Daily Papers

Complex logical reasoning tasks require a long sequence of reasoning, which a large language model (LLM) with chain-of-thought prompting still falls short. To alleviate this issue, neurosymbolic approaches incorporate a symbolic solver. Specifically, an LLM only translates a natural language problem into a satisfiability (SAT) problem that consists of first-order logic formulas, and a sound symbolic solver returns a mathematically correct solution. However, we discover that LLMs have difficulties to capture complex logical semantics hidden in the natural language during translation. To resolve this limitation, we propose a Compositional First-Order Logic Translation. An LLM first parses a natural language sentence into newly defined logical dependency structures that consist of an atomic subsentence and its dependents, then sequentially translate the parsed subsentences. Since multiple logical dependency structures and sequential translations are possible for a single sentence, we also introduce two Verification algorithms to ensure more reliable results. We utilize an SAT solver to rigorously compare semantics of generated first-order logic formulas and select the most probable one. We evaluate the proposed method, dubbed CLOVER, on seven logical reasoning benchmarks and show that it outperforms the previous neurosymbolic approaches and achieves new state-of-the-art results.

We introduce sub-sentence encoder, a contrastively-learned contextual embedding model for fine-grained semantic representation of text. In contrast to the standard practice with sentence embeddings, where the meaning of an entire sequence of text is encoded into a fixed-length vector, the sub-sentence encoder learns to produce distinct contextual embeddings corresponding to different atomic propositions, i.e. atomic units of meaning expressed within a text sequence. The sub-sentence embeddings are contrastively learned to recognize (inferred) semantic equivalence between propositions across different text sequences. Our experiments show the effectiveness of sub-sentence encoders in applications, such as retrieving supporting facts for fine-grained text attribution or recognizing the conditional semantic similarity between texts. In practice, we demonstrate that sub-sentence encoders keep the same level of inference cost and space complexity compared to sentence encoders.

Language-guided human motion synthesis has been a challenging task due to the inherent complexity and diversity of human behaviors. Previous methods face limitations in generalization to novel actions, often resulting in unrealistic or incoherent motion sequences. In this paper, we propose ATOM (ATomic mOtion Modeling) to mitigate this problem, by decomposing actions into atomic actions, and employing a curriculum learning strategy to learn atomic action composition. First, we disentangle complex human motions into a set of atomic actions during learning, and then assemble novel actions using the learned atomic actions, which offers better adaptability to new actions. Moreover, we introduce a curriculum learning training strategy that leverages masked motion modeling with a gradual increase in the mask ratio, and thus facilitates atomic action assembly. This approach mitigates the overfitting problem commonly encountered in previous methods while enforcing the model to learn better motion representations. We demonstrate the effectiveness of ATOM through extensive experiments, including text-to-motion and action-to-motion synthesis tasks. We further illustrate its superiority in synthesizing plausible and coherent text-guided human motion sequences.

The mechanism by which RL contributes to reasoning capabilities-whether it incentivizes the synthesis of new skills or merely amplifies existing behaviors-remains a subject of intense debate. In this work, we investigate this question through the lens of Complementary Reasoning, a complex task that requires integrating internal parametric knowledge with external contextual information. Using a controlled synthetic dataset of human biographies, we strictly decouple this ability into two atomic skills: Parametric Reasoning (relying on internal knowledge) and Contextual Reasoning (depending on external information). To rigorously assess capability boundaries, we evaluate generalization across three distinct levels of difficulty: I.I.D., Composition, and Zero-shot settings. We find that while SFT is sufficient for in-distribution performance, it struggles with O.O.D. generalization, particularly in Zero-shot settings where relational combinations are novel. Crucially, we identify the SFT Generalization Paradox: Models supervised solely on the composite task achieve near-perfect in-distribution accuracy but collapse on out-of-distribution generalization, indicating their reliance on rote memorization of path shortcuts. In contrast, we find that RL acts as a reasoning synthesizer rather than a probability amplifier. However, we uncover a strict atomic prerequisite: RL can only synthesize these complex strategies if the base model has first mastered the independent atomic skills (Parametric and Contextual) via SFT. These findings challenge the view of RL as a mere amplifier, suggesting that given sufficient atomic foundations, RL can actively synthesize complex reasoning strategies from learned primitives without explicit supervision on such complex strategies. This indicates that decoupled atomic training followed by RL offers a scalable path to generalization for complex reasoning tasks.

The fundamental units of internal representations in large language models (LLMs) remain undefined, limiting further understanding of their mechanisms. Neurons or features are often regarded as such units, yet neurons suffer from polysemy, while features face concerns of unreliable reconstruction and instability. To address this issue, we propose the Atoms Theory, which defines such units as atoms. We introduce the atomic inner product (AIP) to correct representation shifting, formally define atoms, and prove the conditions that atoms satisfy the Restricted Isometry Property (RIP), ensuring stable sparse representations over atom set and linking to compressed sensing. Under stronger conditions, we further establish the uniqueness and exact ell_1 recoverability of the sparse representations, and provide guarantees that single-layer sparse autoencoders (SAEs) with threshold activations can reliably identify the atoms. To validate the Atoms Theory, we train threshold-activated SAEs on Gemma2-2B, Gemma2-9B, and Llama3.1-8B, achieving 99.9% sparse reconstruction across layers on average, and more than 99.8% of atoms satisfy the uniqueness condition, compared to 0.5% for neurons and 68.2% for features, showing that atoms more faithfully capture intrinsic representations of LLMs. Scaling experiments further reveal the link between SAEs size and recovery capacity. Overall, this work systematically introduces and validates Atoms Theory of LLMs, providing a theoretical framework for understanding internal representations and a foundation for mechanistic interpretability. Code available at https://github.com/ChenhuiHu/towards_atoms.

In this paper, we address the challenging task of multimodal mathematical reasoning by incorporating the ability of "slow thinking" into multimodal large language models (MLLMs). Our core idea is that different levels of reasoning abilities can be combined dynamically to tackle questions with different complexity. To this end, we propose a paradigm of Self-structured Chain of Thought (SCoT), which is composed of minimal semantic atomic steps. Different from existing methods that rely on structured templates or free-form paradigms, our method can not only generate cognitive CoT structures for various complex tasks but also mitigates the phenomenon of overthinking. To introduce structured reasoning capabilities into visual understanding models, we further design a novel AtomThink framework with four key modules, including (i) a data engine to generate high-quality multimodal reasoning paths; (ii) a supervised fine-tuning process with serialized inference data; (iii) a policy-guided multi-turn inference method; and (iv) an atomic capability metric to evaluate the single step utilization rate. We conduct extensive experiments to show that the proposed AtomThink significantly improves the performance of baseline MLLMs, achieving more than 10\% average accuracy gains on MathVista and MathVerse. Compared to state-of-the-art structured CoT approaches, our method not only achieves higher accuracy but also improves data utilization by 5 times and boosts inference efficiency by 85.3\%. Our code is now public available in https://github.com/Quinn777/AtomThink.

In this paper, we address the challenging task of multimodal mathematical reasoning by incorporating the ability of ``slow thinking" into multimodal large language models (MLLMs). Contrary to existing methods that rely on direct or fast thinking, our key idea is to construct long chains of thought (CoT) consisting of atomic actions in a step-by-step manner, guiding MLLMs to perform complex reasoning. To this end, we design a novel AtomThink framework composed of three key modules: (i) a CoT annotation engine that automatically generates high-quality CoT annotations to address the lack of high-quality visual mathematical data; (ii) an atomic step fine-tuning strategy that jointly optimizes an MLLM and a policy reward model (PRM) for step-wise reasoning; and (iii) four different search strategies that can be applied with the PRM to complete reasoning. Additionally, we propose AtomMATH, a large-scale multimodal dataset of long CoTs, and an atomic capability evaluation metric for mathematical tasks. Extensive experimental results show that the proposed AtomThink significantly improves the performance of baseline MLLMs, achieving approximately 50\% relative accuracy gains on MathVista and 120\% on MathVerse. To support the advancement of multimodal slow-thinking models, we will make our code and dataset publicly available on https://github.com/Quinn777/AtomThink.

Large Language Models (LLMs) achieve superior performance through training-time scaling, and test-time scaling further enhances their capabilities by conducting effective reasoning during inference. However, as the scale of reasoning increases, existing test-time scaling methods suffer from accumulated historical information, which not only wastes computational resources but also interferes with effective reasoning. To address this issue, we observe that complex reasoning progress is often achieved by solving a sequence of independent subquestions, each being self-contained and verifiable. These subquestions are essentially atomic questions, relying primarily on their current state rather than accumulated history, similar to the memoryless transitions in a Markov process. Based on this observation, we propose Atom of Thoughts (AoT), where each state transition in the reasoning process consists of decomposing the current question into a dependency-based directed acyclic graph and contracting its subquestions, forming a new atomic question state. This iterative decomposition-contraction process continues until reaching directly solvable atomic questions, naturally realizing Markov transitions between question states. Furthermore, these atomic questions can be seamlessly integrated into existing test-time scaling methods, enabling AoT to serve as a plug-in enhancement for improving reasoning capabilities. Experiments across six benchmarks demonstrate the effectiveness of AoT both as a standalone framework and a plug-in enhancement. Notably, on HotpotQA, when applied to gpt-4o-mini, AoT achieves an 80.6% F1 score, surpassing o3-mini by 3.4% and DeepSeek-R1 by 10.6%. The code will be available at https://github.com/qixucen/atom.

In today's rapidly expanding data landscape, knowledge extraction from unstructured text is vital for real-time analytics, temporal inference, and dynamic memory frameworks. However, traditional static knowledge graph (KG) construction often overlooks the dynamic and time-sensitive nature of real-world data, limiting adaptability to continuous changes. Moreover, recent zero- or few-shot approaches that avoid domain-specific fine-tuning or reliance on prebuilt ontologies often suffer from instability across multiple runs, as well as incomplete coverage of key facts. To address these challenges, we introduce ATOM (AdapTive and OptiMized), a few-shot and scalable approach that builds and continuously updates Temporal Knowledge Graphs (TKGs) from unstructured texts. ATOM splits input documents into minimal, self-contained "atomic" facts, improving extraction exhaustivity and stability. Then, it constructs atomic TKGs from these facts while employing a dual-time modeling that distinguishes when information is observed from when it is valid. The resulting atomic TKGs are subsequently merged in parallel. Empirical evaluations demonstrate that ATOM achieves ~18% higher exhaustivity, ~17% better stability, and over 90% latency reduction compared to baseline methods, demonstrating a strong scalability potential for dynamic TKG construction.

This paper challenges the recent paradigm in atomic property prediction that links progress to growing dataset sizes and computational resources. We show that pretraining on a carefully selected, task-relevant dataset can match or even surpass large-scale pretraining, while using as little as 1/24th of the computational cost. We introduce the Chemical Similarity Index (CSI), a novel metric inspired by computer vision's Fr\'echet Inception Distance, for molecular graphs which quantifies the alignment between upstream pretraining datasets and downstream tasks. By selecting the most relevant dataset with minimal CSI distance, we show that models pretrained on a smaller, focused dataset consistently outperform those pretrained on massive, mixed datasets such as JMP, even when those larger datasets include the relevant dataset. Counterintuitively, we also find that indiscriminately adding more data can degrade model performance when the additional data poorly aligns with the task at hand. Our findings highlight that quality often outperforms quantity in pretraining for atomic property prediction.

Point defects play a central role in driving the properties of materials. First-principles methods are widely used to compute defect energetics and structures, including at scale for high-throughput defect databases. However, these methods are computationally expensive, making machine-learning force fields (MLFFs) an attractive alternative for accelerating structural relaxations. Most existing MLFFs are based on graph neural networks (GNNs), which can suffer from oversmoothing and poor representation of long-range interactions. Both of these issues are especially of concern when modeling point defects. To address these challenges, we introduce the Accelerated Deep Atomic Potential Transformer (ADAPT), an MLFF that replaces graph representations with a direct coordinates-in-space formulation and explicitly considers all pairwise atomic interactions. Atoms are treated as tokens, with a Transformer encoder modeling their interactions. Applied to a dataset of silicon point defects, ADAPT achieves a roughly 33 percent reduction in both force and energy prediction errors relative to a state-of-the-art GNN-based model, while requiring only a fraction of the computational cost.

Multimodal Large Language Models (MLLMs) have achieved remarkable progress in various multimodal tasks. To pursue higher intelligence in space, MLLMs require integrating multiple atomic spatial capabilities to handle complex and dynamic tasks. However, existing benchmarks struggle to comprehensively evaluate the spatial intelligence of common MLLMs from the atomic level to the compositional level. To fill this gap, we present SpaCE-10, a comprehensive benchmark for compositional spatial evaluations. In SpaCE-10, we define 10 atomic spatial capabilities, which are combined to form 8 compositional capabilities. Based on these definitions, we propose a novel hierarchical annotation pipeline to generate high-quality and diverse question-answer (QA) pairs. With over 150+ hours of human expert effort, we obtain over 5k QA pairs for 811 real indoor scenes in SpaCE-10, which covers various evaluation settings like point cloud input and multi-choice QA. We conduct an extensive evaluation of common MLLMs on SpaCE-10 and find that even the most advanced MLLM still lags behind humans by large margins. Through our careful study, we also draw several significant findings that benefit the MLLM community. For example, we reveal that the shortcoming of counting capability greatly limits the compositional spatial capabilities of existing MLLMs. The evaluation code and benchmark datasets are available at https://github.com/Cuzyoung/SpaCE-10.

The binding energies of the five bound rotational levels J=0-4 in the highest vibrational level v=14 in the X^1Sigma_g^+ ground electronic state of H_2 were measured in a three-step ultraviolet-laser experiment. Two-photon UV-photolysis of H_2S produced population in these high-lying bound states, that were subsequently interrogated at high precision via Doppler-free spectroscopy of the F^1Sigma_g^+ - X^1Sigma_g^+ system. A third UV-laser was used for detection through auto-ionizing resonances. The experimentally determined binding energies were found to be in excellent agreement with calculations based on non-adiabatic perturbation theory, also including relativistic and quantum electrodynamical contributions. The s-wave scattering length of the H + H system is derived from the binding energy of the last bound J=0 level via a direct semi-empirical approach, yielding a value of a_s = 0.2724(5) a_0, in good agreement with a result from a previously followed theoretical approach. The subtle effect of the malpha^4 relativity contribution to a_s was found to be significant. In a similar manner a value for the p-wave scattering volume is determined via the J=1 binding energy yielding a_p = -134.0000(6) a_0^3. The binding energy of the last bound state in H_2, the (v=14, J=4) level, is determined at 0.023(4) cm^{-1}, in good agreement with calculation. The effect of the hyperfine substructure caused by the two hydrogen atoms at large internuclear separation, giving rise to three distinct dissociation limits, is discussed.

Large language models (LLMs) exhibit remarkable problem-solving abilities, but struggle with complex tasks due to static internal knowledge. Retrieval-Augmented Generation (RAG) enhances access to external information, yet remains limited in multi-hop reasoning and strategic search due to rigid workflows. Recent advancements in agentic deep research empower LLMs to autonomously reason, search, and synthesize information. However, current approaches relying on outcome-based reinforcement learning (RL) face critical issues such as conflicting gradients and reward sparsity, limiting performance gains and training efficiency. To address these, we first propose Atomic Thought, a novel LLM thinking paradigm that decomposes reasoning into fine-grained functional units. These units are supervised by Reasoning Reward Models (RRMs), which provide Atomic Thought Rewards (ATR) for fine-grained guidance. Building on this, we propose Atom-Searcher, a novel RL framework for agentic deep research that integrates Atomic Thought and ATR. Atom-Searcher uses a curriculum-inspired reward schedule, prioritizing process-level ATR early and transitioning to outcome rewards, accelerating convergence on effective reasoning paths. Experiments on seven benchmarks show consistent improvements over the state-of-the-art. Key advantages include: (1) Atom-Searcher scales computation at test-time. (2) Atomic Thought provides supervision anchors for RRMs, bridging deep research tasks and RRMs. (3) Atom-Searcher exhibits more interpretable, human-like reasoning patterns.

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

Paraphrases represent a human's intuitive ability to understand expressions presented in various different ways. Current paraphrase evaluations of language models primarily use binary approaches, offering limited interpretability of specific text changes. Atomic paraphrase types (APT) decompose paraphrases into different linguistic changes and offer a granular view of the flexibility in linguistic expression (e.g., a shift in syntax or vocabulary used). In this study, we assess the human preferences towards ChatGPT in generating English paraphrases with ten APTs and five prompting techniques. We introduce APTY (Atomic Paraphrase TYpes), a dataset of 500 sentence-level and word-level annotations by 15 annotators. The dataset also provides a human preference ranking of paraphrases with different types that can be used to fine-tune models with RLHF and DPO methods. Our results reveal that ChatGPT can generate simple APTs, such as additions and deletions, but struggle with complex structures (e.g., subordination changes). This study contributes to understanding which aspects of paraphrasing language models have already succeeded at understanding and what remains elusive. In addition, our curated datasets can be used to develop language models with specific linguistic capabilities.

Full quantum tomography of high-dimensional quantum systems is experimentally infeasible due to the exponential scaling of the number of required measurements on the number of qubits in the system. However, several ideas were proposed recently for predicting the limited number of features for these states, or estimating the expectation values of operators, without the need for full state reconstruction. These ideas go under the general name of shadow tomography. Here we provide an experimental demonstration of property estimation based on classical shadows proposed in [H.-Y. Huang, R. Kueng, J. Preskill. Nat. Phys. https://doi.org/10.1038/s41567-020-0932-7 (2020)] and study its performance in the quantum optical experiment with high-dimensional spatial states of photons. We show on experimental data how this procedure outperforms conventional state reconstruction in fidelity estimation from a limited number of measurements.

Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular energy states from classical mechanics. This limitation results in a significant oversight of quantum mechanical effects, such as quantized (discrete) energy level structures, which offer a more accurate estimation of molecular energy and can be experimentally measured through energy spectra. In this paper, we propose to utilize the energy spectra to enhance the pre-training of 3D molecular representations (MolSpectra), thereby infusing the knowledge of quantum mechanics into the molecular representations. Specifically, we propose SpecFormer, a multi-spectrum encoder for encoding molecular spectra via masked patch reconstruction. By further aligning outputs from the 3D encoder and spectrum encoder using a contrastive objective, we enhance the 3D encoder's understanding of molecules. Evaluations on public benchmarks reveal that our pre-trained representations surpass existing methods in predicting molecular properties and modeling dynamics.

There has recently been considerable interest in incorporating information retrieval into large language models (LLMs). Retrieval from a dynamically expanding external corpus of text allows a model to incorporate current events and can be viewed as a form of episodic memory. Here we demonstrate that pre-processing the external corpus into semi-structured ''atomic facts'' makes retrieval more efficient. More specifically, we demonstrate that our particular form of atomic facts improves performance on various question answering tasks when the amount of retrieved text is limited. Limiting the amount of retrieval reduces the size of the context and improves inference efficiency.

Recently, text-to-motion models have opened new possibilities for creating realistic human motion with greater efficiency and flexibility. However, aligning motion generation with event-level textual descriptions presents unique challenges due to the complex relationship between textual prompts and desired motion outcomes. To address this, we introduce AToM, a framework that enhances the alignment between generated motion and text prompts by leveraging reward from GPT-4Vision. AToM comprises three main stages: Firstly, we construct a dataset MotionPrefer that pairs three types of event-level textual prompts with generated motions, which cover the integrity, temporal relationship and frequency of motion. Secondly, we design a paradigm that utilizes GPT-4Vision for detailed motion annotation, including visual data formatting, task-specific instructions and scoring rules for each sub-task. Finally, we fine-tune an existing text-to-motion model using reinforcement learning guided by this paradigm. Experimental results demonstrate that AToM significantly improves the event-level alignment quality of text-to-motion generation.

The study of the long-time dynamics of quantum systems can be a real challenge, especially in systems like ultracold gases, where the required timescales may be longer than the lifetime of the system itself. In this work, we show that it is possible to access the long-time dynamics of a strongly repulsive atomic gas mixture in shorter times. The shortcut-to-dynamics protocol that we propose does not modify the fate of the observables, but effectively jumps ahead in time without changing the system's inherent evolution. Just like the next-chapter button in a movie player that allows to quickly reach the part of the movie one wants to watch, it is a leap into the future.

Molecule and text representation learning has gained increasing interest due to its potential for enhancing the understanding of chemical information. However, existing models often struggle to capture subtle differences between molecules and their descriptions, as they lack the ability to learn fine-grained alignments between molecular substructures and chemical phrases. To address this limitation, we introduce MolBridge, a novel molecule-text learning framework based on substructure-aware alignments. Specifically, we augment the original molecule-description pairs with additional alignment signals derived from molecular substructures and chemical phrases. To effectively learn from these enriched alignments, MolBridge employs substructure-aware contrastive learning, coupled with a self-refinement mechanism that filters out noisy alignment signals. Experimental results show that MolBridge effectively captures fine-grained correspondences and outperforms state-of-the-art baselines on a wide range of molecular benchmarks, highlighting the significance of substructure-aware alignment in molecule-text learning.

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate change. These calculations are traditionally performed using Density Functional Theory, which is computationally very expensive. Machine learning has the potential to dramatically improve the efficiency of these calculations from days or hours to seconds. We propose the Spherical Channel Network (SCN) to model atomic energies and forces. The SCN is a graph neural network where nodes represent atoms and edges their neighboring atoms. The atom embeddings are a set of spherical functions, called spherical channels, represented using spherical harmonics. We demonstrate, that by rotating the embeddings based on the 3D edge orientation, more information may be utilized while maintaining the rotational equivariance of the messages. While equivariance is a desirable property, we find that by relaxing this constraint in both message passing and aggregation, improved accuracy may be achieved. We demonstrate state-of-the-art results on the large-scale Open Catalyst dataset in both energy and force prediction for numerous tasks and metrics.

We review Bohr's atomic model and its extension by Sommerfeld from a mathematical perspective of wave mechanics. The derivation of quantization rules and energy levels is revisited using semiclassical methods. Sommerfeld-type integrals are evaluated by elementary techniques, and connections with the Schr\"{o}dinger and Dirac equations are established. Historical developments and key transitions from classical to quantum theory are discussed to clarify the structure and significance of the old quantum mechanics.

Generative Flow Networks (GFlowNets) have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from rewards treated as unnormalized distributions. Previous works in this framework often restrict exploration by using predefined molecular fragments as building blocks, limiting the chemical space that can be accessed. In this work, we introduce Atomic GFlowNets (A-GFNs), a foundational generative model leveraging individual atoms as building blocks to explore drug-like chemical space more comprehensively. We propose an unsupervised pre-training approach using drug-like molecule datasets, which teaches A-GFNs about inexpensive yet informative molecular descriptors such as drug-likeliness, topological polar surface area, and synthetic accessibility scores. These properties serve as proxy rewards, guiding A-GFNs towards regions of chemical space that exhibit desirable pharmacological properties. We further implement a goal-conditioned finetuning process, which adapts A-GFNs to optimize for specific target properties. In this work, we pretrain A-GFN on a subset of ZINC dataset, and by employing robust evaluation metrics we show the effectiveness of our approach when compared to other relevant baseline methods for a wide range of drug design tasks. The code is accessible at https://github.com/diamondspark/AGFN.

Machine learning-based interatomic potentials and force fields depend critically on accurate atomic structures, yet such data are scarce due to the limited availability of experimentally resolved crystals. Although atomic-resolution electron microscopy offers a potential source of structural data, converting these images into simulation-ready formats remains labor-intensive and error-prone, creating a bottleneck for model training and validation. We introduce AutoMat, an end-to-end, agent-assisted pipeline that automatically transforms scanning transmission electron microscopy (STEM) images into atomic crystal structures and predicts their physical properties. AutoMat combines pattern-adaptive denoising, physics-guided template retrieval, symmetry-aware atomic reconstruction, fast relaxation and property prediction via MatterSim, and coordinated orchestration across all stages. We propose the first dedicated STEM2Mat-Bench for this task and evaluate performance using lattice RMSD, formation energy MAE, and structure-matching success rate. By orchestrating external tool calls, AutoMat enables a text-only LLM to outperform vision-language models in this domain, achieving closed-loop reasoning throughout the pipeline. In large-scale experiments over 450 structure samples, AutoMat substantially outperforms existing multimodal large language models and tools. These results validate both AutoMat and STEM2Mat-Bench, marking a key step toward bridging microscopy and atomistic simulation in materials science.The code and dataset are publicly available at https://github.com/yyt-2378/AutoMat and https://huggingface.co/datasets/yaotianvector/STEM2Mat.

Discovering novel high-entropy alloys (HEAs) with desirable properties is challenging due to the vast compositional space and complex phase formation mechanisms. Efficient exploration of this space requires a strategic approach that integrates heterogeneous knowledge sources. Here, we propose a framework that systematically combines knowledge extracted from computational material datasets with domain knowledge distilled from scientific literature using large language models (LLMs). A central feature of this approach is the explicit consideration of element substitutability, identifying chemically similar elements that can be interchanged to potentially stabilize desired HEAs. Dempster-Shafer theory, a mathematical framework for reasoning under uncertainty, is employed to model and combine substitutabilities based on aggregated evidence from multiple sources. The framework predicts the phase stability of candidate HEA compositions and is systematically evaluated on both quaternary alloy systems, demonstrating superior performance compared to baseline machine learning models and methods reliant on single-source evidence in cross-validation experiments. By leveraging multi-source knowledge, the framework retains robust predictive power even when key elements are absent from the training data, underscoring its potential for knowledge transfer and extrapolation. Furthermore, the enhanced interpretability of the methodology offers insights into the fundamental factors governing HEA formation. Overall, this work provides a promising strategy for accelerating HEA discovery by integrating computational and textual knowledge sources, enabling efficient exploration of vast compositional spaces with improved generalization and interpretability.

We propose a formal reconstruction of quantum mechanics grounded not in external mathematical abstractions, but in the structured dynamics of subjective experience. The Qualia Abstraction Language (QAL) models physical systems as evolving streams of introspective units, structured sequences of modality, shape, and functional effect, rather than as state vectors in Hilbert space. This approach reimagines core quantum concepts: superposition becomes a form of structured ambiguity; collapse is reframed as an introspective contraction; and entanglement is modeled as semantic resonance across streams of qualia. Drawing on insights from nominalist philosophy and oversight theoretic limits in AI, we argue that the observer paradox in quantum mechanics reflects not an ontological lacuna, but a linguistic one: the absence of a formal vocabulary for modeling first person structure. QAL introduces such a vocabulary, providing a morphodynamic framework that embeds the observer within the system and replaces abstract projection with endogenous transformation. We analyze the alignment of QAL with endophysical approaches, contrast it with standard interpretations of quantum theory, and explore its implications for a post Platonist, introspectively grounded physics.

Molecular structure elucidation involves deducing a molecule's structure from various types of spectral data, which is crucial in chemical experimental analysis. While large language models (LLMs) have shown remarkable proficiency in analyzing and reasoning through complex tasks, they still encounter substantial challenges in molecular structure elucidation. We identify that these challenges largely stem from LLMs' limited grasp of specialized chemical knowledge. In this work, we introduce a Knowledge-enhanced reasoning framework for Molecular Structure Elucidation (K-MSE), leveraging Monte Carlo Tree Search for test-time scaling as a plugin. Specifically, we construct an external molecular substructure knowledge base to extend the LLMs' coverage of the chemical structure space. Furthermore, we design a specialized molecule-spectrum scorer to act as a reward model for the reasoning process, addressing the issue of inaccurate solution evaluation in LLMs. Experimental results show that our approach significantly boosts performance, particularly gaining more than 20% improvement on both GPT-4o-mini and GPT-4o. Our code is available at https://github.com/HICAI-ZJU/K-MSE.

A common approach for teaching large language models (LLMs) to reason is to train on chain-of-thought (CoT) traces of in-distribution reasoning problems, but such annotated data is costly to obtain for every problem of interest. We want reasoning models to generalize beyond their training distribution, and ideally to generalize compositionally: combine atomic reasoning skills to solve harder, unseen reasoning tasks. We take a step towards compositional generalization of reasoning skills when addressing a target compositional task that has no labeled CoT data. We find that simply training models on CoT data of atomic tasks leads to limited generalization, but minimally modifying CoT formats of constituent atomic tasks to be composable can lead to improvements. We can train "atomic CoT" models on the atomic tasks with Composable CoT data and combine them with multitask learning or model merging for better zero-shot performance on the target compositional task. Such a combined model can be further bootstrapped on a small amount of compositional data using rejection sampling fine-tuning (RFT). Results on string operations and natural language skill compositions show that training LLMs on Composable CoT outperforms multitask learning and continued fine-tuning baselines within a given training data budget.

Recent advancements in large language models (LLMs) have led to significant improvements in various natural language processing tasks, but it is still challenging for LLMs to perform knowledge-intensive complex question answering due to LLMs' inefficacy in reasoning planning and the hallucination problem. A typical solution is to employ retrieval-augmented generation (RAG) coupled with chain-of-thought (CoT) reasoning, which decomposes complex questions into chain-like sub-questions and applies iterative RAG at each sub-question. However, prior works exhibit sub-optimal reasoning planning and overlook dynamic knowledge retrieval from heterogeneous sources. In this paper, we propose AtomR, a novel heterogeneous knowledge reasoning framework that conducts multi-source reasoning at the atomic level. Drawing inspiration from the graph modeling of knowledge, AtomR leverages large language models (LLMs) to decompose complex questions into combinations of three atomic knowledge operators, significantly enhancing the reasoning process at both the planning and execution stages. We also introduce BlendQA, a novel evaluation benchmark tailored to assess complex heterogeneous knowledge reasoning. Experiments show that AtomR significantly outperforms state-of-the-art baselines across three single-source and two multi-source reasoning benchmarks, with notable performance gains of 9.4% on 2WikiMultihop and 9.5% on BlendQA.

The AMS-02 experiment recently published time-dependent fluxes of deuterons (D) from May 2011 to April 2021, divided into 33 periods of four Bartels rotations each. These temporal structures are associated with solar modulation. In this study, three modified force-field approximation are employed to examine the long-term behavior of cosmic-ray (CR) isotopes such as D, ^3He, and ^4He, as well as the ratios D/^3He and ^3He/^4He. The solar modulation potential is rigidity-dependent for these modified force-field approximation models. Due to the unknown local interstellar spectrum (LIS) for these isotopes, we utilize the Non-LIS method for solar modulation. By fitting to the AMS-02 time-dependent fluxes, we derive the solar modulation parameters. Our findings prove the assumption in literature that all isotopes can be fitted using the same solar modulation parameters and it shown that the modified FFA models are validated parametrization for solar modulation. Based on these, we forecast the daily fluxes of D, ^3He and ^4He from 2011 to 2020.

Logical reasoning task has attracted great interest since it was proposed. Faced with such a task, current competitive models, even large language models (e.g., ChatGPT and PaLM 2), still perform badly. Previous promising LMs struggle in logical consistency modeling and logical structure perception. To this end, we model the logical reasoning task by transforming each logical sample into reasoning paths and propose an architecture PathReasoner. It addresses the task from the views of both data and model. To expand the diversity of the logical samples, we propose an atom extension strategy supported by equivalent logical formulas, to form new reasoning paths. From the model perspective, we design a stack of transformer-style blocks. In particular, we propose a path-attention module to joint model in-atom and cross-atom relations with the high-order diffusion strategy. Experiments show that PathReasoner achieves competitive performances on two logical reasoning benchmarks and great generalization abilities.

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

Current research on the Decompose-Then-Verify paradigm for evaluating the factuality of long-form text typically treats decomposition and verification in isolation, overlooking their interactions and potential misalignment. We find that existing decomposition policies, typically hand-crafted demonstrations, do not align well with downstream verifiers in terms of atomicity -- a novel metric quantifying information density -- leading to suboptimal verification results. We formulate finding the optimal decomposition policy for optimal verification as a bilevel optimization problem. To approximate a solution for this strongly NP-hard problem, we propose dynamic decomposition, a reinforcement learning framework that leverages verifier feedback to learn a policy for dynamically decomposing claims to verifier-preferred atomicity. Experimental results show that dynamic decomposition outperforms existing decomposition policies, improving verification confidence by 0.07 and accuracy by 0.12 (on a 0-1 scale) on average across varying verifiers, datasets, and atomcities of input claims.

Diffusion models are the standard toolkit for generative modelling of 3D atomic systems. However, for different types of atomic systems - such as molecules and materials - the generative processes are usually highly specific to the target system despite the underlying physics being the same. We introduce the All-atom Diffusion Transformer (ADiT), a unified latent diffusion framework for jointly generating both periodic materials and non-periodic molecular systems using the same model: (1) An autoencoder maps a unified, all-atom representations of molecules and materials to a shared latent embedding space; and (2) A diffusion model is trained to generate new latent embeddings that the autoencoder can decode to sample new molecules or materials. Experiments on QM9 and MP20 datasets demonstrate that jointly trained ADiT generates realistic and valid molecules as well as materials, exceeding state-of-the-art results from molecule and crystal-specific models. ADiT uses standard Transformers for both the autoencoder and diffusion model, resulting in significant speedups during training and inference compared to equivariant diffusion models. Scaling ADiT up to half a billion parameters predictably improves performance, representing a step towards broadly generalizable foundation models for generative chemistry. Open source code: https://github.com/facebookresearch/all-atom-diffusion-transformer

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

Machine learning potentials (MLPs) trained on accurate quantum chemical data can retain the high accuracy, while inflicting little computational demands. On the downside, they need to be trained for each individual system. In recent years, a vast number of MLPs has been trained from scratch because learning additional data typically requires to train again on all data to not forget previously acquired knowledge. Additionally, most common structural descriptors of MLPs cannot represent efficiently a large number of different chemical elements. In this work, we tackle these problems by introducing element-embracing atom-centered symmetry functions (eeACSFs) which combine structural properties and element information from the periodic table. These eeACSFs are a key for our development of a lifelong machine learning potential (lMLP). Uncertainty quantification can be exploited to transgress a fixed, pre-trained MLP to arrive at a continuously adapting lMLP, because a predefined level of accuracy can be ensured. To extend the applicability of an lMLP to new systems, we apply continual learning strategies to enable autonomous and on-the-fly training on a continuous stream of new data. For the training of deep neural networks, we propose the continual resilient (CoRe) optimizer and incremental learning strategies relying on rehearsal of data, regularization of parameters, and the architecture of the model.