arXiv subjects

Shixiang Tang

Publications and source records attributed to Shixiang Tang.

At least 19 recordsLinked to original sources

arXiv2026

ADT: All-Atom Diffusion Tokenizer for 3D Molecular Structures

Discrete structural tokenization provides a promising route to autoregressive 3D molecular generation. Yet, existing tokenizers face a trade-off between compact representation and all-atom reconstruction: atom-level tokens preserve atomic details but produce long sequences, while compact residue-level protein tokens typically omit side-chain geometry. To overcome this limitation, we propose All-atom Diffusion Tokenizer (ADT), which decouples token granularity from reconstruction resolution. ADT uses one structural token per atom for small molecules and one token per protein residue that jointly represents backbone and side-chain geometry. To mitigate geometric distortion introduced by quantization, we leverage the generative capacity of diffusion models to recover fine-grained atomic geometry beyond deterministic decoding from discrete tokens. Extensive experiments across small molecules and proteins demonstrate that ADT achieves strong reconstruction from compact discrete representations while enabling high-quality autoregressive generation of both small molecules and all-atom protein structures. These results establish compact structural tokens as an effective discrete interface for all-atom molecular reconstruction and generation.

cs.LG↗

arXiv2026

Coupled Harness--Model Evolution for Scientific Equation Discovery

Large language models (LLMs) are increasingly used to discover scientific equations from experimental data. Such a discovery system has two parts that must work together: a library of executable computational tools and the model's tool-use policy. The tools supply the solving capability, from diagnosing structure in the data to fitting candidate equations; the policy plans and orchestrates their use. Yet existing systems adapt only one part, keeping either the toolset or the model fixed, which leaves the corresponding failures uncorrectable. We develop a coupled evolution framework that improves both parts from the same verifiable fit-error signal. In the tool-evolution phase, an agent grows an executable tool library from a small set of generic numerical operations by diagnosing its own failures: it authors a new tool when a capability is missing and revises its selection rules when the right tool went unused. In the policy-evolution phase, a small open model (roughly 3B active parameters) is fine-tuned on successful tool-use trajectories collected with the frozen library, on training formulas screened to be disjoint from all evaluation benchmarks. Ablations show the two phases are complementary: with no tool library at all the same model solves almost nothing, the tools account for most of the gain, and trajectory training adds a further gain that is largest on the most difficult problems. The full system solves 79.1/71.3\% of LSR-Synth problems at fit tolerances $10^{-2}$/$10^{-3}$, reaches 63.8\% pooled accuracy on the distributionally different SRSD-Feynman panel, and obtains a normalized CP3-28 aggregate of $-7.27$. These results suggest a broader recipe for scientific agents: let the model and its instruments improve each other under verifiable feedback.

cs.AI↗

arXiv2026

PROTEAN: Beyond De Novo Generation - Can LLM Agents Perform Text-Guided Protein Structure Editing?

Generative AI has achieved remarkable success in de novo protein design, yet protein engineering typically begins with existing, characterized proteins. The primary demand is targeted local editing, e.g., engineering a specific region to optimize affinity, alter immunogenicity, or improve stability, while strictly preserving core catalytic motifs and overall scaffold integrity. However, no standardized framework currently exists for carrying out and evaluating such edits. In current generative-design workflows, researchers often need to manually specify complex low-level parameters and rely on repetitive, trial-and-error sampling and evaluation across generative backends to search for viable conformations. While large language models (LLMs) offer an intuitive interface to express these goals using natural language, prevailing structure-generation models cannot directly interpret high-level human instructions. To bridge this gap, we introduce PROTEAN, a standardized benchmark for text-guided protein structural editing. PROTEAN comprises 380 sub-tasks spanning six intervention families and evaluates a two-stage pipeline in which an LLM translates natural-language goals into backend-specific geometric constraints and a generative model remodels the protein backbone. A two-tier evaluation separates geometric compliance, including target attainment and off-target scope fidelity, from biophysical realizability assessed by inverse folding and refolding consistency. Across five frontier LLMs paired with three backends, strict end-to-end biophysical success starts at just 7.0%. Ablation studies show that LLM constraint compilation is already highly accurate, whereas the main bottlenecks are backend-specific scope leakage and refolding failure. PROTEAN provides an open testbed for developing autonomous, multi-backend macromolecular design agents.

cs.CE↗

arXiv2026

BRIDGE: Selective Boundary Repair with Dependency Graph Evidence in Multi-Agent Systems

Multi-agent collaboration has emerged as a critical paradigm for tackling complex, long-horizon tasks; however, while coordination protocols continue to advance, systemic failures at the inter-agent collaboration interface remain a pervasive bottleneck. In collaborative workflows, systems frequently suffer from \emph{broken handoffs}---where critical task context is omitted, misrouted, or ignored despite each agent emitting locally plausible responses. To address this challenge, we present \method, a verifiable runtime control framework that treats handoff repair as selective intervention over explicit dependency graphs. Central to \method is an integrated fault-attribution and calibration pipeline, \dataset, which decouples execution dependencies and injects counterfactual handoff perturbations to provide empirical supervision for runtime intervention. Leveraging this diagnostic foundation, \method dynamically compiles observable interaction traces into a provenance graph to pinpoint unresolved dependencies, without accessing private agent states. It then evaluates candidate repairs through an empirical gate that weighs expected gains against disruption risks, and executes repairs only when formal local postconditions hold. Extensive evaluations across demanding benchmarks demonstrate that \method boosts task success by up to 12.3 absolute percentage points on SILO-BENCH and 11.1 on TeamBench. Across both backbones, \method maintains strict cost-effectiveness, adding as little as 2.0\% marginal token overhead. Furthermore, on 562 handoff-relevant traces from the MAST benchmark, \method achieves 69.8\% F1 in a single pass, establishing a reliable operational boundary for verifiable coordination repair.

cs.CL↗

arXiv2026

Elucidating the Space of Enzymatic Reaction: A Unified Benchmark and Pretrained Model

Existing reaction models primarily learn molecular transformations, whereas enzy- matic reactions depend jointly on molecular structure and catalytic function. We formulate this problem as learning an enzymatic reaction space linking reactants, products, and Enzyme Commission (EC) annotations. To characterize this space, we introduce VenusRX-Bench, a unified benchmark for forward reaction prediction, single-step retrosynthesis, and EC-number prediction. VenusRX-Bench integrates reactions from multiple biochemical databases with standardized curation, leakage- controlled splits, and consistent evaluation. Benchmarking representative chemical and enzymatic models reveals a clear chemical-to-enzymatic domain gap, driven by limited domain data, catalytic-context dependency, and the difficulty of modeling large biomolecular structures. To bridge this gap, we develop VenusRX, a unified T5-style sequence-to-sequence model for enzymatic reactions. VenusRX jointly learns forward prediction, ret- rosynthesis, and reaction reconstruction, with two-stage training on millions of template-expanded reactions followed by real biochemical reactions. In addition, optional EC conditioning incorporates catalytic context, while Molecule Library- Constrained Decoding improves the generation of complex biomolecules. Across benchmark tasks and challenging generalization splits, VenusRX achieves the best or competitive performance on most evaluated settings over representative chem- ical and enzymatic baselines. Moreover, EC information consistently improves reaction prediction, while learned reaction representations support accurate EC prediction, revealing a bidirectional relationship between reaction structure and catalytic function. Together, VenusRX-Bench and VenusRX provide a unified framework for elucidating and modeling enzymatic reaction space

q-bio.QM↗

arXiv2026

GRAM: Correcting Frozen Time-Series Foundation Models via Graph-Retrieved Amplitude Memory

Time-series foundation models (TSFMs) enable zero-shot forecasting through large-scale cross-domain pretraining, while retrieval augmentation further improves their performance by leveraging historical information. However, existing methods typically correct TSFM forecasts using the ground-truth futures of similar historical windows, which contain both predictive components already captured by the foundation model and sample-specific random fluctuation that is difficult to transfer. In contrast, recurring systematic model bias within prediction errors more directly characterizes the failure modes of a frozen TSFM and therefore provides more valuable correction signals. Effectively exploiting such model bias, however, poses two challenges: prediction errors at different numerical levels are difficult to compare due to scale differences, and the recurring bias must be extracted from prediction errors contaminated by random fluctuation. To address these challenges, we propose GRAM, a general retrieval-augmented framework for frozen TSFMs. GRAM first introduces an Amplitude Memory Module (AMM) that scales prediction errors by amplitude and aggregates them into retrievable prototypes. It then employs a Prototype Graph Module (PGM) to model relations among prototypes to aggregate consistent bias information while suppressing random fluctuation. During online forecasting, GRAM retrieves and expands prototypes relevant to the current query and generates per-horizon corrections to refine the original TSFM forecast. Experiments across multiple datasets and foundation models demonstrate consistent forecasting improvements.

cs.LG↗

arXiv2026

RoboChemGym: A Protocol-Driven Generative Simulation Framework for Long-Horizon Chemical Manipulation

Wet-lab experimentation serves as the gold standard for hypothesis verification in scientific discovery; yet it is inherently labor-intensive, costly, and safety-critical. Embodied agents hold the promise of automating these tedious workflows, but their development is hindered by the scarcity of real-world training data. While simulation offers a scalable alternative for producing demonstrations, current methods primarily target relatively short-horizon tasks with loosely structured interactions, failing to meet the strict procedural constraints and fine-grained manipulation demands of chemical experiments. To bridge this gap, we introduce \textbf{RoboChemGym}, a framework that autonomously generates high-fidelity manipulation demonstrations aligned with real-world experiment protocols, featuring a \textit{self-improving task synthesis} mechanism to iteratively refine task execution and scene configurations, enabling the reliable generation of expert trajectories for complex, multi-object protocols exceeding 10 interaction steps. Furthermore, we introduce a hierarchical benchmark that systematically assesses performance across varying granularities, spanning from atomic operations to full-cycle experimental workflows. RoboChemGym sets a scalable paradigm for the automated data synthesis and capability evaluation of embodied agents in intricate chemical tasks, serving as a critical stepping stone toward fully intelligent laboratories.

cs.RO↗

arXiv2026

UniEvo-VL: An On-policy Self-Distillation Training Recipe for Multimodal Model Self-improvement

Modern multimodal models bring generation and understanding into a single unified system, which enables them to provide and learn from their own feedback. Motivated by this unified capacity, we introduce UniEvo-VL, a self-evolving framework for multimodal models to learn from this constructive self-correction feedback during test-time compute. Instead of relying on a separate, often larger, teacher, we leverage their self-critiques as privileged information and ask a single multimodal model to act as both teacher and student with different contexts. The student only sees the vanilla question, while the teacher conditions on the privileged critique. Then training minimizes the per-state divergence between their denoising diffusion distributions over the student's own sampling trajectories. Experiments demonstrate that UniEvo-VL improves the image generation capabilities of multimodal models, while maintaining their sensitivity to additional reflection information. Specifically, we build on top of the open-source Qwen-image-2512 and observe a significant performance gain from 0.747 to 0.808 on GenEval and from 32.97 to 35.53 on GenEval2 Soft-TIFA. Moreover, attempts with more powerful external critics (e.g., GPT5.6-Luna) show that multimodal models with strong judge capabilities can anticipate a higher self-evolving ceiling. Last but not least, mixed text-rendering outcomes show that our self-improvements may not be uniform across different tasks. Our study aims to shed light on the current hot recursive self-improvement research line to enhance the user experience when using multimodal models without external supervision or guidance.

cs.AI↗

arXiv2026

SymbolicLM: Training Language Models as Symbolic Regressors

Large Language Models (LLMs) have shown promising capabilities in scientific reasoning, yet scientific discovery ultimately requires deriving precise laws directly from observational data, known as Symbolic Regression (SR). This poses a challenge for LLMs due to the gap between probabilistic text generation and the exact structural requirements of SR. Existing approaches rely on complex external scaffolds, which are computationally expensive and separate symbolic reasoning from the model itself. To address this limitation, we propose to directly equip LLMs with symbolic regression capabilities through dedicated numerical-symbolic and physical supervision. We introduce PhysSymbArena, a large-scale benchmark containing over 160,000 equations and 1.8B tokens of numerical-symbolic data with physical descriptions, enabling systematic training and evaluation. Based on PhysSymbArena, we develop SymbolicLM, which enhances the symbolic regression ability of LLMs through mathematical and physical supervision. During inference, we further introduce SymbolicSGA, a refinement framework that leverages quantitative feedback to iteratively improve generated equations. Experiments on multiple symbolic regression benchmarks show that SymbolicLM substantially improves structural recovery while maintaining competitive numerical fitting performance. These results demonstrate that symbolic regression can be explicitly learned as an intrinsic capability of LLMs.

cs.CE↗

arXiv2026

A Comprehensive Survey on Multi-Agent Cooperative Decision-Making: Scenarios, Approaches, Challenges and Perspectives

With the rapid development of artificial intelligence, intelligent decision-making techniques have gradually surpassed human levels in various human-machine competitions, especially in complex multi-agent cooperative task scenarios. Multi-agent cooperative decision-making involves multiple agents working together to complete established tasks and achieve specific objectives. These techniques are widely applicable in real-world scenarios such as autonomous driving, drone navigation, disaster rescue, and simulated military confrontations. This paper begins with a comprehensive survey of the leading simulation environments and platforms used for multi-agent cooperative decision-making. Specifically, we provide an in-depth analysis for these simulation environments from various perspectives, including task formats, reward allocation, and the underlying technologies employed. Subsequently, we provide a comprehensive overview of the mainstream intelligent decision-making approaches, algorithms and models for multi-agent systems (MAS). Theseapproaches can be broadly categorized into five types: rule-based (primarily fuzzy logic), game theory-based, evolutionary algorithms-based, deep multi-agent reinforcement learning (MARL)-based, and large language models(LLMs)reasoning-based. Given the significant advantages of MARL andLLMs-baseddecision-making methods over the traditional rule, game theory, and evolutionary algorithms, this paper focuses on these multi-agent methods utilizing MARL and LLMs-based techniques. We provide an in-depth discussion of these approaches, highlighting their methodology taxonomies, advantages, and drawbacks. Further, several prominent research directions in the future and potential challenges of multi-agent cooperative decision-making are also detailed.

cs.MA↗

arXiv2026

DAPD: Dual-Anchored Policy Distillation

On-policy (self) distillation (OPSD) is increasingly adopted for language-model post-training. It strengthens the teacher with privileged information but can induce a privilege illusion: the student learns privilege-dependent behavior it cannot reproduce from its inference-time context, yet behaves as if the training-time privileged information remained available, ultimately degrading performance. In this paper, we identify information asymmetry between the privileged teacher and the student at inference as the root cause of this failure in OPSD. To resolve this asymmetry, we propose Dual-Anchored Policy Distillation (DAPD), a unified framework with two levels of anchoring. Dual-Path Anchoring (DPA) introduces a self-conditioned bridge and aligns reference and rollout behavior along two matched-information paths, preventing privilege-dependent behavior from being transferred to the inference-time student. Dual-Source Anchoring (DSA) applies these paths in both reference-to-rollout and rollout-to-reference directions, reducing reliance on privileged reference guidance while preserving correctness supervision. Extensive experiments show that DAPD significantly alleviates privilege illusion, outperforming OPSD on Qwen3-4B by +2.00 points on average across tasks. Notably, its gains persist across scales, reaching +2.69 at 4B and +2.78 at 32B.

cs.AI↗

arXiv2026

SciForge: An AI-Native, Multimodal Workbench for Scientific Discovery

Scientific work increasingly spans heterogeneous artifacts -- papers, code, datasets, scientific file formats, model outputs, figures, manuscripts, and team decisions -- yet general-purpose AI assistants rarely preserve these objects as a coherent, auditable research state. We present SciForge, a multimodal research-native AI workbench that reserves the graphical interface for human judgment while search, parsing, model routing, workflow execution, plotting, writing, and presentation generation run as modular agent-accessible services. SciForge is built around five pillars: (i) \emph{goal-scoped scientific decision governance} for \textbf{goal-oriented} research, with review gates and shared review surfaces; (ii) \emph{translate-then-reason} for \textbf{multimodal} input, routing scientific objects through domain translators before the agent reasons; (iii) \emph{evidence governance} for \textbf{auditable} traceability, linking claims to provenance chains and audit findings; (iv) \emph{collaborative team science} for \textbf{collaborative} research, enabling multi-role decision governance, with shared team workspaces planned for future releases; and (v) \emph{real-world application scenarios} for \textbf{practical} impact, demonstrated through eight end-to-end user cases, with flagship demonstrations including multi-day agentic research sprints for gene discovery, AI-guided de novo protein design, molecular optimization, and genome-to-BGC discovery. The system combines a thin interaction layer, contextual research capability patterns, an Agent Runtime and Workflow Engine, an Evidence-DAG audit sidecar and a Scientific Model Router. SciForge currently runs as a desktop application, with mobile supervision support; future releases will deepen team collaboration. The system is open-source and available at https://github.com/AGI4Sci/SciForge

cs.AI↗

arXiv2026

Accurate, Interdisciplinary and Transparent Structure-property Understanding with Deep Native Structural Reasoning

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing $F_{\max}$ from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

cs.CL↗

arXiv2026

ResearchClawBench: A Benchmark for End-to-End Autonomous Scientific Research

AI coding agents are increasingly used for scientific work, but their end-to-end autonomous research capability remains difficult to verify. We present ResearchClawBench, a benchmark for evaluating autonomous scientific research across 40 tasks from 10 scientific domains. Each task is grounded in a real published paper, provides related literature and raw data, and hides the target paper during evaluation. Expert-curated multimodal rubrics decompose the target scientific artifacts into weighted criteria, enabling evaluation of target-paper-level re-discovery while leaving room for new discovery. We evaluate seven autonomous research (auto-research) agents under a unified protocol and seventeen native LLMs through the lightweight ResearchHarness. Current systems remain far from reliable re-discovery: the strongest autonomous agent, Claude Code, averages 21.5, and the strongest ResearchHarness LLM, Claude-Opus-4.7, averages 20.7, with an LLM frontier mean of only 26.5. Error analysis shows that failures concentrate in experimental protocol mismatch, evidence mismatch, and missing scientific core. ResearchClawBench provides a reproducible evaluation frontier for measuring progress toward autonomous scientific research.

cs.LG↗

arXiv2026

MotionGPT-2: A General-Purpose Motion-Language Model for Motion Generation and Understanding

Generating lifelike human motions from descriptive texts has experienced remarkable research focus in the recent years, propelled by the emerging requirements of digital humans.Despite impressive advances, existing approaches are often constrained by limited control modalities, task specificity, and focus solely on body motion representations.In this paper, we present MotionGPT-2, a unified Large Motion-Language Model (LMLM) that addresses these limitations. MotionGPT-2 accommodates multiple motion-relevant tasks and supporting multimodal control conditions through pre-trained Large Language Models (LLMs). It quantizes multimodal inputs-such as text and single-frame poses-into discrete, LLM-interpretable tokens, seamlessly integrating them into the LLM's vocabulary. These tokens are then organized into unified prompts, guiding the LLM to generate motion outputs through a pretraining-then-finetuning paradigm. We also show that the proposed MotionGPT-2 is highly adaptable to the challenging 3D holistic motion generation task, enabled by the innovative motion discretization framework, Part-Aware VQVAE, which ensures fine-grained representations of body and hand movements. Extensive experiments and visualizations validate the effectiveness of our method, demonstrating the adaptability of MotionGPT-2 across motion generation, motion captioning, and generalized motion completion tasks.

cs.CV↗

arXiv2026

S3Mem: Structured Spatiotemporal Scene-Event Memory for Long-Horizon Interactive Question Answering

Long-horizon memory question answering often requires sparse evidence from heterogeneous histories, including events, object states, visual observations, temporal relations, and causal steps. Existing memory interfaces expand reader context, retrieve semantically related chunks, or expose graph neighborhoods, but they are not explicitly designed to select compact evidence for a fixed reader. We propose Structured Spatiotemporal Scene--Event Memory (S3Mem), a query-time memory interface that writes textual, visual, and agent-use histories into structured scene--event units and routes compact evidence packs to the reader. Its router scores candidate units, query anchors, and anchor--support links, enabling both single-hop selection and short multi-hop evidence chains without reader fine-tuning or test-time training. Across LoCoMo, EMemBench Visual Games, and AMA-Bench, S3Mem provides a strong score--token trade-off, with the clearest gains on localized event, state, temporal, causal, or provenance evidence. On LoCoMo, S3Mem reaches $0.48$ F1 and $0.40$ BLEU with (1{,}073) evidence tokens per question, about $15.8\times$ fewer than the LoCoMo reference. On EMemBench Visual Games, it obtains the best F1 and second-best accuracy with only $189$tokens.On AMA-Bench, it is not the highest-scoring method, but remains competitive while using the fewest reader-visible evidence tokens.

cs.CL↗

arXiv2026

Trans2Occ: Voxel Occupancy Estimation and Grasp for Transparent Objects from Simulation to Reality

Transparent objects remain challenging for robotic perception due to unreliable depth sensing caused by refraction and reflection. While prior approaches rely on multi-view reconstruction or depth completion, they are often difficult to scale or deploy in real-world robotic systems. In this paper, we present a practical framework for transparent object perception and manipulation based on single-view RGB input. Our approach predicts voxel-space occupancy directly from a single image, providing a geometry-aware representation that supports downstream robotic grasping. To enable large-scale training, we construct a simulation pipeline that generates paired RGB images and voxel occupancy annotations under diverse materials and lighting conditions. We demonstrate that the predicted occupancy representation is robust to domain shifts and transfers effectively from simulation to real-world robotic setups without fine-tuning. A simple rule-based grasping strategy built on top of the occupancy further achieves reliable grasp performance on transparent objects. Extensive experiments in both simulation and real-world environments show that our framework provides accurate 3D understanding and enables practical manipulation of transparent objects. These results suggest that single-view occupancy prediction offers a scalable and effective solution for transparent object perception in robotics.

cs.RO↗

arXiv2026

UniMedVL: Unifying Medical Multimodal Understanding and Generation through Observation-Knowledge-Analysis

Medical workflows routinely combine reading images with producing visual and textual outputs, making both image understanding and generation central to medical AI. Most existing systems, however, address these abilities in isolated models, losing the shared knowledge that a unified architecture could exploit. To bridge this gap, we present UniMedVL, the first unified medical model that seamlessly integrates multimodal understanding and generation capabilities within a single model without switching weights. We achieve this via a tailored progressive training pipeline where understanding and generation mutually reinforce each other. To effectively train UniMedVL, we curate UniMedVL-5M, the first large-scale medical dataset comprising over 5.6M instances across 8 medical imaging modalities, tailored for multimodal input-output tasks in unified medical understanding and generation. Experimental results demonstrate that UniMedVL achieves competitive performance on five medical understanding benchmarks. Crucially, UniMedVL natively supports diverse interleaved generation tasks, e.g., virtual staining, super-resolution, cross-modal synthesis, essential for complex medical workflows. Our code and dataset are publicly available.

cs.CV↗