arXiv subjects

Jian Ma

Publications and source records attributed to Jian Ma.

At least 19 recordsLinked to original sources

arXiv2026

ProteoCraft: Protein Design as Proposal-Verification Search

Protein-protein interactions underpin nearly all biological processes. Yet, designing proteins with desired interactions remains challenging due to the structural complexity governing molecular recognition. This study views protein design as a search optimization problem over a combinatorial sequence space under expensive structural evaluation. Toward this goal, we introduce a novel tree-based search framework, ProteoCraft, that employs approximate structural gradients from diffusion-based structure predictors as effective proposal policies to specify where the search should explore. Complete no-gradient inference of folding models separately assigns values to the resulting sequences, determining what is good. ProteoCraft allocates this verification budget through a coarse-to-fine paradigm: multi-site edits first explore distinct sequence basins, then verified promising states undergo strict single-site refinement. Across fourteen de novo binder-design settings spanning eight target proteins, five immune-relevant TCR-facing targets, and four localized CDR redesign tasks, ProteoCraft improves design quality and high-confidence yield. These improvements persist under independent AF2-IG and Rosetta-based interface evaluation. Prospective experimental validation further yielded an 82.9% binding hit rate for PD-L1 miniproteins, with a best measured KD of 0.879 nM, and confirmed binding of designed IFNAR2 VHH. Our code is available at https://github.com/smiles724/ProteoCraft_v1.

cs.CE↗

arXiv2026

IMPose: Closed-Loop Correction Propagation for Interactive Multi-Person Pose Annotation

High-quality dynamic human pose annotations provide important supervision for learning fine-grained human motion, yet dense multi-person video annotation remains labor-intensive. Sparse human corrections can reduce this effort, but their propagated locations may become unreliable and ambiguous across identities. Existing interactive refinement and temporal propagation methods do not explicitly address how imperfect propagated corrections should participate in subsequent multi-person pose inference. We propose IMPose, a correction-conditioned temporal inference framework for interactive multi-person pose annotation. IMPose separates temporal correspondence from pose estimation: propagated corrections are treated as geometric priors rather than final predictions and are refined by a correction-aware decoder using target-frame visual evidence. A keypoint-aware identity state further combines structured pose geometry with trajectory history to preserve person- and joint-level correspondence. The refined pose and identity state are fed back to subsequent frames, forming a closed temporal correction loop. Under a controlled sparse-correction protocol on PoseTrack21, one correction improves mean average precision (mAP) from 38.87 to 67.99 and Higher Order Tracking Accuracy (HOTA) from 52.21 to 64.89. At a 20-frame correction interval, IMPose achieves 89.03% keypoint-level Object Keypoint Similarity (K-OKS), compared with 81.41% for CoTracker and 70.12% for PoseWarper-based propagation. We further extend PoseTrack21 with 188K additional person instances through 3.55M annotation updates to keypoints, bounding boxes, and person IDs using 100 annotator-hours. The annotation tool, code, and extended dataset will be released.

cs.CV↗

arXiv2026

Small Edits, Shifting Decisions: Benchmarking LLM Accuracy and Reliability on French Input Variants

French users may omit apostrophes and diacritics or make keyboard typos in everyday input. The effects of these common variations on language model performance and prediction reliability remain insufficiently understood. To address this gap, we construct a controlled French surface-variant benchmark covering seven task types, with 4,200 original-low-high triplets (12,600 input instances). Each high-intensity variant retains all low-intensity edits and adds further changes. We evaluate six models from two LLM families. The results show that accuracy decreases and Brier score and negative log-likelihood (NLL) increase with perturbation intensity. Larger models show smaller accuracy losses under high intensity, but increases in Brier score and NLL do not consistently decrease with scale. Keyboard typos cause the largest losses in accuracy and the quality of predicted probabilities at the predefined high-intensity settings. Finally, calibration temperatures fitted on original inputs transfer effectively to surface variants. Combining calibration with input restoration further improves Brier score and NLL over either method alone while preserving restored accuracy. Our benchmark provides a unified framework for jointly evaluating task accuracy and prediction reliability under common French surface variations.

cs.CL↗

arXiv2026

Beyond the Vote: When Do LLMs Add Value to Retrieval-Based Tabular Classification?

Retrieval-based in-context learning (ICL) enables large language models (LLMs) to predict tabular labels from similar examples, but it remains unclear whether LLM inference improves on direct voting over those same examples. We address this question by comparing four general-purpose LLMs with distance-weighted nearest-neighbor voting (Distance-KNN) using identical retrieved neighbors across 19 tabular classification datasets. With the number of demonstrations fixed, enlarging the retrieval candidate pool improves accuracy for all predictors, yet Distance-KNN achieves the highest mean accuracy at every pool size. More detailed analyses reveal that LLM gains are concentrated where retrieved neighbors exhibit low label consensus and vary across models. These gains further depend on the average feature-space distance to the test query: under low label consensus, some LLMs outperform Distance-KNN in close and intermediate neighborhoods, but all fall behind on average in the most distant group. Complementary experiments on the number of demonstrations, prompt formulation, retrieval representation, and label-balanced demonstration selection largely preserve the overall findings. These results characterize when LLM inference adds predictive value beyond distance-weighted voting in retrieval-based tabular ICL.

cs.IR↗

arXiv2026

Can Agents Price a Reaction? Evaluating LLMs on Chemical Cost Reasoning

Large Language Models (LLMs) have become increasingly capable as tool-using agents, with benchmarks spanning diverse general agentic tasks. Yet rigorous evaluation of scientific tool use remains limited. In chemistry, recent agents can plan syntheses and invoke domain-specific tools, but evaluations often rely on curated demonstrations, expert assessment, or LLM-as-judge scoring rather than exact, judge-free ground truth. We address this gap with chemical procurement cost estimation, a practical task in which an agent must ground chemical identities, retrieve supplier quotes, select valid purchasable packs, normalize quantities, and compute cost from a reaction description. We introduce ChemCost, a benchmark of 1,427 evaluable reactions grounded to a frozen pricing snapshot covering 2,261 chemicals and 230,775 supplier quotes, supporting scalar scoring and stage-level diagnosis of grounding, retrieval, procurement, and arithmetic failures. To evaluate robustness, we further construct controlled noise-injected views that perturb chemical aliases, quantity expressions, missing fields, and input formatting. Experiments with frontier, open-weight, and chemistry-specialized LLM agents show that tool access is necessary but insufficient for solving the task. The strongest agents reach only 50.6% accuracy within 25% relative error on clean inputs and degrade substantially with realistic noise. Stage-level analysis further shows that failures arise from brittle parsing, ineffective evidence integration, invalid pack selection, and non-convergent tool use.

cs.AI↗

arXiv2026

A Physics-Constrained Implicit Profile Network for Continuous Reconstruction of Tropical Cyclone Near-Surface Wind Profiles

Near the ocean surface, tropical cyclone winds change rapidly with height, but direct measurements are limited because aircraft dropsondes provide only sparse and irregular observations. Continuous wind profiles are important for understanding hurricane boundary-layer processes, improving storm-surge prediction, supporting offshore engineering, and assessing coastal hazards. In this study, we developed an artificial intelligence model that combines machine learning with physical principles to reconstruct continuous wind profiles from sparse observations. The model is designed to preserve the observed surface winds while generating realistic changes in wind speed and direction with height. Tests using more than two decades of NOAA hurricane observations show that the method accurately reproduces the vertical structure of tropical cyclone winds over a wide range of storm intensities. The framework can also extend satellite-derived surface wind measurements into three-dimensional near-surface wind fields, providing new opportunities for hurricane research, operational forecasting, and engineering applications.

physics.ao-ph↗

arXiv2026

An LLM-powered Agent Framework for Heterogeneous Evacuation Behavior Modeling under a Moving Threat in a Public Plaza

Modeling heterogeneous evacuation behavior under a moving threat is difficult because human perception, memory, and evidence evaluation are not well captured by fixed rules. We propose a novel LLM-powered agent-based framework to represent these internal decision processes. Each pedestrian agent perceives a private symbolic ASCII view, maintains a Memory-based Knowledge Graph derived solely from individual observations, and makes decisions through persona-conditioned prompts under a common sampling configuration. A compressed decision context with stateless memory preserves trial-and-error experience across turns while excluding reasoning traces, and a validation engine separates behavioral choice from physical feasibility by executing routes only over observed terrain. We evaluated eight personality compositions in eight paired randomized blocks within a simulated public plaza. Usable-exit knowledge was strongly associated with evacuation success: 89.5% of agents possessing such knowledge evacuated, compared with 1.05% of those without it. Personality compositions also differed in their evaluation of remembered threat evidence: the proportion of danger assessments varied by 0.265, while high-urgency, low-directness decisions ranged from 11.41% to 34.33%. After direct threat sightings, responses converged, with 99.6% of assessments classifying the situation as dangerous. Movement was selected in 99.8% of decisions. Overall, evacuation outcomes were strongly associated with information access, while evacuation time was jointly associated with spatial geometry, information, and affect. The framework provides an auditable approach to generating endogenous behavioral heterogeneity through persona-conditioned LLM agents in crowd-evacuation simulations.

physics.soc-ph↗

arXiv2026

MMLDSum-LLM: Multimodal Long-Document Summarization with Visual-Alignment and Keyword-Aware

Multimodal long documents are core carriers of professional knowledge, where critical evidence is sparsely distributed across paragraphs and modalities. This easily causes key information omission and cross-modal hallucinations in summarization by multimodal LLMs. These issues stem from attention drift in long-range dependency modeling and gaps in inter-modal alignment. To address this, we introduce MMLDSum-Bench, a high-quality benchmark for multimodal long-document summarization, covering multiple domains, context-length scales, and visual-textual modality distributions. We further propose MMLDSum-LLM, a reproducible two-stage training framework that combines supervised fine-tuning with visual-alignment weighted loss and keyword-aware weighted loss, followed by GRPO with a multi-objective reward (keyword coverage, image-text alignment, ROUGE, and length control). Extensive experiments on MMLDSum-Bench, comparing against leading closed-source and open-source multimodal models under a unified evaluation protocol - including LLM-as-a-judge scoring, atomic-claim precision/recall, image-text alignment (ITA), and ROUGE - demonstrate that our approach significantly improves key-information coverage and cross-modal consistency.

cs.AI↗

arXiv2026

Detector Development for HUBS I: Initial Testing of Small-Area TES Microcalorimeters

We report progress on the ongoing development of microcalorimeter detector technology for the Hot Universe Baryon Surveyor (HUBS) mission. We show the results from testing and characterizing selected pixels in a 10$\times$10 microcalorimeter array. The microcalorimeter is based on a Mo/Cu transition-edge sensor (TES) coupled to an Au absorber. To better understand the properties of the devices, we have first measured the energy resolution of a selected pixel in a TES array of the same design with a pulsed laser system that produces 3 eV photons, and found that individual photon peaks are easily resolved with the TES, indicating good performance. We have then exposed the microcalorimeter array to radiation from a $^{55}$Fe source, and found that the pixels tested show energy resolutions as good as 3.7$\pm$0.1 eV at 5.9 keV. The energy resolution is found to vary monotonically with the bias point for all the devices, showing little evidence for the presence of the so-called excess noise. This is consistent with the results from modeling the measured noise spectrum. The effects of thermal crosstalk are evident, leading to the degradation of energy resolution.

astro-ph.IM↗

arXiv2026

AgentCo-op: Retrieval-Based Synthesis of Interoperable Multi-Agent Workflows

Designing multi-agent workflows is especially difficult in open-ended scientific settings where tasks lack curated training sets, reliable scalar evaluation metrics, and standardized interfaces between existing tools and agents. We propose AgentCo-op, a retrieval-based synthesis framework that composes reusable skills, tools, and external agents into executable workflows through typed artifact handoffs, then applies bounded self-guided local repair to implicated components when execution evidence indicates failure. In two open-world genomics case studies, AgentCo-op composes independently developed scientific agents and external tool repositories into auditable workflows without redesigning them or running global topology search. It coordinates specialized agents for spatial transcriptomics and gene-set interpretation to enable collaborative discovery from spatial transcriptomics data, and builds a parallel workflow for cross-modality marker analysis on single-cell multiome data. AgentCo-op can also import a searched workflow as a structural prior and improve it by grounding nodes with retrieved components and applying local repair, showing that synthesis and search are complementary. On six coding, math, and question-answering benchmarks, AgentCo-op achieves the best result on four benchmarks and the best average score under a unified backbone setting, while consistently reducing per-task cost relative to multi-agent baselines. Together, these results suggest that retrieval-based synthesis can extend automated agentic workflow design beyond benchmark-optimized agent graphs to open-world workflows built from existing agents, tools, and typed artifacts.

cs.AI↗

arXiv2026

expo: Exploration-prioritized policy optimization via adaptive kl regulation and gaussian curriculum sampling

Reinforcement Learning with Verifiable Rewards (RLVR) has become the standard paradigm for LLM mathematical reasoning, where Group Relative Policy Optimization (GRPO) serves as the mainstream algorithm. We point out two understudied inefficiencies existing in GRPO. First, the fixed KL penalty coefficient overly restricts policy exploration at stages where the model requires significant deviation from the reference policy. Second, uniform sampling of training questions ignores that moderately difficult problems provide the most informative gradient signals for optimization. We propose Exploration-Prioritized Policy Optimization (EXPO) with two lightweight plug-in modules. The Accuracy-Conditioned KL Scaling (AKL) dynamically adjusts KL regularization strength through a smooth nonlinear function of batch average accuracy, relaxing the penalty when the model underperforms and strengthening it when the model achieves good results. The Gaussian Curriculum Sampling (GCS) assigns sampling weights to questions following a Gaussian distribution centered at moderate accuracy around 0.5, focusing training on the model's learning frontier. We conduct extensive experiments on DeepSeek-R1-Distill-Qwen-1.5B and Qwen3-8B-Base over six mathematical reasoning benchmarks. The results show EXPO steadily surpasses vanilla GRPO. It obtains an absolute gain of 13.34 on AIME 2025 pass@32, rising from 63.33 percent to 76.67 percent, and achieves an average pass@32 improvement of 2.66 on the 8B model. The much larger performance gains on pass@32 compared with pass@1 demonstrate that EXPO effectively enlarges the model's exploration boundary under a fixed inference cost budget.

cs.AI↗

arXiv2026

fg-expo: Frontier-guided exploration-prioritized policy optimization via adaptive kl and gaussian curriculum

Reinforcement Learning with Verifiable Rewards (RLVR) has become the standard paradigm for LLM mathematical reasoning, with Group Relative Policy Optimization (GRPO) serving as the dominant algorithm. We identify two overlooked inefficiencies inherent in GRPO. First, a fixed KL coefficient overly restricts policy exploration at moments when the model needs to diverge significantly from the reference policy. Second, uniform question sampling overlooks that moderately difficult problems produce the most informative gradient signals. We propose FG-ExPO, short for Frontier-Guided Exploration-Prioritized Policy Optimization, which integrates two lightweight components. Accuracy-Conditioned KL Scaling (AKL) adjusts the KL penalty strength through a smooth nonlinear function of batch average accuracy, loosening the constraint when the model performs poorly and strengthening it when the model achieves satisfactory results. Gaussian Curriculum Sampling (GCS) assigns sampling weights to questions following a Gaussian distribution centered at a moderate accuracy level around 0.5, focusing model training on its learning frontier. We conduct evaluations on DeepSeek-R1-Distill-Qwen-1.5B and Qwen3-8B-Base across six mainstream mathematical reasoning benchmarks. Experimental results demonstrate that FG-ExPO consistently outperforms vanilla GRPO. It delivers an absolute improvement of 13.34 on the AIME 2025 pass@32 metric, rising from 63.33 percent to 76.67 percent, and obtains an average pass@32 gain of 2.66 on the 8B model. The substantially larger performance gains observed on pass@32 compared to pass@1 verify that FG-ExPO enlarges the model's effective exploration space under a fixed inference budget.

cs.LG↗

arXiv2026

SKILLFOUNDRY: Building Self-Evolving Agent Skill Libraries from Heterogeneous Scientific Resources

Modern scientific ecosystems are rich in procedural knowledge across repositories, APIs, scripts, notebooks, documentation, databases, and papers, yet much of this knowledge remains fragmented across heterogeneous artifacts that agents cannot readily operationalize. This gap between abundant scientific know-how and usable agent capabilities is a key bottleneck for building effective scientific agents. We present SkillFoundry, a self-evolving framework that converts such resources into validated agent skills, reusable packages that encode task scope, inputs and outputs, execution steps, environment assumptions, provenance, and tests. SkillFoundry organizes a target domain as a domain knowledge tree, mines resources from high-value branches, extracts operational contracts, compiles them into executable skill packages, and then iteratively expands, repairs, merges, or prunes the resulting library through a closed-loop validation process. SkillFoundry produces a substantially novel and internally valid skill library, with 71.1\% of mined skills differing from existing skill libraries such as SkillHub and SkillSMP. We demonstrate that these mined skills improve coding agent performance on five of the six MoSciBench datasets. We further show that SkillFoundry can design new task-specific skills on demand for concrete scientific objectives, and that the resulting skills substantially improve performance on two challenging genomics tasks: cell type annotation and the scDRS workflow. Together, these results show that automatically mined skills improve agent performance on benchmarks and domain-specific tasks, expand coverage beyond hand-crafted skill libraries, and provide a practical foundation for more capable scientific agents.

cs.AI↗

arXiv2026

CLEAR-Mamba:Towards Accurate, Adaptive and Trustworthy Multi-Sequence Ophthalmic Angiography Classification

Medical image classification is a core task in computer-aided diagnosis (CAD), playing a pivotal role in early disease detection, treatment planning, and patient prognosis assessment. In ophthalmic practice, fluorescein fundus angiography (FFA) and indocyanine green angiography (ICGA) provide hemodynamic and lesion-structural information that conventional fundus photography cannot capture. However, due to the single-modality nature, subtle lesion patterns, and significant inter-device variability, existing methods still face limitations in generalization and high-confidence prediction. To address these challenges, we propose CLEAR-Mamba, an enhanced framework built upon MedMamba with optimizations in both architecture and training strategy. Architecturally, we introduce HaC, a hypernetwork-based adaptive conditioning layer that dynamically generates parameters according to input feature distributions, thereby improving cross-domain adaptability. From a training perspective, we develop RaP, a reliability-aware prediction scheme built upon evidential uncertainty learning, which encourages the model to emphasize low-confidence samples and improves overall stability and reliability. We further construct a large-scale ophthalmic angiography dataset covering both FFA and ICGA modalities, comprising multiple retinal disease categories for model training and evaluation. Experimental results demonstrate that CLEAR-Mamba consistently outperforms multiple baseline models, including the original MedMamba, across various metrics-showing particular advantages in multi-disease classification and reliability-aware prediction. This study provides an effective solution that balances generalizability and reliability for modality-specific medical image classification tasks. Our project can be accessed at https://github.com/ZJU4HealthCare/CLEAR-Mamba.

cs.CV↗

arXiv2026

Pluggable Pruning with Contiguous Layer Distillation for Diffusion Transformers

Diffusion Transformers (DiTs) have shown exceptional performance in image generation, yet their large parameter counts incur high computational costs, impeding deployment in resource-constrained settings. To address this, we propose Pluggable Pruning with Contiguous Layer Distillation (PPCL), a flexible structured pruning framework specifically designed for DiT architectures. First, we identify redundant layer intervals through a linear probing mechanism combined with the first-order differential trend analysis of similarity metrics. Subsequently, we propose a plug-and-play teacher-student alternating distillation scheme tailored to integrate depth-wise and width-wise pruning within a single training phase. This distillation framework enables flexible knowledge transfer across diverse pruning ratios, eliminating the need for per-configuration retraining. Extensive experiments on multiple Multi-Modal Diffusion Transformer architecture models demonstrate that PPCL achieves a 50\% reduction in parameter count compared to the full model, with less than 3\% degradation in key objective metrics. Notably, our method maintains high-quality image generation capabilities while achieving higher compression ratios, rendering it well-suited for resource-constrained environments. The open-source code, checkpoints for PPCL can be found at the following link: https://github.com/OPPO-Mente-Lab/Qwen-Image-Pruning.

cs.CV↗

arXiv2026

Learning from Prompt itself: the Hierarchical Attribution Prompt Optimization

Optimization is fundamental across numerous disciplines, typically following an iterative process of refining an initial solution to enhance performance. This principle is equally critical in prompt engineering, where designing effective prompts for large language models constitutes a complex optimization challenge. A structured optimization approach requires automated or semi-automated procedures to develop improved prompts, thereby reducing manual effort, improving performance, and yielding an interpretable process. However, current prompt optimization methods often induce prompt drift, where new prompts fix prior failures but impair performance on previously successful tasks. Additionally, generating prompts from scratch can compromise interpretability. To address these limitations, this study proposes the Hierarchical Attribution Prompt Optimization (HAPO) framework, which introduces three innovations: (1) a dynamic attribution mechanism targeting error patterns in training data and prompting history, (2) semantic-unit optimization for editing functional prompt segments, and (3) multimodal-friendly progression supporting both end-to-end LLM and LLM-MLLM workflows. Applied in contexts like single/multi-image QA (e.g., OCRV2) and complex task analysis (e.g., BBH), HAPO demonstrates enhanced optimization efficiency, outperforming comparable automated prompt optimization methods and establishing an extensible paradigm for scalable prompt engineering.

cs.AI↗

arXiv2026

IKFST: IOO and KOO Algorithms for Accelerated and Precise WFST-based End-to-End Automatic Speech Recognition

End-to-end automatic speech recognition has become the dominant paradigm in both academia and industry. To enhance recognition performance, the Weighted Finite-State Transducer (WFST) is widely adopted to integrate acoustic and language models through static graph composition, providing robust decoding and effective error correction. However, WFST decoding relies on a frame-by-frame autoregressive search over CTC posterior probabilities, which severely limits inference efficiency. Motivated by establishing a more principled compatibility between WFST decoding and CTC modeling, we systematically study the two fundamental components of CTC outputs, namely blank and non-blank frames, and identify a key insight: blank frames primarily encode positional information, while non-blank frames carry semantic content. Building on this observation, we introduce Keep-Only-One and Insert-Only-One, two decoding algorithms that explicitly exploit the structural roles of blank and non-blank frames to achieve significantly faster WFST-based inference without compromising recognition accuracy. Experiments on large-scale in-house, AISHELL-1, and LibriSpeech datasets demonstrate state-of-the-art recognition accuracy with substantially reduced decoding latency, enabling truly efficient and high-performance WFST decoding in modern speech recognition systems.

cs.SD↗

arXiv2025

DICE: Discrete Interpretable Comparative Evaluation with Probabilistic Scoring for Retrieval-Augmented Generation

As Retrieval-Augmented Generation (RAG) systems evolve toward more sophisticated architectures, ensuring their trustworthiness through explainable and robust evaluation becomes critical. Existing scalar metrics suffer from limited interpretability, inadequate uncertainty quantification, and computational inefficiency in multi-system comparisons, hindering responsible deployment of RAG technologies. We introduce DICE (Discrete Interpretable Comparative Evaluation), a two-stage, evidence-coupled framework that advances explainability and robustness in RAG evaluation. DICE combines deep analytical reasoning with probabilistic $\{A, B, Tie\}$ scoring to produce transparent, confidence-aware judgments that support accountable system improvement through interpretable reasoning traces, enabling systematic error diagnosis and actionable insights. To address efficiency challenges at scale, DICE employs a Swiss-system tournament that reduces computational complexity from $O(N^2)$ to $O(N \log N)$, achieving a 42.9% reduction in our eight-system evaluation while preserving ranking fidelity. Validation on a curated Chinese financial QA dataset demonstrates that DICE achieves 85.7% agreement with human experts, substantially outperforming existing LLM-based metrics such as RAGAS. Our results establish DICE as a responsible, explainable, and efficient paradigm for trustworthy RAG system assessment.

cs.AI↗