arXiv subjects

Jia Li

Publications and source records attributed to Jia Li.

At least 127 records · Page 7Linked to original sources

arXiv2026

Learning the Interaction Prior for Protein-Protein Interaction Prediction: A Model-Agnostic Approach

Protein-protein interactions (PPIs) are fundamental to cellular function and disease mechanisms. Current learning-based PPI predictors focus on learning powerful protein representations but neglect designing specialized classification heads. They mainly rely on generic aggregating methods like concatenation or dot products, which lack biological insight. Motivated by the biological "L3 rule", where multiple length-3 paths between a pair of proteins indicate their interaction likelihood, our study addresses this gap by designing a biologically informed PPI classifier. In this paper, we provide empirical evidence that popular PPI datasets strongly support the L3 rule. We propose an L3-path-regularized graph prompt learning method called L3-PPI, which can generate a prompt graph with virtual L3 paths based on protein representations and controls the number of paths. L3-PPI reformulates the classification of protein embedding pairs into a graph-level classification task over the generated prompt graph. This lightweight module seamlessly integrates with PPI predictors as a plug-and-play component, injecting the interaction prior of complementarity to enhance performance. Extensive experiments show that L3-PPI achieves superior performance enhancements over advanced competitors.

cs.AI↗

arXiv2026

SDTalk: Structured Facial Priors and Dual-Branch Motion Fields for Generalizable Gaussian Talking Head Synthesis

High-quality, real-time talking head synthesis remains a fundamental challenge in computer vision. Existing reconstruction- and rendering-based methods typically rely on identity-specific models, limiting cross-identity generalization. To address this issue, we propose SDTalk, a one-shot 3D Gaussian Splatting (3DGS)-based framework that generalizes to unseen identities without personalized training or fine-tuning. Our framework comprises two modules with a two-stage training strategy. In the first stage, we incorporate structured facial priors into the reconstruction module and separately predict 3DGS parameters for visible and occluded regions, enabling complete head reconstruction from a single image. In the second stage, we introduce a dual-branch motion field to model coarse and fine facial dynamics, improving detail fidelity and lip synchronization. Experiments demonstrate that SDTalk surpasses existing methods in both visual quality and inference efficiency.

cs.CV↗

arXiv2026

ProteinOPD: Towards Effective and Efficient Preference Alignment for Protein Design

Designing proteins with desired functions or properties represents a core goal in synthetic biology and drug discovery. Recent advances in protein language models (PLMs) have enabled the generation of highly designable protein sequences, while preference alignment provides a promising way to steer designs toward desired functions and properties. Nevertheless, they often trigger catastrophic forgetting of pretrained knowledge, degrading basic designability and failing to balance multiple competing objectives. To address these issues, we draw inspiration from On-Policy Distillation (OPD), an advanced post-training method renowned for mitigating catastrophic forgetting through its mode-seeking nature. In this work, we propose ProteinOPD, a multi-objective preference alignment framework that can effectively balance multiple preference objectives while maintaining the inherent designability of PLMs. ProteinOPD adapts a pretrained PLM into preference-specific teachers and distills their knowledge into a shared student via token-level OPD on the student's own trajectories. During this process, the student is aligned to a unique normalized geometric consensus of weighted teachers while ensuring bounded optimization under conflicts. This bridges the gap for OPD in multi-objective/teacher alignment. Extensive experiments show that ProteinOPD achieves substantial gains on target preference objectives without compromising the designability, with an 8x training speedup over RL-based alignment competitors.

cs.LG↗

arXiv2026

Signal Reshaping for GRPO in Weak-Feedback Agentic Code Repair

Code-agent RL often receives weak feedback: rollout-time signals are reliable and executable, but capture only necessary or surface conditions for task success rather than the target semantic predicate. Using agentic compile-fix as the setting, we study signal reshaping for standard GRPO under such feedback. Our central claim is that GRPO's within-group comparison is meaningful only after three kinds of signals are reshaped: outcome rewards recover semantic ranking, process signals localize intra-trajectory credit, and rollouts from the same prompt remain execution-comparable. We operationalize these conditions with a minimal signal-reshaping construction that leaves GRPO's group-normalized advantage construction unchanged: compile-and-semantic layered rewards reshape trajectory ranking, step-level process scores outside group reward normalization reshape within-trajectory update strength, and failure-cause-aware rollout governance reshapes within-group comparability. Experiments show a clear end-to-end gain: full signal-reshaped GRPO improves strict compile-and-semantic accuracy from the base model's zero-shot $0.385$ to $0.535$. Controlled comparisons further explain the source of this gain: binary rewards remove the compile-only middle tier and degrade trajectory control; on top of layered rewards, process-score weighting further improves accuracy from $0.48$ to $0.53$ and reduces average evaluation steps from $23.50$ to $17.02$. As a boundary comparison, privileged-prompt token-level distillation mainly optimizes local distributional alignment; in long tool-use trajectories, this signal is diluted by non-critical tokens and cannot replace outcome semantics, process credit, or within-group comparability.

cs.AI↗

arXiv2026

WeatherSyn: An Instruction Tuning MLLM For Weather Forecasting Report Generation

Accurate weather forecast reporting enables individuals and communities to better plan daily activities and agricultural operations. However, the current reporting process primarily relies on manual analysis of multi-source data, which leads to information overload and reduced efficiency. With the development of multimodal large language models (MLLMs), leveraging data-driven models to analyze and generate reports in the weather forecasting domain remains largely underexplored. In this work, we propose the Weather Forecasting Report (WFR) task and construct the first instruction-tuning dataset for this task, named~\DatasetNameL, which covers 31 cities in America and 8 weather aspects. Based on this corpus, we develop the first model, \ModelNameL, specialized in generating weather forecast reports. Evaluation across multiple metrics on our dataset shows that \ModelNameL~ consistently outperforms leading closed-source MLLMs, particularly on structurally complex weather aspects. We further analyze its performance across diverse geographic regions and weather aspects. \ModelNameL~ demonstrates strong transferability across different regions, highlighting its zero-shot generalization capability. \ModelNameL~offers valuable insight for developing MLLMs specialized in weather report generation. .

cs.CL↗

arXiv2026

DOGMA: Weaving Structural Information into Data-centric Single-cell Transcriptomics Analysis

Recently, data-centric AI methodology has been a dominant paradigm in single-cell transcriptomics analysis, which treats data representation rather than model complexity as the fundamental bottleneck. In the review of current studies, earlier sequence methods treat cells as independent entities and adapt prevalent ML models to analyze their directly inherited sequence data. Despite their simplicity and intuition, these methods overlook the latent intercellular relationships driven by the functional mechanisms of biological systems and the inherent quality issues of the raw sequencing data. Therefore, a series of structured methods has emerged. Although they employ various heuristic rules to capture intricate intercellular relationships and enhance the raw sequencing data, these methods often neglect biological prior knowledge. This omission incurs substantial overhead and yields suboptimal graph representations, hindering the utility of ML models. To address these issues, we propose DOGMA, a data-centric framework designed for the structural reshaping and semantic enhancement of raw data through multi-level biological prior knowledge. Transcending reliance on purely data-driven heuristics, DOGMA provides a prior-guided graph construction pipeline that integrates statistical alignment with Cell Ontology and phylogenetic structure for biologically grounded cell-graph construction and robust cross-species alignment. Furthermore, Gene Ontology is utilized to bridge the feature-level semantic gap by incorporating functional priors. In complex multi-species and multi-organ benchmarks, DOGMA exhibits strong robustness in strict zero-shot cell-type evaluation and sample efficiency while using substantially lower GPU memory and inference time in downstream evaluation.

cs.LG↗

arXiv2026

Adaptive Physical-Facial Representation Fusion via Subject-Invariant Cross-Modal Prompt Tuning for Video-Based Emotion Recognition

Emotion recognition from facial videos enables non-contact inference of human emotional states. Although facial expressions are widely used cues, they cannot fully reflect intrinsic affective states. Remote photoplethysmography (rPPG) provides complementary physiological information, but it is highly susceptible to noise and inter-subject variability, limiting generalization to unseen individuals. Existing multimodal methods combine facial and rPPG features, yet their fusion strategies often disrupt pretrained facial representations and lack explicit mechanisms to suppress subject-specific variations. To address these issues, we propose a subject-invariant cross-modal prompt-tuning framework for video-based emotion recognition. Specifically, rPPG waveforms are transformed into noise-robust time-frequency representations (TFRs), from which modality-complementary prompts are generated to modulate facial tokens within a frozen Vision Transformer (ViT). This design enables effective cross-modal interaction while preserving the generalizable facial representations learned by the pretrained backbone. In addition, we introduce a decoupled shared-specific adapter (DSSA) into each ViT layer to explicitly separate subject-shared and subject-specific components, thereby improving cross-subject generalization. Experiments on the MAHNOB-HCI and DEAP benchmarks demonstrate that the proposed method consistently outperforms strong baselines in both recognition accuracy and generalization ability, highlighting its effectiveness for video-based emotion recognition.

cs.CV↗

arXiv2026

An Empirical Study of Proactive Coding Assistants in Real-World Software Development

Large language model (LLM)-based coding assistants have made substantial progress, yet most systems remain reactive, requiring developers to explicitly formulate their needs. Proactive coding assistants aim to infer latent developer intent from integrated development environment (IDE) interactions and repository context, thereby reducing interaction overhead and supporting more seamless assistance. However, research in this direction is limited by the scarcity of large-scale real-world developer behavior data. Existing studies therefore often rely on LLM-simulated IDE traces, whose fidelity to real development behavior remains unclear. In this paper, we investigate this simulation-to-reality gap through a large-scale empirical study. We collect real IDE interaction traces from 1{,}246 experienced industry developers over three consecutive days using a custom Visual Studio Code extension, and construct paired LLM-simulated traces for controlled comparison. Our analysis shows that simulated traces differ substantially from real traces in behavioral diversity, temporal structure, and exploratory patterns. Based on the collected data, we introduce \textbf{ProCodeBench}, a real-world benchmark for proactive intent prediction. Experiments with representative LLMs, retrieval-augmented methods, and agentic baselines show that current approaches remain far from reliable under real IDE traces, suggesting that simulation-based evaluation can overestimate real-world performance. Finally, our training study shows that simulated data cannot replace real data, but can complement it when used before real-world fine-tuning. These findings highlight the importance of real developer behavior data for evaluating and training proactive coding assistants.

cs.SE↗

arXiv2026

To Fuse or to Drop? Dual-Path Learning for Resolving Modality Conflicts in Multimodal Emotion Recognition

Multimodal emotion recognition (MER) benefits from combining text, audio, and vision, yet standard fusion often fails when modalities conflict. Crucially, conflicts differ in resolvability: benign conflicts stem from missing, weak, or ambiguous cues and can be mitigated by cross-modal calibration, while severe conflicts arise from intrinsically contradictory (e.g., sarcasm) or misleading signals, for which forced fusion may amplify errors. Recognizing this, we propose Dual-Path Conflict Resolution (DCR), a unified framework that learns when to fuse and when to drop modalities. Path I (Affective Fusion Distiller, AFD) performs reverse distillation from audio/visual teachers to a textual student using temporally weighted class evidence, thereby enhancing representation-level calibration and improving fusion when alignment is beneficial. Path II (Affective Discernment Agent, ADA) formulates MER as a contextual bandit that selects among fusion and unimodal predictions based on a dual-view state and a calibration-aware reward, enabling decision-level arbitration under irreconcilable conflicts without requiring per-modality reliability labels. By taking into account the full multimodal context and coupling soft calibration with hard arbitration, DCR reconciles conflicts that can be aligned while bypassing misleading modalities when fusion is harmful. Across five benchmarks covering both dialogue-level and clip-level MER, DCR consistently outperforms competitive baselines or achieves highly competitive results. Further ablations, conflict-specific subset evaluation, and modality-selection analysis verify that AFD and ADA are complementary and jointly improve robust conflict-aware emotion recognition.

cs.MM↗

arXiv2026

From Laboratory to Real-World Applications: Benchmarking Agentic Code Reasoning at the Repository Level

As large language models (LLMs) evolve into autonomous agents, evaluating repository-level reasoning, the ability to maintain logical consistency across massive, real-world, interdependent file systems, has become critical. Current benchmarks typically fluctuate between isolated code snippets and black-box evaluations. We present RepoReason, a white-box diagnostic benchmark centered on abductive assertion verification. To eliminate memorization while preserving authentic logical depth, we implement an execution-driven mutation framework that utilizes the environment as a semantic oracle to regenerate ground-truth states. Furthermore, we establish a fine-grained diagnostic system using dynamic program slicing, quantifying reasoning via three orthogonal metrics: $ESV$ (reading load), $MCL$ (simulation depth), and $DFI$ (integration width). Comprehensive evaluations of frontier models (e.g., Claude-4.5-Sonnet, DeepSeek-v3.1-Terminus) reveal a prevalent aggregation deficit, where integration width serves as the primary cognitive bottleneck. Our findings provide granular white-box insights for optimizing the next generation of agentic software engineering.

cs.SE↗

arXiv2026

Genetic Programming for Self-Adaptive Auto-Scaling of Microservices

Microservice architecture is widely adopted in modern systems, where auto-scaling is critical for satisfying service-level objectives (SLOs). However, determining optimal scaling for microservices is difficult, and reactive resource allocation often leads to costly over- or under-provisioning. We propose AutoSLO, a learning-based, self-adaptive scaling framework that dynamically adjusts microservice replicas to meet SLOs while minimizing resource usage. AutoSLO uses a continuous monitoring-adaptation feedback loop and leverages genetic programming to learn and evolve scaling logic, enabling the deployed microservice system to proactively prevent SLO violations rather than repeatedly searching for one-off scaling actions. We evaluate AutoSLO on two case-study systems -- an online shopping platform and a chatbot based on large language models -- and show that this framework substantially reduces resource usage while maintaining a low frequency of SLO violations, all of which are resolved within a short time window.

cs.SE↗

arXiv2026

CURE-OOD: Benchmarking Out-of-Distribution Detection for Survival Prediction

``How long can I live and remain free of cancer?'' is often the first question a patient asks after receiving a cancer diagnosis and treatment. Accurate survival prediction helps alleviate psychological distress and supports risk stratification and personalized treatment planning. Recent survival prediction frameworks have shown strong performance using computed tomography (CT) images. However, variations in imaging acquisition introduce out-of-distribution (OOD) samples caused by covariate shifts that undermine model reliability. Despite this challenge, to our knowledge, no existing benchmark systematically studies OOD detection in cancer survival prediction. To address this gap, we introduce the Cancer sURvival bEnchmark for OOD Detection (CURE-OOD), the first benchmark for systematically evaluating OOD detection in survival prediction under controlled acquisition-induced distribution shifts. CURE-OOD defines scanner-parameter-based training, in-distribution (ID), and OOD test splits across four survival prediction tasks. Our experiments show that covariate shifts notably reduce survival prediction performance. It also shows that mainstream classification-oriented OOD detectors can fail in survival prediction. Finally, we include HazardDev as a simple survival-aware reference baseline for OOD detection. CURE-OOD enables systematic analysis of how distribution shifts affect both downstream survival performance and OOD detectability.

cs.CV↗

arXiv2026

KOCO-BENCH: Can Large Language Models Leverage Domain Knowledge in Software Development?

Large language models (LLMs) excel at general programming but struggle with domain-specific software development, necessitating domain specialization methods for LLMs to learn and utilize domain knowledge and data. However, existing domain-specific code benchmarks cannot evaluate the effectiveness of domain specialization methods, which focus on assessing what knowledge LLMs possess rather than how they acquire and apply new knowledge, lacking explicit knowledge corpora for developing domain specialization methods. To this end, we present KOCO-BENCH, a novel benchmark designed for evaluating domain specialization methods in real-world software development. KOCO-BENCH contains 6 emerging domains with 11 software frameworks and 25 projects, featuring curated knowledge corpora alongside multi-granularity evaluation tasks including domain code generation (from function-level to project-level with rigorous test suites) and domain knowledge understanding (via multiple-choice Q&A). Unlike previous benchmarks that only provide test sets for direct evaluation, KOCO-BENCH requires acquiring and applying diverse domain knowledge (APIs, rules, constraints, etc.) from knowledge corpora to solve evaluation tasks. Our evaluations reveal that KOCO-BENCH poses significant challenges to state-of-the-art LLMs. Even with domain specialization methods (e.g., SFT, RAG, kNN-LM) applied, improvements remain marginal. Best-performing coding agent, Claude Code, achieves only 34.2%, highlighting the urgent need for more effective domain specialization methods. We release KOCO-BENCH, evaluation code, and baselines to advance further research at https://github.com/jiangxxxue/KOCO-bench.

cs.SE↗

arXiv2026

DebugRepair: Enhancing LLM-Based Automated Program Repair via Self-Directed Debugging

Automated Program Repair (APR) has benefited from the code understanding and generation capabilities of Large Language Models (LLMs). Existing feedback-based APR methods iteratively refine candidate patches using test execution feedback and have shown promising results. However, most rely on outcome-level failure symptoms, such as stack traces, which show how failures are observed but fail to expose the intermediate runtime states critical for root-cause analysis. As a result, LLMs often infer bug causes without sufficient runtime evidence, leading to incorrect patches. To address this limitation, we propose DebugRepair, a self-directed debugging framework for LLM-based APR. DebugRepair enhances patch refinement with intermediate runtime evidence collected through simulated debugging. It consists of three components: test semantic purification, simulated instrumentation, and debugging-driven conversational repair. Together, they reduce noisy test context, collect runtime traces through targeted debugging statements with rule-based fallback, and progressively refine candidate patches using prior attempts and newly observed runtime states. We evaluate DebugRepair on three benchmarks across Java and Python. Experiments show that DebugRepair achieves state-of-the-art performance against 15 approaches. With GPT-3.5, it correctly fixes 224 bugs on Defects4J, outperforming prior SOTA LLM-based methods by 26.2%. With DeepSeek-V3, it correctly fixes 295 Defects4J bugs, surpassing the second-best baseline by 59 bugs. Across five additional backbone LLMs, DebugRepair improves repair performance by 51.3% over vanilla settings. Ablation studies further confirm the effectiveness of all components.

cs.SE↗

arXiv2026

EvoCoT: Overcoming the Exploration Bottleneck in Reinforcement Learning

Reinforcement learning with verifiable reward (RLVR) has become a promising paradigm for post-training large language models (LLMs) to improve their reasoning capability. However, when the rollout accuracy is low on hard problems, the reward becomes sparse, limiting learning efficiency and causing exploration bottlenecks. Existing approaches either rely on teacher models for distillation or filter out difficult problems, which limits scalability or restricts reasoning improvement through exploration. We propose EvoCoT, a self-evolving curriculum learning framework based on two-stage chain-of-thought (CoT) reasoning optimization. EvoCoT constrains the exploration space by self-generating and verifying CoT trajectories, then gradually shortens CoT steps to expand the space in a controlled way. The framework enables LLMs to stably learn from initially unsolved hard problems under sparse rewards. We apply EvoCoT to multiple LLM families, including Qwen, DeepSeek, and Llama. Experiments show that EvoCoT enables LLMs to solve previously unsolved problems, improves reasoning capability without external CoT supervision, and is compatible with various RL fine-tuning methods. We release the source code to support future research.

cs.LG↗

arXiv2026

LoReC: Rethinking Large Language Models for Graph Data Analysis

The advent of Large Language Models (LLMs) has fundamentally reshaped the way we interact with graphs, giving rise to a new paradigm called GraphLLM. As revealed in recent studies, graph learning can benefit from LLMs. However, we observe limited benefits when we directly utilize LLMs to make predictions for graph-related tasks within GraphLLM paradigm, which even yields suboptimal results compared to conventional GNN-based approaches. Through in-depth analysis, we find this failure can be attributed to LLMs' limited capability for processing graph data and their tendency to overlook graph information. To address this issue, we propose LoReC (Look, Remember, and Contrast), a novel plug-and-play method for GraphLLM paradigm, which enhances LLM's understanding of graph data through three stages: (1) Look: redistributing attention to graph; (2) Remember: re-injecting graph information into the Feed-Forward Network (FFN); (3) Contrast: rectifying the vanilla logits produced in the decoding process. Extensive experiments demonstrate that LoReC brings notable improvements over current GraphLLM methods and outperforms GNN-based approaches across diverse datasets. The implementation is available at https://github.com/Git-King-Zhan/LoReC.

cs.LG↗

arXiv2026

Training LLM Agents for Spontaneous, Reward-Free Self-Evolution via World Knowledge Exploration

Most agents today ``self-evolve'' by following rewards and rules defined by humans. However, this process remains fundamentally dependent on external supervision; without human guidance, the evolution stops. In this work, we train agents to possess an intrinsic meta-evolution capability to spontaneously learn about unseen environments prior to task execution. To instill this ability, we design an outcome-based reward mechanism that measures how much an agent's self-generated world knowledge improves its success rate on downstream tasks. This reward signal is used exclusively during the training phase to teach the model how to explore and summarize effectively. At inference time, the agent requires no external rewards or human instructions. It spontaneously performs native self-evolution to adapt to unknown environments using its internal parameters. When applied to Qwen3-30B and Seed-OSS-36B, this shift to native evolution yields a 20% performance increase on WebVoyager and WebWalker. Most strikingly, the generated world knowledge even enables a compact 14B Qwen3 model to outperform the unassisted Gemini-2.5-Flash, establishing a new paradigm for truly evolving agents.

cs.AI↗

arXiv2026

Bridging the Gap between User Intent and LLM: A Requirement Alignment Approach for Code Generation

Code generation refers to automatically producing executable programs from user requirements. Recently, researchers have explored approaches to enhance the correctness of generated code with advanced large language models. Although achieving improvements, existing approaches focus on designing reasoning strategies or post-refinement methods to enhance code generation performance. Despite their differences, all these methods share a common assumption: the LLM can correctly understand the given requirement. However, this assumption does not always hold. To fill this gap, we propose REA-Coder, a requirement alignment approach to enhance the code generation performance of LLMs. REA-Coder involves first identifying the requirement content that does not align with LLMs and aligning the requirements. Then, based on the aligned requirements, LLMs generate code and further verify whether the generated code aligns with the requirements, iterating this process of requirement alignment and code generation until generating correct code or achieving the maximum number of iterations. Experimental results show that REA-Coder outperforms all advanced baselines on four LLMs across five programming benchmarks. Concretely, REA-Coder achieves average improvements of 7.93%, 30.25%, 26.75%, 8.59%, and 8.64% on the five benchmark datasets, demonstrating the effectiveness of requirement alignment for improving the code generation performance of LLMs.

cs.SE↗