and C QPOs in this source, the rms spectrum of the imaginary QPO increases with energy. The lags of the imaginary QPO are similar to those of the type-B and C QPOs above 2 keV but differ from the lags of those other QPOs below that energy. While the properties of this imaginary QPO resemble those of type-C QPOs, we cannot rule out that it is a new type of QPO.

Dynamical systems with complex behaviours, e.g. immune system cells interacting with a pathogen, are commonly modelled by splitting the behaviour into different regimes, or modes, each with simpler dynamics, and then learning the switching behaviour from one mode to another. Switching Dynamical Systems (SDS) are a powerful tool that automatically discovers these modes and mode-switching behaviour from time series data. While effective, these methods focus on independent objects, where the modes of one object are independent of the modes of the other objects. In this paper, we focus on the more general interacting object setting for switching dynamical systems, where the per-object dynamics also depends on an unknown and dynamically changing subset of other objects and their modes. To this end, we propose a novel graph-based approach for switching dynamical systems, GRAph Switching dynamical Systems (GRASS), in which we use a dynamic graph to characterize interactions between objects and learn both intra-object and inter-object mode-switching behaviour. We introduce two new datasets for this setting, a synthesized ODE-driven particles dataset and a real-world Salsa Couple Dancing dataset. Experiments show that GRASS can consistently outperforms previous state-of-the-art methods.

Standing as one of the most significant barriers to reaching quantum advantage, state-preparation fidelities on noisy intermediate-scale quantum processors suffer from quantum-gate errors, which accumulate over time. A potential remedy is pulse-based state preparation. We numerically investigate the minimal evolution times (METs) attainable by optimizing (microwave and exchange) pulses on silicon hardware. We investigate two state preparation tasks. First, we consider the preparation of molecular ground states and find the METs for H_2, HeH^+, and LiH to be 2.4 ns, 4.4 ns, and 27.2 ns, respectively. Second, we consider transitions between arbitrary states and find the METs for transitions between arbitrary four-qubit states to be below 50 ns. For comparison, connecting arbitrary two-qubit states via one- and two-qubit gates on the same silicon processor requires approximately 200 ns. This comparison indicates that pulse-based state preparation is likely to utilize the coherence times of silicon hardware more efficiently than gate-based state preparation. Finally, we quantify the effect of silicon device parameters on the MET. We show that increasing the maximal exchange amplitude from 10 MHz to 1 GHz accelerates the METs, e.g., for H_2 from 84.3 ns to 2.4 ns. This demonstrates the importance of fast exchange. We also show that increasing the maximal amplitude of the microwave drive from 884 kHz to 56.6 MHz shortens state transitions, e.g., for two-qubit states from 1000 ns to 25 ns. Our results bound both the state-preparation times for general quantum algorithms and the execution times of variational quantum algorithms with silicon spin qubits.

Neural networks acquire structured representations at specific moments during training, yet identifying these transitions typically relies on retrospective, label-dependent metrics. We introduce a bifurcation theory of representation dynamics to detect these moments in real time. Analyzing a passive GMM probe attached to the evolving encoder, we show the onset of structure corresponds to a supercritical pitchfork bifurcation driven by the loss Hessian. The system exhibits a theoretically predictable zero-crossing (β_c) that, compared to the network's current state (β), yields a dynamic ratio β(t)/β_c(t): a universal, label-free phase coordinate for representation dynamics, computable entirely from hidden states. We empirically validate four distinct transition regimes predicted by this coordinate across diverse settings: SAEs on language models (Pythia), SSL (CIFAR), and grokking (modular arithmetic). Crucially, under finite dissipation, macroscopic symmetry-breaking can lag the initial zero-crossing by orders of magnitude, which providing a rigorous dynamical account of the delayed escape observed in grokking. Microscopically, the bifurcation creates a shared unstable subspace, forcing collective symmetry breaking. We term this the "feature lottery" in SAE training: a feature's terminal interpretability becomes predictable remarkably early. By only 5% of training, early atom purity robustly predicts final convergence purity, with top-decile early atoms achieving over 12x the baseline purity at convergence. Beyond explaining concept emergence, β/β_c provides a practical early-warning indicator for training health, detecting the onset of usable structure, the crystallization of feature identity, and representational collapse epochs before downstream metrics react.

Previous theoretical and experimental research has shown that current NISQ devices constitute powerful platforms for analogue quantum simulation. With the exquisite level of control offered by state-of-the-art quantum computers, we show that one can go further and implement a wide class of Floquet Hamiltonians, or timedependent Hamiltonians in general. We then implement a single-qubit version of these models in the IBM Quantum Experience and experimentally realize a temporal version of the Bernevig-Hughes-Zhang Chern insulator. From our data we can infer the presence of a topological transition, thus realizing an earlier proposal of topological frequency conversion by Martin, Refael, and Halperin. Our study highlights promises and limitations when studying many-body systems through multi-frequency driving of quantum computers.

It is shown that in the complex trajectory representation of quantum mechanics, the Born's Psi^{\star}Ψprobability density can be obtained from the imaginary part of the velocity field of particles on the real axis. Extending this probability axiom to the complex plane, we first attempt to find a probability density by solving an appropriate conservation equation. The characteristic curves of this conservation equation are found to be the same as the complex paths of particles in the new representation. The boundary condition in this case is that the extended probability density should agree with the quantum probability rule along the real line. For the simple, time-independent, one-dimensional problems worked out here, we find that a conserved probability density can be derived from the velocity field of particles, except in regions where the trajectories were previously suspected to be nonviable. An alternative method to find this probability density in terms of a trajectory integral, which is easier to implement on a computer and useful for single particle solutions, is also presented. Most importantly, we show, by using the complex extension of Schrodinger equation, that the desired conservation equation can be derived from this definition of probability density.

Chemical reaction networks can undergo nonequilibrium phase transitions upon variation of external control parameters like the chemical potential of a species. We investigate the flux in the associated chemostats that is proportional to the entropy production and its critical fluctuations within the Schlögl model. Numerical simulations show that the corresponding diffusion coefficient diverges at the critical point as a function of system size. In the vicinity of the critical point, the diffusion coefficient follows a scaling form. We develop an analytical approach based on the chemical Langevin equation and van Kampen's system size expansion that yields the corresponding exponents in the monostable regime. In the bistable regime, we rely on a two-state approximation in order to analytically describe the critical behavior.

The structure-function relationship is at the heart of biology and major protein deformations are correlated to specific functions. In the case of heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobin, while ruffling has been correlated with electron transfer processes, such as in the case of Cytochrome c (Cyt c). The latter has indeed evolved to become an important electron transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe K-edge X-ray absorption near-edge structure (XANES) studies and femtosecond Fe Kalpha and Kbeta X-ray emission spectroscopy (XES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the Iron ion, causing the ferric heme to undergo doming, which we identify for the first time. We also argue that this pattern is common to all ferric haems, raising the question of the biological relevance of doming in such proteins.

Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from being proven. One challenge in engineering and understanding biochemical computation is the intrinsic noise due to chemical fluctuations. In this paper, we draw insights from machine learning theory, chemical reaction network theory, and statistical physics to show that the broad and biologically relevant class of detailed balanced chemical reaction networks is capable of representing and conditioning complex distributions. These results illustrate how a biochemical computer can use intrinsic chemical noise to perform complex computations. Furthermore, we use our explicit physical model to derive thermodynamic costs of inference.

We introduce an experimentally accessible network representation for many-body quantum states based on entanglement between all pairs of its constituents. We illustrate the power of this representation by applying it to a paradigmatic spin chain model, the XX model, and showing that it brings to light new phenomena. The analysis of these entanglement networks reveals that the gradual establishment of quasi-long range order is accompanied by a symmetry regarding single-spin concurrence distributions, as well as by instabilities in the network topology. Moreover, we identify the existence of emergent entanglement structures, spatially localised communities enforced by the global symmetry of the system that can be revealed by model-agnostic community detection algorithms. The network representation further unveils the existence of structural classes and a cyclic self-similarity in the state, which we conjecture to be intimately linked to the community structure. Our results demonstrate that the use of tools and concepts from complex network theory enables the discovery, understanding, and description of new physical phenomena even in models studied for decades.

When agents are acting together, they may need a simple mechanism to decide on joint actions. One possibility is to have the agents express their preferences in the form of a ballot and use a voting rule to decide the winning action(s). Unfortunately, agents may try to manipulate such an election by misreporting their preferences. Fortunately, it has been shown that it is NP-hard to compute how to manipulate a number of different voting rules. However, NP-hardness only bounds the worst-case complexity. Recent theoretical results suggest that manipulation may often be easy in practice. To address this issue, I suggest studying empirically if computational complexity is in practice a barrier to manipulation. The basic tool used in my investigations is the identification of computational "phase transitions". Such an approach has been fruitful in identifying hard instances of propositional satisfiability and other NP-hard problems. I show that phase transition behaviour gives insight into the hardness of manipulating voting rules, increasing concern that computational complexity is indeed any sort of barrier. Finally, I look at the problem of computing manipulation of other, related problems like stable marriage and tournament problems.

In complex systems, we often observe complex global behavior emerge from a collection of agents interacting with each other in their environment, with each individual agent acting only on locally available information, without knowing the full picture. Such systems have inspired development of artificial intelligence algorithms in areas such as swarm optimization and cellular automata. Motivated by the emergence of collective behavior from complex cellular systems, we build systems that feed each sensory input from the environment into distinct, but identical neural networks, each with no fixed relationship with one another. We show that these sensory networks can be trained to integrate information received locally, and through communication via an attention mechanism, can collectively produce a globally coherent policy. Moreover, the system can still perform its task even if the ordering of its inputs is randomly permuted several times during an episode. These permutation invariant systems also display useful robustness and generalization properties that are broadly applicable. Interactive demo and videos of our results: https://attentionneuron.github.io/

The simulation of large-scale systems with complex electron interactions remains one of the greatest challenges for the atomistic modeling of materials. Although classical force fields often fail to describe the coupling between electronic states and ionic rearrangements, the more accurate ab-initio molecular dynamics suffers from computational complexity that prevents long-time and large-scale simulations, which are essential to study many technologically relevant phenomena, such as reactions, ion migrations, phase transformations, and degradation. In this work, we present the Crystal Hamiltonian Graph neural Network (CHGNet) as a novel machine-learning interatomic potential (MLIP), using a graph-neural-network-based force field to model a universal potential energy surface. CHGNet is pretrained on the energies, forces, stresses, and magnetic moments from the Materials Project Trajectory Dataset, which consists of over 10 years of density functional theory static and relaxation trajectories of sim 1.5 million inorganic structures. The explicit inclusion of magnetic moments enables CHGNet to learn and accurately represent the orbital occupancy of electrons, enhancing its capability to describe both atomic and electronic degrees of freedom. We demonstrate several applications of CHGNet in solid-state materials, including charge-informed molecular dynamics in Li_xMnO_2, the finite temperature phase diagram for Li_xFePO_4 and Li diffusion in garnet conductors. We critically analyze the significance of including charge information for capturing appropriate chemistry, and we provide new insights into ionic systems with additional electronic degrees of freedom that can not be observed by previous MLIPs.

In contrast to entropy, which increases monotonically, the "complexity" or "interestingness" of closed systems seems intuitively to increase at first and then decrease as equilibrium is approached. For example, our universe lacked complex structures at the Big Bang and will also lack them after black holes evaporate and particles are dispersed. This paper makes an initial attempt to quantify this pattern. As a model system, we use a simple, two-dimensional cellular automaton that simulates the mixing of two liquids ("coffee" and "cream"). A plausible complexity measure is then the Kolmogorov complexity of a coarse-grained approximation of the automaton's state, which we dub the "apparent complexity." We study this complexity measure, and show analytically that it never becomes large when the liquid particles are non-interacting. By contrast, when the particles do interact, we give numerical evidence that the complexity reaches a maximum comparable to the "coffee cup's" horizontal dimension. We raise the problem of proving this behavior analytically.

Communication requires a shared code, and any change to it must be coordinated between senders and receivers to avoid a breakdown of communication. The honeybee waggle dance illustrates this problem: species with horizontal combs point directly at a food source, while species with vertical combs cannot point directly and instead reference the dance to gravity, decoded against the position of the sun. We model the emergence and evolutionary transition between these two codes in populations of bee-like agents, with selection acting at the level of colonies. In a horizontal-comb model, we find that direct pointing evolves readily when food is moderately hard to find by random search alone, whether because sites are few and large or many and small, and fails when food is too sparse to spark dances or so abundant that it is found without signaling. Adding an exogenous benefit for vertical combs, we then find that the transition to the gravity-referenced code is driven mainly by the mutation rate and the magnitude of this benefit, with the coupling between sender and receiver mutations playing a further role at low mutation rates. Given a favorable confluence of these factors, the transition proceeds reliably and without a breakdown of communication.

Scientific discovery is not only answer generation but revision of the representational regime in which evidence, artifacts, operations, and verifiers are typed. We develop a category-theoretic account of agentic discovery for materials science. In a fixed regime b with schema category S_b, the system state is a copresheaf I_t: S_b -> Set, and provenance is the category of elements \int_{S_b} I_t. Fixed-regime operation is an update on such states, endofunctorial only when provenance-preserving refinements are specified and preserved. Discovery is instead a verified regime transition u: S_b -> S_b': old artifacts are preserved, transported by the left Kan extension Lan_u I_t, and compared with the post-transition state to identify residual content beyond functorial transport. This separates retrieval, search, and discovery without subjective novelty. We instantiate the framework in two systems. In Builder/Breaker, a protein-mechanics world model is revised under a Minimum Description Length gate; the accepted law expresses within-chain flexibility as all-mode elastic compliance conditioned by slow collective-mode participation, or mode-conditioned compliance. In CategoryScienceClaw, typed skills, artifacts, open needs, workflow mutation, gates, stress tests, and public discourse become a proof-carrying knowledge-computation graph. A fiber-network example records candidate models, rejected alternatives, an AIC gate, perturbation tests, and an accepted orientation-tensor anisotropic stiffness surrogate over an isotropic fiber-count descriptor. Together, the cases show how category theory can be both a mathematical language for discovery and an engineering specification for self-revising AI discovery systems.

All known up to now models of chemical oscillations are based exclusively on kinetic considerations. The chemical gross-process equation is split usually by elementary steps, each step is supplied by an arrow and a differential equation, joint solution to such a construction under certain, often ad hoc chosen conditions and with ad hoc numerical coefficients leads to chemical oscillations. Kinetic perception of chemical oscillations reigns without exclusions. However, as it was recently shown by the author for the laser and for the electrochemical systems, chemical oscillations follow also from solutions to the basic expressions of discrete thermodynamics of chemical equilibria. Graphically those solutions are various fork bifurcation diagrams, and, in certain types of chemical systems, oscillations are well pronounced in the bistable bifurcation areas. In this work we describe a general thermodynamic approach to chemical oscillations as opposite to kinetic models, and depict some of their new features like spontaneity and fractality. The paper doubts exclusivity of the kinetic approach to chemical oscillations, and its aim is to discuss and exemplify thermodynamically predicted chemical oscillations in closed chemical systems.

Water looks unchanged as it warms, then at a critical point it boils. We ask whether long-horizon language agents show an analogous transition in their implicit world models. In some parameter settings, changing state load by a small amount, or adding a single step of horizon, leaves behavior nearly unchanged; near a critical boundary, the same small change causes a sudden world collapse. We study this effect in a deterministic task family with exact per-step gold state. A large grid search over state cardinality, dependency density, horizon, branching, observation mode, and mutation rate reveals a phase diagram: a solved plateau, a narrow transition band, and a collapse floor. Per-step traces show the mechanism: world-state fidelity fails before action validity, so the agent is not merely choosing a bad action; it is acting from a corrupted world. Stronger models translate the critical boundary but do not remove the qualitative transition. These results make world-model collapse a measurable bottleneck for long-horizon agents.

Tunnelling reactions of molecules embedded on cryogenic noble-gas matrices are being used in fundamental studies of how reactivity varies with the nature of the supposedly inert matrix as well as pointers to the chemistry occurring in the interstellar medium on ice-grains. To these ends we present chemical kinetic rate constants for the cis to trans isomerisation of seleno-, thio- and monomeric formic acids and that of their three dimeric species, based on multidimensional calculations in the gas-phase, from 10~K to 300~K as a guide to the matrix reactions.

World models for embodied AI must be physically viable: constructed to answer intervention queries by representing the physical structure governing action outcomes, rather than merely predicting future observations. Existing observation-predictive world models can produce visually plausible but physically wrong rollouts. This failure is structural; distinct physical systems can look identical yet diverge under intervention. We expose this problem with controlled benchmarks that fix the visible scene while varying latent physics. We show that such models may recommend infeasible actions, mispredict interaction outcomes, or certify unsafe behavior. We argue that embodied AI requires world models that identify the simplest physical abstraction sufficient to answer an intervention query. Such a model comprises modular components, including environment representation, latent state and parameter estimation, action specification, interventional dynamics, and query-level response. An autonomous orchestrator should identify the relevant abstraction and compose compatible learned and structured components per query. When closed-form physics is unavailable, uncertain, or costly, the transition model may be analytic, simulated, learned, or hybrid, but it must preserve the structure that determines interventional outcomes. This decomposition makes the model interpretable, its components verifiable, and its outputs auditable against the query. It also provides a design principle for new world models and a feasibility test for existing ones: the right abstraction is not the most detailed model of the world, but the simplest model that preserves the distinctions relevant to the query. We demonstrate this approach on queries that existing systems fail to answer correctly, and outline how an orchestrator can dynamically assemble and adapt physically viable models for planning, control, and verification.

Quantum algorithms for probing ground-state properties of quantum systems require good initial states. Projection-based methods such as eigenvalue filtering rely on inputs that have a significant overlap with the low-energy subspace, which can be challenging for large, strongly-correlated systems. This issue has motivated the study of physically-inspired dynamical approaches such as thermodynamic cooling. In this work, we introduce a ground-state preparation algorithm based on the simulation of quantum dynamics. Our main insight is to transform the Hamiltonian by a shifted sign function via quantum signal processing, effectively mapping eigenvalues into positive and negative subspaces separated by a large gap. This automatically ensures that all states within each subspace conserve energy with respect to the transformed Hamiltonian. Subsequent time-evolution with a perturbed Hamiltonian induces transitions to lower-energy states while preventing unwanted jumps to higher energy states. The approach does not rely on a priori knowledge of energy gaps and requires no additional qubits to model a bath. Furthermore, it makes mathcal{O}(d^{,3/2}/epsilon) queries to the time-evolution operator of the system and mathcal{O}(d^{,3/2}) queries to a block-encoding of the perturbation, for d cooling steps and an epsilon-accurate energy resolution. Our results provide a framework for combining quantum signal processing and Hamiltonian simulation to design heuristic quantum algorithms for ground-state preparation.

The use of machine learning algorithms to investigate phase transitions in physical systems is a valuable way to better understand the characteristics of these systems. Neural networks have been used to extract information of phases and phase transitions directly from many-body configurations. However, one limitation of neural networks is that they require the definition of the model architecture and parameters previous to their application, and such determination is itself a difficult problem. In this paper, we investigate for the first time the relationship between the accuracy of neural networks for information of phases and the network configuration (that comprises the architecture and hyperparameters). We formulate the phase analysis as a regression task, address the question of generating data that reflects the different states of the physical system, and evaluate the performance of neural architecture search for this task. After obtaining the optimized architectures, we further implement smart data processing and analytics by means of neuron coverage metrics, assessing the capability of these metrics to estimate phase transitions. Our results identify the neuron coverage metric as promising for detecting phase transitions in physical systems.

The local structure of V_{2}O_{3}, an archetypal strongly correlated electron system that displays a metal-insulator transition around 160 K, has been investigated via pair distribution function (PDF) analysis of neutron and x-ray total scattering data. The rhombohedral-to-monoclinic structural phase transition manifests as an abrupt change on all length scales in the observed PDF. No monoclinic distortions of the local structure are found above the transition, although coexisting regions of phase-separated rhombohedral and monoclinic symmetry are observed between 150 K and 160 K. This lack of structural fluctuations above the transition contrasts with the known presence of magnetic fluctuations in the high-temperature state, suggesting that the lattice degree of freedom plays a secondary role behind the spin degree of freedom in the transition mechanism.

Physics is based on probabilities as fundamental entities of a mathematical description. Expectation values of observables are computed according to the classical statistical rule. The overall probability distribution for one world covers all times. The quantum formalism arises once one focuses on the evolution of the time-local probabilistic information. Wave functions or the density matrix allow the formulation of a general linear evolution law for classical statistics. The quantum formalism for classical statistics is a powerful tool which allows us to implement for generalized Ising models the momentum observable with the associated Fourier representation. The association of operators to observables permits the computation of expectation values in terms of the density matrix by the usual quantum rule. We show that probabilistic cellular automata are quantum systems in a formulation with discrete time steps and real wave functions. With a complex structure the evolution operator for automata can be expressed in terms of a Hamiltonian involving fermionic creation and annihilation operators. The time-local probabilistic information amounts to a subsystem of the overall probabilistic system which is correlated with its environment consisting of the past and future. Such subsystems typically involve probabilistic observables for which only a probability distribution for their possible measurement values is available. Incomplete statistics does not permit to compute classical correlation functions for arbitrary subsystem-observables. Bell's inequalities are not generally applicable.

Simulating trajectories of multi-particle systems on complex energy landscapes is a central task in molecular dynamics (MD) and drug discovery, but remains challenging at scale due to computationally expensive and long simulations. Previous approaches leverage techniques such as flow or Schrödinger bridge matching to implicitly learn joint trajectories through data snapshots. However, many systems, including biomolecular systems and heterogeneous cell populations, undergo dynamic interactions that evolve over their trajectory and cannot be captured through static snapshots. To close this gap, we introduce Entangled Schrödinger Bridge Matching (EntangledSBM), a framework that learns the first- and second-order stochastic dynamics of interacting, multi-particle systems where the direction and magnitude of each particle's path depend dynamically on the paths of the other particles. We define the Entangled Schrödinger Bridge (EntangledSB) problem as solving a coupled system of bias forces that entangle particle velocities. We show that our framework accurately simulates heterogeneous cell populations under perturbations and rare transitions in high-dimensional biomolecular systems.

Critical temperature, T_c, and the transition width, ΔT_c, are two primary parameters of the superconducting transition. The latter parameter reflects the superconducting state disturbance originating from the thermodynamic fluctuations, atomic disorder, applied magnetic field, the presence of secondary crystalline phases, applied pressure, etc. Recently, Hirsch and Marsiglio (2020 arXiv:2012.12796) performed an analysis of the transition width in several near-room-temperature superconductors (NRTS) and reported that the reduced transition width, ΔT_c/T_c, in these materials does not follow a conventional trend of transition width broadening on applied magnetic field observed in low- and high-T_c superconductors. Here we present thorough mathematical analysis of the magnetoresistive data, R(T,B), for the high-entropy alloy (ScZrNb)_{0.65}[RhPd]_{0.35} and hydrogen-rich superconductors of Im-3m-H_{3}S, C2/m-LaH_{10} and P63/mmc-CeH_9. We found that the reduced transition width, ΔT_c/T_c, in these materials does follow a conventional broadening trend on applied magnetic field.

Closed-loop human-AI systems generate high-dimensional behavioural trajectories whose collective dynamics remain obscure. Using 297,915 learners' adaptive-tutoring histories, we define semantic order variables before model fitting and test them in user-disjoint cohorts. The state exhibits reproducible basin-like flow and operationally defined, state-heterogeneous metastable-like kinetics. A construction-matched null distinguishes normalised-memory relaxation from a reproducible excess field. A four-term conditional mechanism recovers population drift (r = 0.946; learner-bootstrap 95% CI, 0.935-0.955). Predictive event-level self-supervised learning recovers the state and learned-plane flow; null-referenced corrections retain directional, partial-amplitude excess-field structure without full calibration. Shuffled-order training reverses learned-plane flow on ordered trajectories; support-alignment randomisation selectively reduces inward transport. Both axes remain linearly accessible without state supervision. Without cross-model fitting, the models share leading population drift (r = 0.866; learner-bootstrap 95% CI, 0.857-0.875) and persistence ordering; residual directions remain model-specific. These results identify an externally anchored leading-order effective field linking empirical dynamics, an interpretable mechanism and neural computation.

In geometrically frustrated magnetic systems, weak interactions or slight changes to the structure can tip the delicate balance of exchange interactions, sending the system into a different ground state. Brochantite, Cu_4SO_4(OH)_6, has a copper sublattice composed of distorted triangles, making it a likely host for frustrated magnetism, but exhibits stacking disorder. The lack of synthetic single crystals has limited research on the magnetism in brochantite to powders and natural mineral crystals. We grew crystals which we find to be a new polytype with a tendency toward ABAC stacking and some anion disorder, alongside the expected stacking disorder. Comparison to previous results on natural mineral specimens suggests that cation disorder is more deleterious to the magnetism than anion and stacking disorder. Our specific heat data suggest a double transition on cooling into the magnetically ordered state.

The final state interactions (FSI) model in which soft rescattering of low mass intermediate states dominates is suggested. It explains why the strong interaction phases are large in the B_dtopipi channel and are considerably smaller in the B_dtorhorho one. Direct CP asymmetries of B_dtopipi decays which are determined by FSI phases are considered as well.

We provide a theoretical analysis for a recently demonstrated cooling method. Two-level particles undergo successive adiabatic transfers upon interaction with counter-propagating laser beams that are repeatedly swept over the transition frequency. We show that particles with narrow linewidth transitions can be cooled to near the recoil limit. This cooling mechanism has a reduced reliance on spontaneous emission compared to Doppler cooling, and hence shows promise for application to systems lacking closed cycling transitions, such as molecules.

In this paper we study the out-of-equilibrium phase diagram of the quantum version of Derrida's Random Energy Model, which is the simplest model of mean-field spin glasses. We interpret its corresponding quantum dynamics in Fock space as a one-particle problem in very high dimension to which we apply different theoretical methods tailored for high-dimensional lattices: the Forward-Scattering Approximation, a mapping to the Rosenzweig-Porter model, and the cavity method. Our results indicate the existence of two transition lines and three distinct dynamical phases: a completely many-body localized phase at low energy, a fully ergodic phase at high energy, and a multifractal "bad metal" phase at intermediate energy. In the latter, eigenfunctions occupy a diverging volume, yet an exponentially vanishing fraction of the total Hilbert space. We discuss the limitations of our approximations and the relationship with previous studies.

This chapter provides a pedagogical introduction and overview of spatial and temporal correlation and fluctuation effects resulting from the fundamentally stochastic kinetics underlying chemical reactions and the dynamics of populations or epidemics. After reviewing the assumptions and mean-field type approximations involved in the construction of chemical rate equations for uniform reactant densities, we first discuss spatial clustering in birth-death systems, where non-linearities are introduced through either density-limiting pair reactions, or equivalently via local imposition of finite carrying capacities. The competition of offspring production, death, and non-linear inhibition induces a population extinction threshold, which represents a non-equilibrium phase transition that separates active from absorbing states. This continuous transition is characterized by the universal scaling exponents of critical directed percolation clusters. Next we focus on the emergence of depletion zones in single-species annihilation processes and spatial population segregation with the associated reaction fronts in two-species pair annihilation. These strong (anti-)correlation effects are dynamically generated by the underlying stochastic kinetics. Finally, we address noise-induced and fluctuation-stabilized spatio-temporal patterns in basic predator-prey systems, exemplified by spreading activity fronts in the two-species Lotka-Volterra model as well as spiral structures in the May-Leonard variant of cyclically competing three-species systems akin to rock-paper-scissors games.

Macroscopic entropy production σ^{(tot)} in the general nonlinear isothermal chemical reaction system with mass action kinetics is decomposed into a free energy dissipation and a house-keeping heat: σ^{(tot)}=σ^{(fd)}+σ^{(hk)}; σ^{(fd)}=-rd A/rd t, where A is a generalized free energy function. This yields a novel nonequilibrium free energy balance equation rd A/rd t=-σ^{(tot)}+σ^{(hk)}, which is on a par with celebrated entropy balance equation rd S/rd t=σ^{(tot)}+η^{(ex)} where η^{(ex)} is the rate of entropy exchange with the environment.For kinetic systems with complex balance, σ^{(fd)} and σ^{(hk)} are the macroscopic limits of stochastic free energy dissipation and house-keeping heat, which are both nonnegative, in the Delbrück-Gillespie description of the stochastic chemical kinetics.Therefore, we show that a full kinetic and thermodynamic theory of chemical reaction systems that transcends mesoscopic and macroscopic levels emerges.

Ferrofluids show unusual hydrodynamic effects due to the magnetic nature of their constituents. For increasing magnetization a classical ferrofluid undergoes a Rosensweig instability and creates self-organized ordered surface structures or droplet crystals. A Bose-Einstein condensate with strong dipolar interactions is a quantum ferrofluid that also shows superfluidity. The field of dipolar quantum gases is motivated by the search for new phases that break continuous symmetries. The simultaneous breaking of continuous symmetries like the phase invariance for the superfluid state and the translational symmetry for a crystal provides the basis of novel states of matter. However, interaction-induced crystallization in a superfluid has not been observed. Here we use in situ imaging to directly observe the spontaneous transition from an unstructured superfluid to an ordered arrangement of droplets in an atomic dysprosium Bose-Einstein condensate. By utilizing a Feshbach resonance to control the interparticle interactions, we induce a finite-wavelength instability and observe discrete droplets in a triangular structure, growing with increasing atom number. We find that these states are surprisingly long-lived and measure a hysteretic behaviour, which is typical for a crystallization process and in close analogy to the Rosensweig instability. Our system can show both superfluidity and, as shown here, spontaneous translational symmetry breaking. The presented observations do not probe superfluidity in the structured states, but if the droplets establish a common phase via weak links, this system is a very good candidate for a supersolid ground state.

Complex prediction models such as deep learning are the output from fitting machine learning, neural networks, or AI models to a set of training data. These are now standard tools in science. A key challenge with the current generation of models is that they are highly parameterized, which makes describing and interpreting the prediction strategies difficult. We use topological data analysis to transform these complex prediction models into pictures representing a topological view. The result is a map of the predictions that enables inspection. The methods scale up to large datasets across different domains and enable us to detect labeling errors in training data, understand generalization in image classification, and inspect predictions of likely pathogenic mutations in the BRCA1 gene.

Four lectures on holography and the AdS/CFT correspondence applied to condensed matter systems. The first lecture introduces the concept of a quantum phase transition. The second lecture discusses linear response theory and Ward identities. The third lecture presents transport coefficients derived from AdS/CFT that should be applicable in the quantum critical region associated to a quantum phase transition. The fourth lecture builds in the physics of a superconducting or superfluid phase transition to the simple holographic model of the third lecture.

While attaining external field control of bimolecular chemical reactions has long been a coveted goal of physics and chemistry, the role of hyperfine interactions and dc magnetic fields in achieving such control has remained elusive. We develop an extended coupled-channel statistical theory of barrierless atom-diatom chemical reactions, and apply it to elucidate the effects of magnetic fields and hyperfine interactions on the ultracold chemical reaction Li(^2S_{1/2}) + CaH(^2Σ^+) to LiH(^1Σ^+) + Ca(^1S_{0}) on a newly developed set of ab initio potential energy surfaces. We observe large field effects on the reaction cross sections, opening up the possibility of controlling ultracold barrierless chemical reactions by tuning selected hyperfine states of the reactants with an external magnetic field.

Previously, methods for learning marginally stable linear dynamical systems either required the transition matrix to be symmetric or incurred regret bounds that scale polynomially with the system's hidden dimension. In this work, we introduce a novel method that overcomes this trade-off, achieving dimension-free regret despite the presence of asymmetric matrices and marginal stability. Our method combines spectral filtering with linear predictors and employs Chebyshev polynomials in the complex plane to construct a novel spectral filtering basis. This construction guarantees sublinear regret in an online learning framework, without relying on any statistical or generative assumptions. Specifically, we prove that as long as the transition matrix has eigenvalues with complex component bounded by 1/poly log T, then our method achieves regret O(T^{9/10}) when compared to the best linear dynamical predictor in hindsight.

The study demonstrates the capabilities of a vector-based approach for calculating stoichiometric coefficients in chemical equations, using black powder as an illustrative example. A method is proposed for selecting and constraining intermediate interactions between reactants, as well as for identifying final products. It is shown that even a small number of components can lead to a large number of final and intermediate products. Through concrete calculations, a correlation is established between the number of possible chemical equations and the number of reactants. A methodology is proposed for computing all possible chemical equations within a reaction system for arbitrary component ratios, enabling the derivation of all feasible chemical reactions. Additionally, a method is developed for calculating the chemical composition for a fixed set of reactants, allowing for the evaluation of the set of products resulting from all possible chemical interactions given a specified initial composition.

We theoretically identify the noise-induced coherent contribution to the ergotropy of a four-level quantum heat engine coupled to a unimodal quantum cavity. We utilize a protocol where the passive state's quasiprobabilities can be analytically identified from the population-coherence coupled reduced density matrix. The reduced density matrix elements are evaluated using a microscopic quantum master equation formalism. Multiple ergotropies within the same coherence interval, each characterized by a positive and pronounced coherent contribution, are observed. These ergotropies are a result of population inversion as well as quasiprobability-population inversion, controllable through the coherence measure parameters. The optimal flux and power of the engine are found to be at moderate values of ergotropy with increasing values of noise-induced coherence. The optimal power at different coherences is found to possess a constant ergotropy.

Early warning signals have been proposed to forecast the possibility of a critical transition, such as the eutrophication of a lake, the collapse of a coral reef, or the end of a glacial period. Because such transitions often unfold on temporal and spatial scales that can be difficult to approach by experimental manipulation, research has often relied on historical observations as a source of natural experiments. Here we examine a critical difference between selecting systems for study based on the fact that we have observed a critical transition and those systems for which we wish to forecast the approach of a transition. This difference arises by conditionally selecting systems known to experience a transition of some sort and failing to account for the bias this introduces -- a statistical error often known as the Prosecutor's Fallacy. By analysing simulated systems that have experienced transitions purely by chance, we reveal an elevated rate of false positives in common warning signal statistics. We further demonstrate a model-based approach that is less subject to this bias than these more commonly used summary statistics. We note that experimental studies with replicates avoid this pitfall entirely.

Predicting properties of complex, large-scale quantum systems is essential for developing quantum technologies. We present an efficient method for constructing an approximate classical description of a quantum state using very few measurements of the state. This description, called a classical shadow, can be used to predict many different properties: order log M measurements suffice to accurately predict M different functions of the state with high success probability. The number of measurements is independent of the system size, and saturates information-theoretic lower bounds. Moreover, target properties to predict can be selected after the measurements are completed. We support our theoretical findings with extensive numerical experiments. We apply classical shadows to predict quantum fidelities, entanglement entropies, two-point correlation functions, expectation values of local observables, and the energy variance of many-body local Hamiltonians. The numerical results highlight the advantages of classical shadows relative to previously known methods.

The paper has two goals: It presents basic ideas, notions, and methods for reduction of reaction kinetics models: quasi-steady-state, quasi-equilibrium, slow invariant manifolds, and limiting steps. It describes briefly the current state of the art and some latest achievements in the broad area of model reduction in chemical and biochemical kinetics, including new results in methods of invariant manifolds, computation singular perturbation, bottleneck methods, asymptotology, tropical equilibration, and reaction mechanism skeletonisation.

The mobility edge (ME) is a critical energy delineates the boundary between extended and localized states within the energy spectrum, and it plays a crucial role in understanding the metal-insulator transition in disordered or quasiperiodic systems. While there have been extensive studies on MEs in one-dimensional non-Hermitian (NH) quasiperiodic lattices recently, the investigation of exact NH MEs in two-dimensional (2D) cases remains rare. In the present study, we introduce a 2D dissipative Lieb lattice (DLL) model with imaginary quasiperiodic potentials applied solely to the vertices of the Lieb lattice. By mapping this DLL model to the 2D NH Aubry-Andr{é}-Harper (AAH) model, we analytically derive the exact ME and find it associated with the absolute eigenenergies. We find that the eigenvalues of extended states are purely imaginary when the quasiperiodic potential is strong enough. Additionally, we demonstrate that the introduction of imaginary quasiperiodic potentials does not disrupt the flat bands inherent in the system. Finally, we propose a theoretical framework for realizing our model using the Lindblad master equation. Our results pave the way for further investigation of exact NH MEs and flat bands in 2D dissipative quasiperiodic systems.

Motivated by recent observations of symmtry broken phases in lightly-doped multilayer graphene, we investigate magnetic phase transitions in a generalized electron gas model with four-component electron spin. This model simplifies the problem with a parabolic dispersion band, abstracting away the details of the graphene band structure to focus solely on the effects of the Coulomb interaction. We report four findings: 1) In the Hartree-Fock approximation, we observe that the paramagnetic state undergoes a sequence of density-driven, first-order phase transitions, progressively depopulating electrons from each spin component until achieving complete polarization within a very narrow density window where 1.2<r_s<2 (r_s being the electron gas parameter). 2) Further incorporating the correlation energy via the Bohm-Pines random-phase approximation shows that the cascade of transitions obtained within Hartree-Fock approximation is replaced by a single ferromagnetic phase transition at r_s = 6.12. 3) The disappearance of cascade is due to the correlation energy difference between the four-component paramagnetic state and symmetry-broken phases, which is nearly an order of magnitude more negative than the corresponding Hartree-Fock energy difference for 1.2 < r_s < 2. 4) The transition from the paramagnetic state to the fully polarized state at r_s=6.12 is governed by the balance between exchange and correlation energies, a competition that cannot be captured by mean-field approximations to models featuring effective (density-dependent) delta-function interactions, such as the Stoner model. We use the insights from our model to comment on the phase diagram of multilayer graphene electron gas.

We study the emergence of multi-step reasoning in deep Transformer language models through a geometric and statistical-physics lens. Treating the hidden-state trajectory as a flow on an implicit Riemannian manifold, we analyze the layerwise covariance spectrum of activations, where C^{(ell)}=E[h^{(ell)}h^{(ell)top}], and track deviations from a random-matrix bulk. Across model scales (1.5B--30B), we observe a sharp reduction in effective dimensionality consistent with a phase transition: an order parameter based on sparsity/localization, Ω(h)=1-|h|_1/(d|h|_2), exhibits a discontinuity near a critical normalized depth γ_capprox 0.42 in sufficiently large models. We formalize the forward pass as a discrete coarse-graining map and relate the appearance of stable "concept basins" to fixed points of this renormalization-like dynamics. The resulting low-entropy regime is characterized by a spectral tail collapse and by the formation of transient, reusable object-like structures in representation space, which we call Transient Class Objects (TCOs). We provide theoretical conditions connecting logical separability to spectral decay and validate the predicted signatures with layerwise probes on multiple open-weight model families.

In recent years, there has been tremendous progress in the development of quantum computing hardware, algorithms and services leading to the expectation that in the near future quantum computers will be capable of performing simulations for natural science applications, operations research, and machine learning at scales mostly inaccessible to classical computers. Whereas the impact of quantum computing has already started to be recognized in fields such as cryptanalysis, natural science simulations, and optimization among others, very little is known about the full potential of quantum computing simulations and machine learning in the realm of healthcare and life science (HCLS). Herein, we discuss the transformational changes we expect from the use of quantum computation for HCLS research, more specifically in the field of cell-centric therapeutics. Moreover, we identify and elaborate open problems in cell engineering, tissue modeling, perturbation modeling, and bio-topology while discussing candidate quantum algorithms for research on these topics and their potential advantages over classical computational approaches.

Temporal causal representation learning methods assume that causal mechanisms switch instantaneously between discrete domains, yet real-world systems often exhibit continuous mechanism transitions. For example, a vehicle's dynamics evolve gradually through a turning maneuver, and human gait shifts smoothly from walking to running. We formalize this setting by modeling transitional mechanisms as convex combinations of finitely many atomic mechanisms, governed by time-varying mixing coefficients. Our theoretical contributions establish that both the latent causal variables and the continuous mixing trajectory are jointly identifiable. We further propose TRACE, a Mixture-of-Experts framework where each expert learns one atomic mechanism during training, enabling recovery of mechanism trajectories at test time. This formulation generalizes to intermediate mechanism states never observed during training. Experiments on synthetic and real-world data demonstrate that TRACE recovers mixing trajectories with up to 0.99 correlation, substantially outperforming discrete-switching baselines.

In fault-tolerant quantum computing with the surface code, non-Clifford gates are crucial for universal computation. However, implementing these gates using methods like magic state distillation and code switching requires significant resources. In this work, we propose a new protocol that combines magic state preparation and code switching to realize logical non-Clifford operations with the potential for fault tolerance. Our approach begins with a special logical state in the Z_4 surface code. By applying a sequence of transformations, the system goes through different topological codes, including the non-Abelian D_4 quantum double model. This process ultimately produces a magic state in a condensed Z_2 surface code, which enables the implementation of a logical T gate in the standard Z_2 surface code. In our analysis, we employ a framework where the topological codes are represented by their topological orders and all the transformations are considered as topological manipulations such as gauging symmetries and condensing anyons. This perspective is particularly useful for understanding code switching between topological codes.

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

This paper introduces a continuous-time stochastic dynamical framework for understanding how large language models (LLMs) may self-amplify latent biases or toxicity through their own chain-of-thought reasoning. The model posits an instantaneous "severity" variable x(t) in [0,1] evolving under a stochastic differential equation (SDE) with a drift term μ(x) and diffusion σ(x). Crucially, such a process can be consistently analyzed via the Fokker--Planck approach if each incremental step behaves nearly Markovian in severity space. The analysis investigates critical phenomena, showing that certain parameter regimes create phase transitions from subcritical (self-correcting) to supercritical (runaway severity). The paper derives stationary distributions, first-passage times to harmful thresholds, and scaling laws near critical points. Finally, it highlights implications for agents and extended LLM reasoning models: in principle, these equations might serve as a basis for formal verification of whether a model remains stable or propagates bias over repeated inferences.

We introduce a new predator-prey model by replacing the growth and predation constant by a square matrix, and the population density as a population vector. The classical Lotka-Volterra model describes a population that either modulates or converges. Stability analysis of such models have been extensively studied by the works of Merdan (https://doi.org/10.1016/j.chaos.2007.06.062). The new model adds complexity by introducing an age group structure where the population of each age group evolves as prescribed by the Leslie matrix. The added complexity changes the behavior of the model such that the population either displays roughly an exponential growth or decay. We first provide an exact equation that describes a time evolution and use analytic techniques to obtain an approximate growth factor. We also discuss the variants of the Leslie model, i.e., the complex value predator-prey model and the competitive model. We then prove the Last Species Standing theorem that determines the dominant population in the large time limit. The recursive structure of the model denies the application of simple regression. We discuss a machine learning scheme that allows an admissible fit for the population evolution of Paramecium Aurelia and Paramecium Caudatum. Another potential avenue to simplify the computation is to use the machinery of quantum operators. We demonstrate the potential of this approach by computing the Hamiltonian of a simple Leslie system.

A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105 585-593 (2003), Annu. Rev. Phys. Chem. 58 113-142 (2007)], emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It utilizes multiple kinetic cycles in time, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein. In the present paper, we thoroughly investigate both the deterministic (microscopic) and stochastic (mesoscopic) models, and focus on the identification of the source of temporal cooperativity via comparing with allosteric cooperativity. A thermodynamic analysis confirms again the claim that the chemical equilibrium state exists if and only if the phosphorylation potential triangle G=0, in which case the amplification of sensitivity is completely abolished. Then we provide comprehensive theoretical and numerical analysis with the first-order and zero-order assumptions in phosphorylation-dephosphorylation cycle respectively. Furthermore, it is interestingly found that the underlying mathematics of temporal cooperativity and allosteric cooperativity are equivalent, and both of them can be expressed by "dissociation constants", which also characterizes the essential differences between the simple and ultrasensitive PdPC switches. Nevertheless, the degree of allosteric cooperativity is restricted by the total number of sites in a single enzyme molecule which can not be freely regulated, while temporal cooperativity is only restricted by the total number of molecules of the target protein which can be regulated in a wide range and gives rise to the ultrasensitivity phenomenon.