arXiv subjects

Jia Li

Publications and source records attributed to Jia Li.

At least 289 records · Page 16Linked to original sources

arXiv2025

InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.

cs.LG↗

arXiv2025

Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model

Effective generation of molecular structures, or new chemical entities, that bind to target proteins is crucial for lead identification and optimization in drug discovery. Despite advancements in atom- and motif-wise deep learning models for 3D molecular generation, current methods often struggle with validity and reliability. To address these issues, we develop the Atom-Motif Consistency Diffusion Model (AMDiff), utilizing a joint-training paradigm for multi-view learning. This model features a hierarchical diffusion architecture that integrates both atom- and motif-level views of molecules, allowing for comprehensive exploration of complementary information. By leveraging classifier-free guidance and incorporating binding site features as conditional inputs, AMDiff ensures robust molecule generation across diverse targets. Compared to existing approaches, AMDiff exhibits superior validity and novelty in generating molecules tailored to fit various protein pockets. Case studies targeting protein kinases, including Anaplastic Lymphoma Kinase (ALK) and Cyclin-dependent kinase 4 (CDK4), demonstrate the model's capability in structure-based de novo drug design. Overall, AMDiff bridges the gap between atom-view and motif-view drug discovery and speeds up the process of target-aware molecular generation.

cs.LG↗

arXiv2025

Building Trust in Mental Health Chatbots: Safety Metrics and LLM-Based Evaluation Tools

Objective: This study aims to develop and validate an evaluation framework to ensure the safety and reliability of mental health chatbots, which are increasingly popular due to their accessibility, human-like interactions, and context-aware support. Materials and Methods: We created an evaluation framework with 100 benchmark questions and ideal responses, and five guideline questions for chatbot responses. This framework, validated by mental health experts, was tested on a GPT-3.5-turbo-based chatbot. Automated evaluation methods explored included large language model (LLM)-based scoring, an agentic approach using real-time data, and embedding models to compare chatbot responses against ground truth standards. Results: The results highlight the importance of guidelines and ground truth for improving LLM evaluation accuracy. The agentic method, dynamically accessing reliable information, demonstrated the best alignment with human assessments. Adherence to a standardized, expert-validated framework significantly enhanced chatbot response safety and reliability. Discussion: Our findings emphasize the need for comprehensive, expert-tailored safety evaluation metrics for mental health chatbots. While LLMs have significant potential, careful implementation is necessary to mitigate risks. The superior performance of the agentic approach underscores the importance of real-time data access in enhancing chatbot reliability. Conclusion: The study validated an evaluation framework for mental health chatbots, proving its effectiveness in improving safety and reliability. Future work should extend evaluations to accuracy, bias, empathy, and privacy to ensure holistic assessment and responsible integration into healthcare. Standardized evaluations will build trust among users and professionals, facilitating broader adoption and improved mental health support through technology.

cs.CL↗

arXiv2025

Convex inequalities in Hilbert $C^*$-modules

The H$\ddot{\rm o}$lder-McCarty inequalities are originally derived in the Hilbert space case and have been generalized via a convex inequality. The main purpose of this paper is to extend this convex inequality to the Hilbert $C^*$-module case, and meanwhile to make some investigations on the H$\ddot{\rm o}$lder-McCarty inequalities in the Hilbert $C^*$-module case.

math.FA↗

arXiv2025

CirT: Global Subseasonal-to-Seasonal Forecasting with Geometry-inspired Transformer

Accurate Subseasonal-to-Seasonal (S2S) climate forecasting is pivotal for decision-making including agriculture planning and disaster preparedness but is known to be challenging due to its chaotic nature. Although recent data-driven models have shown promising results, their performance is limited by inadequate consideration of geometric inductive biases. Usually, they treat the spherical weather data as planar images, resulting in an inaccurate representation of locations and spatial relations. In this work, we propose the geometric-inspired Circular Transformer (CirT) to model the cyclic characteristic of the graticule, consisting of two key designs: (1) Decomposing the weather data by latitude into circular patches that serve as input tokens to the Transformer; (2) Leveraging Fourier transform in self-attention to capture the global information and model the spatial periodicity. Extensive experiments on the Earth Reanalysis 5 (ERA5) reanalysis dataset demonstrate our model yields a significant improvement over the advanced data-driven models, including PanguWeather and GraphCast, as well as skillful ECMWF systems. Additionally, we empirically show the effectiveness of our model designs and high-quality prediction over spatial and temporal dimensions.

cs.LG↗

arXiv2025

Evidence and quantification of cooperation of driving agents in mixed traffic flow

Cooperation is a ubiquitous phenomenon in many natural, social, and engineered systems with multiple agents. Understanding the formation of cooperation in mixed traffic is of theoretical interest in its own right, and could also benefit the design and operations of future automated and mixed-autonomy transportation systems. However, how cooperativeness of driving agents can be defined and identified from empirical data seems ambiguous and this hinders further empirical characterizations of the phenomenon and revealing its behavior mechanisms. Towards mitigating this gap, in this paper, we propose a unified conceptual framework to identify collective cooperativeness of driving agents. This framework expands the concept of collective rationality from our recent model (Li et al. 2022a), making it empirically identifiable and behaviorally interpretable in realistic (microscopic and dynamic) settings. This framework integrates mixed traffic observations at both microscopic and macroscopic scales to estimate critical behavioral parameters that describe the collective cooperativeness of driving agents. Applying this framework to NGSIM I-80 trajectory data, we empirically confirm the existence of collective cooperation and quantify the condition and likelihood of its emergence. This study provides the first empirical understanding of collective cooperativeness in human-driven mixed traffic and points to new possibilities to manage mixed autonomy traffic systems.

physics.soc-ph↗

arXiv2025

Do Audio-Visual Segmentation Models Truly Segment Sounding Objects?

Unlike traditional visual segmentation, audio-visual segmentation (AVS) requires the model not only to identify and segment objects but also to determine whether they are sound sources. Recent AVS approaches, leveraging transformer architectures and powerful foundation models like SAM, have achieved impressive performance on standard benchmarks. Yet, an important question remains: Do these models genuinely integrate audio-visual cues to segment sounding objects? In this paper, we systematically investigate this issue in the context of robust AVS. Our study reveals a fundamental bias in current methods: they tend to generate segmentation masks based predominantly on visual salience, irrespective of the audio context. This bias results in unreliable predictions when sounds are absent or irrelevant. To address this challenge, we introduce AVSBench-Robust, a comprehensive benchmark incorporating diverse negative audio scenarios including silence, ambient noise, and off-screen sounds. We also propose a simple yet effective approach combining balanced training with negative samples and classifier-guided similarity learning. Our extensive experiments show that state-of-theart AVS methods consistently fail under negative audio conditions, demonstrating the prevalence of visual bias. In contrast, our approach achieves remarkable improvements in both standard metrics and robustness measures, maintaining near-perfect false positive rates while preserving highquality segmentation performance.

cs.SD↗

arXiv2025

G-Refer: Graph Retrieval-Augmented Large Language Model for Explainable Recommendation

Explainable recommendation has demonstrated significant advantages in informing users about the logic behind recommendations, thereby increasing system transparency, effectiveness, and trustworthiness. To provide personalized and interpretable explanations, existing works often combine the generation capabilities of large language models (LLMs) with collaborative filtering (CF) information. CF information extracted from the user-item interaction graph captures the user behaviors and preferences, which is crucial for providing informative explanations. However, due to the complexity of graph structure, effectively extracting the CF information from graphs still remains a challenge. Moreover, existing methods often struggle with the integration of extracted CF information with LLMs due to its implicit representation and the modality gap between graph structures and natural language explanations. To address these challenges, we propose G-Refer, a framework using graph retrieval-augmented large language models (LLMs) for explainable recommendation. Specifically, we first employ a hybrid graph retrieval mechanism to retrieve explicit CF signals from both structural and semantic perspectives. The retrieved CF information is explicitly formulated as human-understandable text by the proposed graph translation and accounts for the explanations generated by LLMs. To bridge the modality gap, we introduce knowledge pruning and retrieval-augmented fine-tuning to enhance the ability of LLMs to process and utilize the retrieved CF information to generate explanations. Extensive experiments show that G-Refer achieves superior performance compared with existing methods in both explainability and stability. Codes and data are available at https://github.com/Yuhan1i/G-Refer.

cs.IR↗

arXiv2025

S$^2$R: Teaching LLMs to Self-verify and Self-correct via Reinforcement Learning

Recent studies have demonstrated the effectiveness of LLM test-time scaling. However, existing approaches to incentivize LLMs' deep thinking abilities generally require large-scale data or significant training efforts. Meanwhile, it remains unclear how to improve the thinking abilities of less powerful base models. In this work, we introduce S$^2$R, an efficient framework that enhances LLM reasoning by teaching models to self-verify and self-correct during inference. Specifically, we first initialize LLMs with iterative self-verification and self-correction behaviors through supervised fine-tuning on carefully curated data. The self-verification and self-correction skills are then further strengthened by both outcome-level and process-level reinforcement learning, with minimized resource requirements, enabling the model to adaptively refine its reasoning process during inference. Our results demonstrate that, with only 3.1k self-verifying and self-correcting behavior initialization samples, Qwen2.5-math-7B achieves an accuracy improvement from 51.0\% to 81.6\%, outperforming models trained on an equivalent amount of long-CoT distilled data. Extensive experiments and analysis based on three base models across both in-domain and out-of-domain benchmarks validate the effectiveness of S$^2$R. Our code and data are available at https://github.com/NineAbyss/S2R.

cs.CL↗

arXiv2025

SimXRD-4M: Big Simulated X-ray Diffraction Data Accelerate the Crystal Symmetry Classification

Spectroscopic data, particularly diffraction data, contain detailed crystal and microstructure information and thus are crucial for materials discovery. Powder X-ray diffraction (XRD) patterns are greatly effective in identifying crystals. Although machine learning (ML) has significantly advanced the analysis of powder XRD patterns, the progress is hindered by a lack of training data. To address this, we introduce SimXRD, the largest open-source simulated XRD pattern dataset so far, to accelerate the development of crystallographic informatics. SimXRD comprises 4,065,346 simulated powder X-ray diffraction patterns, representing 119,569 distinct crystal structures under 33 simulated conditions that mimic real-world variations. We find that the crystal symmetry inherently follows a long-tailed distribution and evaluate 21 sequence learning models on SimXRD. The results indicate that existing neural networks struggle with low-frequency crystal classifications. The present work highlights the academic significance and the engineering novelty of simulated XRD patterns in this interdisciplinary field.

cond-mat.mtrl-sci↗

arXiv2025

GraphArena: Evaluating and Exploring Large Language Models on Graph Computation

The ``arms race'' of Large Language Models (LLMs) demands new benchmarks to examine their progresses. In this paper, we introduce GraphArena, a benchmarking tool designed to evaluate LLMs on real-world graph computational problems. It offers a suite of four polynomial-time tasks (e.g., Shortest Distance) and six NP-complete challenges (e.g., Traveling Salesman Problem). GraphArena features a rigorous evaluation framework that classifies LLM outputs as correct, suboptimal (feasible but not optimal), hallucinatory (properly formatted but infeasible), or missing. Evaluation of over 10 LLMs reveals that even top-performing LLMs struggle with larger, more complex graph problems and exhibit hallucination issues. We further explore four potential solutions to address this issue and improve LLMs on graph computation, including chain-of-thought prompting, instruction tuning, code writing, and scaling test-time compute, each demonstrating unique strengths and limitations. GraphArena complements the existing LLM benchmarks and is open-sourced at https://github.com/squareRoot3/GraphArena.

cs.AI↗

arXiv2025

Constructing Cell-type Taxonomy by Optimal Transport with Relaxed Marginal Constraints

The rapid emergence of single-cell data has facilitated the study of many different biological conditions at the cellular level. Cluster analysis has been widely applied to identify cell types, capturing the essential patterns of the original data in a much more concise form. One challenge in the cluster analysis of cells is matching clusters extracted from datasets of different origins or conditions. Many existing algorithms cannot recognize new cell types present in only one of the two samples when establishing a correspondence between clusters obtained from two samples. Additionally, when there are more than two samples, it is advantageous to align clusters across all samples simultaneously rather than performing pairwise alignment. Our approach aims to construct a taxonomy for cell clusters across all samples to better annotate these clusters and effectively extract features for downstream analysis. A new system for constructing cell-type taxonomy has been developed by combining the technique of Optimal Transport with Relaxed Marginal Constraints (OT-RMC) and the simultaneous alignment of clusters across multiple samples. OT-RMC allows us to address challenges that arise when the proportions of clusters vary substantially between samples or when some clusters do not appear in all the samples. Experiments on more than twenty datasets demonstrate that the taxonomy constructed by this new system can yield highly accurate annotation of cell types. Additionally, sample-level features extracted based on the taxonomy result in accurate classification of samples.

q-bio.GN↗

arXiv2025

InfoBFR: Real-World Blind Face Restoration via Information Bottleneck

Blind face restoration (BFR) is a highly challenging problem due to the uncertainty of data degradation patterns. Current BFR methods have realized certain restored productions but with inherent neural degradations that limit real-world generalization in complicated scenarios. In this paper, we propose a plug-and-play framework InfoBFR to tackle neural degradations, e.g., prior bias, topological distortion, textural distortion, and artifact residues, which achieves high-generalization face restoration in diverse wild and heterogeneous scenes. Specifically, based on the results from pre-trained BFR models, InfoBFR considers information compression using manifold information bottleneck (MIB) and information compensation with efficient diffusion LoRA to conduct information optimization. InfoBFR effectively synthesizes high-fidelity faces without attribute and identity distortions. Comprehensive experimental results demonstrate the superiority of InfoBFR over state-of-the-art GAN-based and diffusion-based BFR methods, with around 70ms consumption, 16M trainable parameters, and nearly 85% BFR-boosting. It is promising that InfoBFR will be the first plug-and-play restorer universally employed by diverse BFR models to conquer neural degradations.

cs.CV↗

arXiv2025

GAD-NR: Graph Anomaly Detection via Neighborhood Reconstruction

Graph Anomaly Detection (GAD) is a technique used to identify abnormal nodes within graphs, finding applications in network security, fraud detection, social media spam detection, and various other domains. A common method for GAD is Graph Auto-Encoders (GAEs), which encode graph data into node representations and identify anomalies by assessing the reconstruction quality of the graphs based on these representations. However, existing GAE models are primarily optimized for direct link reconstruction, resulting in nodes connected in the graph being clustered in the latent space. As a result, they excel at detecting cluster-type structural anomalies but struggle with more complex structural anomalies that do not conform to clusters. To address this limitation, we propose a novel solution called GAD-NR, a new variant of GAE that incorporates neighborhood reconstruction for graph anomaly detection. GAD-NR aims to reconstruct the entire neighborhood of a node, encompassing the local structure, self-attributes, and neighbor attributes, based on the corresponding node representation. By comparing the neighborhood reconstruction loss between anomalous nodes and normal nodes, GAD-NR can effectively detect any anomalies. Extensive experimentation conducted on six real-world datasets validates the effectiveness of GAD-NR, showcasing significant improvements (by up to 30% in AUC) over state-of-the-art competitors. The source code for GAD-NR is openly available. Importantly, the comparative analysis reveals that the existing methods perform well only in detecting one or two types of anomalies out of the three types studied. In contrast, GAD-NR excels at detecting all three types of anomalies across the datasets, demonstrating its comprehensive anomaly detection capabilities.

cs.LG↗

arXiv2025

aiXcoder-7B: A Lightweight and Effective Large Language Model for Code Processing

Large Language Models (LLMs) have been widely used in code completion, and researchers are focusing on scaling up LLMs to improve their accuracy. However, larger LLMs have lower inference efficiency, affecting developers' experience and productivity. In this paper, we propose a lightweight and effective LLM for code completion named aiXcoder-7B. Compared to existing LLMs, aiXcoder-7B achieves higher code completion accuracy while having smaller scales (i.e., 7 billion parameters). We attribute the superiority of aiXcoder-7B to three key factors: (1) Multi-objective training. We employ three training objectives, one of which is our proposed Structured Fill-In-the-Middle (SFIM). SFIM considers the syntax structures in code and effectively improves the performance of LLMs for code. (2) Diverse data sampling strategies. They consider inter-file relationships and enhance the capability of LLMs in understanding cross-file contexts. (3) Extensive high-quality data. We establish a rigorous data collection pipeline and consume a total of 1.2 trillion unique tokens for training aiXcoder-7B. This vast volume of data enables aiXcoder-7B to learn a broad distribution of code. We evaluate aiXcoder-7B in five popular code completion benchmarks and a new benchmark collected by this paper. The results show that aiXcoder-7B outperforms the latest six LLMs with similar sizes and even surpasses four larger LLMs (e.g., StarCoder2-15B and CodeLlama-34B), positioning aiXcoder-7B as a lightweight and effective LLM for academia and industry. Finally, we summarize three valuable insights for helping practitioners train the next generations of LLMs for code. aiXcoder-7B has been open-souced and gained significant attention. Until January 2025, aiXcoder-7B has received 2,226 GitHub Stars.

cs.CL↗

arXiv2025

4-bit Shampoo for Memory-Efficient Network Training

Second-order optimizers, maintaining a matrix termed a preconditioner, are superior to first-order optimizers in both theory and practice. The states forming the preconditioner and its inverse root restrict the maximum size of models trained by second-order optimizers. To address this, compressing 32-bit optimizer states to lower bitwidths has shown promise in reducing memory usage. However, current approaches only pertain to first-order optimizers. In this paper, we propose the first 4-bit second-order optimizers, exemplified by 4-bit Shampoo, maintaining performance similar to that of 32-bit ones. We show that quantizing the eigenvector matrix of the preconditioner in 4-bit Shampoo is remarkably better than quantizing the preconditioner itself both theoretically and experimentally. By rectifying the orthogonality of the quantized eigenvector matrix, we enhance the approximation of the preconditioner's eigenvector matrix, which also benefits the computation of its inverse 4-th root. Besides, we find that linear square quantization slightly outperforms dynamic tree quantization when quantizing second-order optimizer states. Evaluation on various networks for image classification and natural language modeling demonstrates that our 4-bit Shampoo achieves comparable performance to its 32-bit counterpart while being more memory-efficient.

cs.LG↗

arXiv2025

The Oscars of AI Theater: A Survey on Role-Playing with Language Models

This survey explores the burgeoning field of role-playing with language models, focusing on their development from early persona-based models to advanced character-driven simulations facilitated by Large Language Models (LLMs). Initially confined to simple persona consistency due to limited model capabilities, role-playing tasks have now expanded to embrace complex character portrayals involving character consistency, behavioral alignment, and overall attractiveness. We provide a comprehensive taxonomy of the critical components in designing these systems, including data, models and alignment, agent architecture and evaluation. This survey not only outlines the current methodologies and challenges, such as managing dynamic personal profiles and achieving high-level persona consistency but also suggests avenues for future research in improving the depth and realism of role-playing applications. The goal is to guide future research by offering a structured overview of current methodologies and identifying potential areas for improvement. Related resources and papers are available at https://github.com/nuochenpku/Awesome-Role-Play-Papers.

cs.AI↗

arXiv2025

Language-Inspired Relation Transfer for Few-shot Class-Incremental Learning

Depicting novel classes with language descriptions by observing few-shot samples is inherent in human-learning systems. This lifelong learning capability helps to distinguish new knowledge from old ones through the increase of open-world learning, namely Few-Shot Class-Incremental Learning (FSCIL). Existing works to solve this problem mainly rely on the careful tuning of visual encoders, which shows an evident trade-off between the base knowledge and incremental ones. Motivated by human learning systems, we propose a new Language-inspired Relation Transfer (LRT) paradigm to understand objects by joint visual clues and text depictions, composed of two major steps. We first transfer the pretrained text knowledge to the visual domains by proposing a graph relation transformation module and then fuse the visual and language embedding by a text-vision prototypical fusion module. Second, to mitigate the domain gap caused by visual finetuning, we propose context prompt learning for fast domain alignment and imagined contrastive learning to alleviate the insufficient text data during alignment. With collaborative learning of domain alignments and text-image transfer, our proposed LRT outperforms the state-of-the-art models by over $13\%$ and $7\%$ on the final session of mini-ImageNet and CIFAR-100 FSCIL benchmarks.

cs.CV↗