Search arXiv⌕ Search

arXiv subjects

Yuqiang Li

Publications and source records attributed to Yuqiang Li.

At least 19 recordsLinked to original sources
arXiv2026

Minimal Witness Reinforcement Learning

``What are the irreducible conditions that are sufficient to produce an outcome?'' is one of the most common questions that recur across computation and science. Its answers, the minimal sufficient witnesses, are what we mean by explanations, mechanisms and reasons. These problems usually ask for multiple minimal witnesses, yet standard RL methods may reveal only one solution or redundant ones. We formalize this problem as minimal-witness identification and introduce Minimal-Witness Reinforcement Learning (MWRL). MWRL takes the union of the sets certified by successful proposals sampled from the policy and credits each proposal for the coverage the group union would lose without that proposal. This credit assignment, derived directly from the problem definition, unifies the demands for minimality and recovery of alternatives from a single black-box verifier bit. Under this principle, we derive a value iteration planner that recovers the entire family of witnesses and a policy gradient method that can scale to large language models. Across different experimental settings, MWRL recovers most minimal witnesses, while other methods return redundant supersets or a single witness. By making witness families learnable from verifier feedback, MWRL expands the scope of reinforcement learning beyond single-solution optimization. Our code is available at https://github.com/TSUITUENYUE/MWRL.

cs.LG↗
arXiv2026

Sage-A1.5: From Long-Horizon Execution to Scientific Exploration with Capability Composition

In this report, we introduce Sage-A1.5, a 35B Mixture-of-Experts agentic model that builds on A1 to advance long-horizon problem solving through adaptive capability composition. Compared with A1, Sage-A1.5 learns not only to solve individual tasks, but also to organize work and revise its approach during execution. Sage-A1.5 highlights three improvements: agentic orchestration, verification, and open scientific discovery. First, agentic orchestration extends single-agent execution through task delegation and parallel collaboration among subagents with isolated contexts, enabling complex tasks to be decomposed and addressed concurrently and supporting efficient execution while reducing interference across concurrent subagents. Second, agentic verification strengthens long-horizon reliability through progress checking, evidence validation, and reflective strategy revision, allowing the agent to recognize unproductive search paths and pursue alternative approaches. Third, open scientific discovery extends agentic capabilities beyond answering predefined questions to conducting exploratory research, connecting scientific inquiry with interactive analysis and inspectable research artifacts. We showcase these capabilities through complicated agentic tasks and multidisciplinary scientific applications. Besides, we hope Sage-A1.5 provides the community with an accessible foundation for open scientific discovery, offering a practical path from long-horizon task execution to collaborative, verifiable, and inspectable scientific exploration.

cs.AI↗
arXiv2026

DrugHarness: An Evolvable Agent Harness for Computational Drug Discovery

Computational drug discovery requires agents to compose scientific operations and adapt to changing evidence and constraints. Here we introduce DrugHarness, an evolvable agent harness coupling composable scientific execution with conditional skill induction. Its environment integrates over 80 scientific operations, biomedical resources and task-specific code, preserving associations among candidates, results and artifacts. From execution trajectories and outcome feedback, DrugHarness induces action hypotheses with observable applicability conditions, recommended actions and supporting evidence. An independent review agent evaluates candidate skills derived from these hypotheses through source verification and, when needed, targeted execution trials. Admitted skills guide subsequent tasks and are revised through feedback. Evaluation on MolBench and SMDD-Bench demonstrates capabilities in molecular screening, optimization and constrained design. Without evolution, DrugHarness exceeds reported MolClaw-CC results by 10.8 percentage points in affinity-comparison accuracy and 55% in mean top-three active hits on MolBench. Retrospective evaluation on skill-development tasks shows that evolution increases Qwen's affinity-comparison accuracy from 62.2% to 81.1% and optimization success from 79.5% to 87.2%. In a prospective HPK1 study, DrugHarness achieves a more favorable median docking score than Biomni among system-specific candidates. A synthesized compound achieves a cellular IC50 of 14.19 nM, a 2.64-fold potency improvement over the best input reference, with activity competitive with two selected compounds designed by experienced medicinal chemists. These results support conditional skill evolution for scientific agents and demonstrate a workflow connecting computational drug design with experimental validation.

cs.AI↗
arXiv2026

Constrain the Size of Broad Line Region in NGC 1068 Using Sub-millimeter Excess

Constraining the size of broad-line region (BLR) close to the accretion disk in active galactic nuclei (AGNs) is key to understand the central engine and evolution of AGN. We propose a new method to constrain the BLR size, based on millimeter to sub-millimeter spectral energy distribution (SED), from which a sub-millimeter excess may be found. Such excess can be used to determine the solid angle of the free-free emission region from BLR, as a region with high electron density and optically thick at sub-millimeter wavelength for free-free continuum. Millimeter to sub-millimeter SED analysis toward the central source S1 in a nearby type II AGN NGC 1068 was done, which gave an upper limit on the solid angle of BLR region as(4.94 +/- 0.61) *10^-6 arcsec^2, corresponding to a radius no more than 0.085 pc. Such a constraint on the BLR size is important for estimating the masses of central supermassive black holes in AGNs.

astro-ph.GA↗
arXiv2026

Honeycomb Crystal in a Mass-Asymmetric Electron-Hole Bilayer

A two-dimensional electron gas in a uniform neutralizing background forms a triangular Wigner crystal at low density. In a strongly mass-asymmetric electron-hole bilayer, localized heavy holes instead provide a nonuniform positive background that supports an electron crystal at densities two orders of magnitude higher than for a homogeneous electron gas in the same material. Here we show that correlated mobile electrons can overturn the preference for triangular order, stabilizing a honeycomb electron-hole crystal. Using the powerful real-space neural-network variational Monte Carlo in the Born-Oppenheimer limit with fixed holes, we find that increasing the density drives a transition from a triangular electron-hole crystal to a honeycomb crystal, which eventually melts into itinerant electrons coexisting with the honeycomb or the triangular hole lattice at fixed interlayer separation. Relative to triangular order, honeycomb order emerges when gains in electronic kinetic energy and electron-hole attraction outweigh its higher intralayer Coulomb repulsion, a threshold never reached in the rigid point-dipole model. Moreover, the honeycomb hole lattice supports paramagnetic, antiferromagnetic, and stripe-ordered spin states. Complex polarization indicates a metal-insulator transition, while the states on the honeycomb hole lattice are consistent with a stripe-ordered Dirac semimetal and paramagnetic or antiferromagnetic Mott insulators via mapping to the half-filled Hubbard model. We further propose a BLG/hBN/WS$_2$-WSe$_2$ heterostructure as a platform for the predicted honeycomb crystal, at an experimentally feasible density $n\sim10^{11}~\text{cm}^{-2}$.

cond-mat.str-el↗
arXiv2026

Thermochemically Constrained Multiscale Laplace Neural Operator to Learn Stiff Chemical Kinetics with Conditional Diffusion Model Sampling

Stiff chemical kinetics is a major computational bottleneck in reacting-flow simulations, while data-driven solvers remain sensitive to training-state coverage and chemical dynamics. This work combines conditional diffusion sampling with a thermochemically constrained multiscale Laplace neural operator (TC-MLNO) for chemistry ODE integration. The diffusion model learns the equivalence-ratio-conditioned joint distribution of temperature and species from low-dimensional flame data, augmenting the state space without independent perturbations. TC-MLNO represents transient, non-periodic responses through pole-residue Laplace layers and assigns fast, medium, and slow species to separate branches. Thermochemical constraints are imposed through losses for mass and elemental conservation and heat release rate. The framework is evaluated in 1D premixed flames, a 2D developing jet, and a 3D turbulent burner flame. With equal-sized datasets, diffusion sampling reduces the 95th-percentile distance to the base flame manifold by up to 37.5% and the a posteriori full-species macro-average error by up to 92.7% versus random sampling, especially for minor species and radicals. TC-LNO yields smaller errors than the DeepONet baseline for 84.9% of retained modes and reduces the 95th-percentile error for the most attenuated modes from 0.372 to 0.081. In multidimensional flames, TC-MLNO better preserves reaction-zone locations, heat-release structures, and chemically sensitive species than DeepONet. Errors of representative radical and nitrogen-containing species in the 3D flame decrease by 88.0%-88.9%. Compared with direct CVODE integration, TC-MLNO reduces mean chemistry and total solution times by 90.1% and 62.6%, respectively. These results show that distribution-aware sampling and Laplace neural operator learning provide an accurate and efficient alternative for stiff chemical ODE integration.

physics.comp-ph↗
arXiv2026

Revisiting the Broken Symmetry Phase of Solid Hydrogen: A Neural Network Variational Monte Carlo Study

The crystal structure of high-pressure solid hydrogen remains a fundamental open problem. Although the research frontier has mostly shifted toward ultra-high pressure phases above 400 GPa, we show that even the broken symmetry phase observed around 130~GPa requires revisiting due to its intricate coupling of electronic and nuclear degrees of freedom. Here, we develop a first principle quantum Monte Carlo framework based on a deep neural network wave function that treats both electrons and nuclei quantum mechanically within the constant pressure ensemble. Our calculations reveal an unreported ground-state structure candidate for the broken symmetry phase with $Cmcm$ space group symmetry, and we test its stability up to 96 atoms. The predicted structure quantitatively matches the experimental equation of state and gives the closest x-ray diffraction peak-position match among the tested candidates. Furthermore, our group-theoretical analysis provides a symmetry-counting compatibility check between the $Cmcm$ structure and existing Raman and infrared spectroscopic data. Crucially, static density functional theory calculation reveals the $Cmcm$ structure as a dynamically unstable saddle point on the Born-Oppenheimer potential energy surface, demonstrating that a full quantum many-body treatment of the problem is necessary. These results shed new light on the phase diagram of high-pressure hydrogen and call for further experimental verifications.

cond-mat.str-el↗
arXiv2026

MatToolBench: Benchmarking Multimodal Agents in Real-World Materials Science Workflows

Multimodal GUI agents have achieved impressive results on general software benchmarks, yet their ability to operate professional scientific software remains largely unexplored. In materials science, sparse domain-specific web data, specialized interfaces, and tacit workflow conventions create blind spots that general-purpose pretraining cannot readily bridge. We present MatToolBench, the first real-environment benchmark for evaluating multimodal GUI agents on professional materials science software, comprising 204 tasks across 10 tools in three modalities: GUI operation, OriginPro scripting, and code-based database queries, all executed inside a Windows 11 VM. Each task is decomposed into fine-grained sub-criteria by domain experts, enabling interpretable partial-credit scoring; the GUI component of our multi-level evaluation pipeline achieves an average F1 of 0.98. For OriginPro figure-generation tasks, we further conduct a human-LLM agreement study to validate the use of a multimodal judge for secondary aesthetic assessment. Our experiments show that strong performance on general benchmarks does not transfer to professional scientific workflows, and that this gap is not a visual-grounding problem alone: failures arise from domain-specific operational knowledge, sparse pretraining coverage of scientific software, weak cross-tool artifact handoff, and critical states exposed only visually. Even the best model reaches only 25% success rate on GUI tasks and 45% on code tasks. MatToolBench therefore serves as a challenging diagnostic benchmark and real-environment testbed for data-scarce, knowledge-intensive scientific workflows.

cs.AI↗
arXiv2026

RxnOptBench: Benchmarking LLMs for Reaction-Condition Optimization in Organic Methodology

Chemical reaction-condition optimization -- choosing the catalyst, ligand, solvent, reagent, temperature, time, and atmosphere that jointly maximize yield and stereoselectivity -- is a central, judgement-laden subtask of organic methodology research that large language models are increasingly expected to support. Yet existing chemistry benchmarks evaluate reaction-class labelling, retrosynthesis, or SMILES manipulation, and do not ask models to read a real condition-screening table and pick the best set. We introduce RxnOptBench, a benchmark whose every option and precedent is a real wet-lab entry mined from the optimization tables of organic-methodology papers published in 2025, graded by a continuous relative score derived from a declared headline utility that combines reported yield with enantiomeric excess (ee), diastereomeric ratio (dr), and regioisomeric ratio (rr), and equipped with a paired precedents-vs-no-precedents design that isolates in-context use of literature evidence from parametric memorization. Across nine frontier LLMs and three Chemistry LLMs, even the best models leave substantial headroom: chemistry-specialized models fall to the random-baseline floor on multi-axis selection, while open-weight models have closed most of the gap to proprietary frontier models. We release the final human-reviewed benchmark test set and evaluation code.

physics.chem-ph↗
arXiv2026

Equivariant Neural Primal-Dual Assignment for Maximum Common Edge Subgraphs

Maximum common edge subgraph (MCES) matching finds a partial vertex correspondence between two labeled graphs that preserves as many labeled edges as possible. Molecular similarity search requires matching many graph pairs, making the cost of repeated queries important. The strongest baseline attains accurate MCES solutions but trains a separate network for each pair. We introduce Equivariant Neural Primal-Dual Assignment (ENPDA), which learns a shared matching policy and applies it to new pairs without further training, answering queries roughly three orders of magnitude faster and recovering its training cost after a few dozen queries. The policy recomputes exact objective marginals for candidate matches and learns corrections and step sizes that update their scores. Target prices respond to competition when several source vertices favor the same target. Four update rounds and a Hungarian projection produce a partial one-to-one matching. We prove per-pair guarantees that hold for any network parameters. In exact arithmetic, reordering either graph permutes the assignment and price states, the projected matching is one-to-one, and repaired prices give a valid MCES upper bound. Subtracting the preserved-edge count bounds the optimality gap; combined with structural caps, these certificates prove global optimality for 60 of 291 native test pairs. On three molecular benchmarks with disjoint train/validation/test splits, ENPDA improves over an analytic counterpart with the same update and projection budget by 7.4-8.6 accuracy points; after one second of refinement search, 2.5-3 points of the gain remain. Transferred without fine-tuning to edge-deletion tasks from social and protein graphs, the policy gains 9.1-17.6 points over the analytic counterpart. When output matchings must keep aromatic rings intact, ENPDA recovers more reference bonds than the baselines on all three datasets.

cs.LG↗
arXiv2026

ChemMLLM: Chemical Multimodal Large Language Model

Recent years have seen rapid progress in multimodal large language models (MLLMs) in the field of chemistry. However, chemical MLLMs that can handle cross-modal understanding and generation remain underexplored. To fill this gap, we propose ChemMLLM, a unified chemical multimodal large language model for molecule understanding and generation. In this work, we design five types of multimodal tasks across text, molecular SMILES strings and images, and curate the datasets. We benchmark ChemMLLM against a range of general leading MLLMs, Chemical LLMs and specialized models on these tasks. Experimental results show that ChemMLLM achieves superior performance among general-purpose MLLMs and close performance to specialized models across all evaluated tasks. Our work extends the capabilities of chemical multimodal large language models to the realm of image generation, demonstrating the feasibility of unifying multiple cross-modal chemical tasks within a single foundation model and enabling more intuitive, visual human-AI interaction.

cs.LG↗
arXiv2026

Model-based Bootstrap for Offline Policy Evaluation in Tabular Reinforcement Learning

Offline policy evaluation (OPE) is crucial in high-stakes reinforcement learning applications, where new policies must be assessed reliably before deployment. In such settings, point estimates alone are insufficient; principled uncertainty quantification, such as confidence intervals and variance estimates, is essential for safe and risk-aware decision-making. A comprehensive way to unify these tasks is to estimate the sampling distribution of the evaluation error. Existing approaches, however, often suffer from limited robustness, scalability, or finite-sample validity. In this paper, we propose a model-based bootstrap framework for uncertainty quantification of OPE in finite-horizon, time-inhomogeneous Markov decision processes (MDPs). Unlike classical bootstrap methods that rely on resampling complete episodes, the proposed method regenerates trajectories from an estimated MDP and can therefore accommodate a much broader range of offline data formats, including complete trajectories, transition-level observations, and trajectory fragments. This flexibility further improves finite-sample statistical efficiency. We establish bootstrap distributional consistency, asymptotically valid confidence intervals, and consistent variance estimation for the target policy value. Extensive simulations show that the proposed method accurately captures the sampling distribution of the OPE estimator, yielding tighter confidence intervals and more accurate variance estimates in most settings.

stat.ML↗
arXiv2026

Water maser detections toward 70 $μ$m infrared dark clumps at early star formation stage

Water masers provided powerful probes of shocked gas and protostellar activity during the early stages of star formation. Using VLA K-band observations of the 22 GHz water line, we report the first detections of water masers toward dense cores in five 70 $μ$m infrared dark clumps, providing evidence for active star formation at an early evolutionary stage. We detected ten unresolved maser spots comprising thirteen velocity components, with peak flux densities of 13--499 mJy and deconvolved full widths at half maximum (FWHMs) of 0.51--3.54 km s-1. Eleven components had FWHMs below 1 km s-1, while their velocity offsets from the systemic velocities traced by the NH3(1,1) main line ranged from 0.83 to 50.73 km s-1. Four water maser spots were associated with 1.3 mm continuum emission, three of which were also associated with molecular outflows traced by CO 2-1 emission. No CO outflow signature was detected toward the remaining spots within the observed field of view, suggesting that water masers could trace deeply embedded protostellar activity whose outflows were not yet detectable in CO emission. For AGAL031, the non-detection of StokesV emission toward the strongest maser component yields an upper limit on the line of sight magnetic field strength on the order of a few hundred mG. Our results showed that star formation was already active in 70 $μ$m infrared dark clumps and that 22 GHz water masers provided insights into early protostellar environments that remained difficult to probe with common star formation tracers.

astro-ph.GA↗
arXiv2026

Autonomous Chemical Mechanistic Discovery through Agentic Reasoning and Validation

Unraveling reaction mechanisms is central to modern chemistry, yet automating these investigations remains challenging because computational workflows still rely heavily on expert intervention. Here we introduce ARCHE, an autonomous agentic system that integrates a general-purpose reasoning model, a domain-specialized computational chemistry model, and a structured tool registry to transform mechanistic inquiry into a scalable, self-validating process. ARCHE interprets scientific questions, generates and prioritizes mechanistic hypotheses, orchestrates computational workflows, and iteratively refines conclusions based on computed evidence within a closed loop. We validate its capabilities across three increasingly demanding scenarios: reconstructing stereocontrolling transition states and validating the corresponding reaction mechanism in a previously reported asymmetric catalytic reaction; proposing and validating a plausible radical pathway through iterative hypothesis refinement for a recently discovered but unpublished $α$-iodoboronate C-I cleavage reaction; and identifying a chemically interpretable descriptor that governs selectivity in nickel-catalysed migratory cross-coupling reactions. By coupling agentic reasoning with rigorous computational validation, ARCHE advances autonomous mechanistic discovery and establishes a foundation for broader machine-assisted chemical research. The code for ARCHE is publicly available at https://github.com/JetAstra/Arche-Harness.

cs.AI↗
arXiv2026

DianShi-RxnDB: A Large-Scale, Fine-Grained Organic Reaction Data Platform Built via a Fully Automated Pipeline for Researchers and AI Agents

High-quality structured organic reaction data are essential for developing artificial intelligence for chemistry (AI4Chem), yet much of this knowledge remains dispersed across patent text, images, and reaction schemes. We present DianShi-RxnDB, a large-scale, fine-grained organic reaction data platform built via a fully automated extraction and normalization pipeline integrating patent text, images, and reaction schemes. Its corpus covers organic synthesis patents from the USPTO and EPO published between 1976 and 2025, yielding approximately 24 million reaction instances, of which approximately 14.8 million (61.7%) pass automated qualification checks. Each instance represents a specific single-step experiment recording participants, roles, quantities, temperatures, reaction times, yields, experimental procedures, and provenance links to source patents. In a manual evaluation of 1,300 sampled qualified instances, the micro-averaged field-level accuracy was 92.95%. A matched comparison with Pistachio further indicated advantages in deduplicated record counts, representation granularity, and field-level exact agreement. The platform provides a Web research workbench for searching, filtering, comparing, and source-verifying records, and a Model Context Protocol (MCP) service offering AI agents composable structured retrieval tools. DianShi-RxnDB is available at https://dianshi.opendatalab.org.cn/ .

cs.CL↗
arXiv2026

Molecular LLM Agents: From Architectural Design to Scientific Autonomy

Molecular science represents an important frontier for LLM-based agents. Unlike general agents that mainly operate over natural language, code, or web environments, molecular LLM agents must perceive, reason about, and act upon chemical objects across symbolic strings, molecular graphs, 3D conformations, spectra, simulations, and wet-lab measurements. Their capabilities depend on chemically faithful molecular perception, an LLM-centered agent framework, domain-specific tool grounding, and computational or experimental feedback, in addition to planning and tool use. This work develops a conceptual framework for molecular LLM agents from two complementary perspectives. First, we introduce an architectural view of molecular-agent design, covering molecular representation and perception, the agent framework, domain-specific toolboxes, and learning and optimization. Second, we propose a scientific autonomy ladder inspired by staged autonomy in engineering systems, categorizing agents into four levels: L1 assistive or fixed workflows, L2 adaptive computational agents, L3 feedback-aware physical experiment agents, and L4 scientific-agenda agents. Together, these two perspectives establish a comprehensive framework for comparing existing molecular LLM agents, identifying missing capabilities and deployment risks, and guiding the design, evaluation, and deployment of future agents in molecular discovery workflows.

cs.CL↗
arXiv2026

MinerU.Chem: A High-Precision System for Optical Chemical Structure and Reaction Recognition

In organic chemistry papers and patents, molecular structures, reaction schemes, and experimental conditions are often presented as molecular structure depictions, reaction diagrams, and complex tables or figures. Such information is difficult for general-purpose document parsing systems to directly convert into machine-readable data. This limits data production for organic chemistry knowledge base construction and for AI for Chemistry tasks such as reaction prediction, retrosynthesis, condition recommendation, molecular property prediction, and drug molecule design. This report introduces MinerU-Chem, a document parsing system for organic chemistry literature integrated into the MinerU online platform. Built on top of MinerU's general document parsing pipeline, MinerU-Chem adds five chemistry-specific modules: chemistry relevance filtering, molecular structure detection, molecule identifier extraction, molecular structure recognition, and reaction scheme parsing. Together, these modules convert organic-chemistry-related image regions in documents into a Molecule Summary List and a Reaction Summary List. For molecular structure recognition, MinerU-Chem uses CARBON (Complex Atomic Representation and Bonding Object Notation) as its core representation. CARBON enables recognition results to preserve both the visual layout of the original image and complex chemical semantics, while supporting the export of standard downstream formats such as MolFile and SMILES. On the SMILES-evaluable subset of MolRecBench-Wild (N=2,392), MinerU-Chem's molecular structure recognition module achieves a SMILES exact-match accuracy of 93.02%, outperforming the best evaluated comparison system, GPT-5.6-Sol (74.87%), by 18.15 percentage points. The system has been integrated into the MinerU online platform and is available at https://mineru.net/OpenSourceTools/Extractor .

cs.CV↗
arXiv2026

Simulation-to-real transfer learning for infrared spectroscopic chemical sensing and analysis from molecules to complex samples

Infrared (IR) spectroscopy is widely used for chemical sensing, but extracting reliable chemical information from spectra remains challenging. Conventional interpretation is labor-intensive, relies on prior knowledge and reference spectra, and is difficult to scale, whereas most machine-learning methods are tailored to individual tasks or datasets, require large labeled training sets, and transfer poorly across analytical objectives and experimental datasets. Here we introduce UltraIR, a foundation model for IR spectroscopy with more than 100 million parameters that enables simulation-to-real transfer learning for chemical sensing and analysis from molecules to complex samples. UltraIR is pretrained on approximately 60 million simulated IR spectra using spectral reconstruction, molecular fingerprint similarity alignment, and functional-group prediction, then adapted to downstream objectives with task-specific labels or targets. Across functional-group prediction, molecular structure elucidation, physicochemical property prediction, mixture-component identification and quantification, bacterial classification, medicinal-herb geographic origin traceability and constituent quantification, microplastics classification, and soil property prediction, UltraIR outperforms conventional machine-learning and task-specific deep-learning baselines. It performs strongly with limited labeled experimental spectra and in zero-shot inference for the same analytical task across Fourier-transform infrared spectrometers and laboratories, providing a route to adaptable, data-efficient chemical sensing from complex real-world samples.

cs.LG↗