arXiv subjects

Tianlong Chen

Publications and source records attributed to Tianlong Chen.

At least 181 records · Page 10Linked to original sources

arXiv2025

GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: $3.6\%$ increase in drug response prediction correlation, $9.6\%$ improvement in single-cell drug classification AUC, and $1.1\%$ average gain in gene perturbation prediction accuracy.

cs.LG↗

arXiv2025

NeuroSymAD: A Neuro-Symbolic Framework for Interpretable Alzheimer's Disease Diagnosis

Alzheimer's disease (AD) diagnosis is complex, requiring the integration of imaging and clinical data for accurate assessment. While deep learning has shown promise in brain MRI analysis, it often functions as a black box, limiting interpretability and lacking mechanisms to effectively integrate critical clinical data such as biomarkers, medical history, and demographic information. To bridge this gap, we propose NeuroSymAD, a neuro-symbolic framework that synergizes neural networks with symbolic reasoning. A neural network percepts brain MRI scans, while a large language model (LLM) distills medical rules to guide a symbolic system in reasoning over biomarkers and medical history. This structured integration enhances both diagnostic accuracy and explainability. Experiments on the ADNI dataset demonstrate that NeuroSymAD outperforms state-of-the-art methods by up to 2.91% in accuracy and 3.43% in F1-score while providing transparent and interpretable diagnosis.

eess.IV↗

arXiv2025

QuantMoE-Bench: Examining Post-Training Quantization for Mixture-of-Experts

Mixture-of-Experts (MoE) is a promising way to scale up the learning capacity of large language models. It increases the number of parameters while keeping FLOPs nearly constant during inference through sparse activation. Yet, it still suffers from significant memory overheads due to the vast parameter size, necessitating model compression techniques. Post-training quantization offers a powerful approach for model compression. Existing methods adopt a fixed quantization precision for the entire MoE model. This rigid setup can lead to suboptimal performance, without considering the inherent sparse structure. For example, MoE's sparse routing mechanism leads to different activation patterns, where shared experts are accessed by all tokens while token-conditioned experts are selectively activated. This activation disparity suggests different quantization requirements, with consistently activated shared experts potentially needing higher precision to maintain model quality. In this paper, we study a fine-grained precision setup for MoE quantization. We explore MoE structure-aware quantization heuristics, ranging from coarse (e.g., MoE layers) to fine granularity (e.g., linear layers). Our investigations reveal critical principles, where different MoE structures require varying numbers of bits for effective quantization. Conclusions are supported by extensive benchmarking across two representative MoE models and six tasks including commonsense reasoning and natural language understanding. We further show that an MoE quantized in a fined-grained mixed precision achieved state-of-the-art 65.35% performance on average compared to the baseline 64.30% (i.e., GPTQ). Moreover, based on the findings, we introduce novel data-driven techniques for optimizing bit allocation in MoE quantization, including the outlier-aware linear layer scorer and MoE block importance predictor.

cs.LG↗

arXiv2025

BPO: Towards Balanced Preference Optimization between Knowledge Breadth and Depth in Alignment

Reinforcement Learning with Human Feedback (RLHF) is the key to the success of large language models (LLMs) in recent years. In this work, we first introduce the concepts of knowledge breadth and knowledge depth, which measure the comprehensiveness and depth of an LLM or knowledge source respectively. We reveal that the imbalance in the number of prompts and responses can lead to a potential disparity in breadth and depth learning within alignment tuning datasets by showing that even a simple uniform method for balancing the number of instructions and responses can lead to significant improvements. Building on this, we further propose Balanced Preference Optimization (BPO), designed to dynamically augment the knowledge depth of each sample. BPO is motivated by the observation that the usefulness of knowledge varies across samples, necessitating tailored learning of knowledge depth. To achieve this, we introduce gradient-based clustering, estimating the knowledge informativeness and usefulness of each augmented sample based on the model's optimization direction. Our experimental results across various benchmarks demonstrate that BPO outperforms other baseline methods in alignment tuning while maintaining training efficiency. Furthermore, we conduct a detailed analysis of each component of BPO, providing guidelines for future research in preference data optimization.

cs.CL↗

arXiv2025

MedHallu: A Comprehensive Benchmark for Detecting Medical Hallucinations in Large Language Models

Advancements in Large Language Models (LLMs) and their increasing use in medical question-answering necessitate rigorous evaluation of their reliability. A critical challenge lies in hallucination, where models generate plausible yet factually incorrect outputs. In the medical domain, this poses serious risks to patient safety and clinical decision-making. To address this, we introduce MedHallu, the first benchmark specifically designed for medical hallucination detection. MedHallu comprises 10,000 high-quality question-answer pairs derived from PubMedQA, with hallucinated answers systematically generated through a controlled pipeline. Our experiments show that state-of-the-art LLMs, including GPT-4o, Llama-3.1, and the medically fine-tuned UltraMedical, struggle with this binary hallucination detection task, with the best model achieving an F1 score as low as 0.625 for detecting "hard" category hallucinations. Using bidirectional entailment clustering, we show that harder-to-detect hallucinations are semantically closer to ground truth. Through experiments, we also show incorporating domain-specific knowledge and introducing a "not sure" category as one of the answer categories improves the precision and F1 scores by up to 38% relative to baselines.

cs.CL↗

arXiv2025

Cross-Lingual Multi-Hop Knowledge Editing

Large language models are often expected to constantly adapt to new sources of knowledge and knowledge editing techniques aim to efficiently patch the outdated model knowledge, with minimal modification. Most prior works focus on monolingual knowledge editing in English, even though new information can emerge in any language from any part of the world. We propose the Cross-Lingual Multi-Hop Knowledge Editing paradigm, for measuring and analyzing the performance of various SoTA knowledge editing techniques in a cross-lingual setup. Specifically, we create a parallel cross-lingual benchmark, CROLIN-MQUAKE for measuring the knowledge editing capabilities. Our extensive analysis over various knowledge editing techniques uncover significant gaps in performance between the cross-lingual and English-centric setting. Following this, we propose a significantly improved system for cross-lingual multi-hop knowledge editing, CLEVER-CKE. CLEVER-CKE is based on a retrieve, verify and generate knowledge editing framework, where a retriever is formulated to recall edited facts and support an LLM to adhere to knowledge edits. We develop language-aware and hard-negative based contrastive objectives for improving the cross-lingual and fine-grained fact retrieval and verification process used in this framework. Extensive experiments on three LLMs, eight languages, and two datasets show CLEVER-CKE's significant gains of up to 30% over prior methods.

cs.CL↗

arXiv2025

GroverGPT: A Large Language Model with 8 Billion Parameters for Quantum Searching

Quantum computing is an exciting non-Von Neumann paradigm, offering provable speedups over classical computing for specific problems. However, the practical limits of classical simulatability for quantum circuits remain unclear, especially with current noisy quantum devices. In this work, we explore the potential of leveraging Large Language Models (LLMs) to simulate the output of a quantum Turing machine using Grover's quantum circuits, known to provide quadratic speedups over classical counterparts. To this end, we developed GroverGPT, a specialized model based on LLaMA's 8-billion-parameter architecture, trained on over 15 trillion tokens. Unlike brute-force state-vector simulations, which demand substantial computational resources, GroverGPT employs pattern recognition to approximate quantum search algorithms without explicitly representing quantum states. Analyzing 97K quantum search instances, GroverGPT consistently outperformed OpenAI's GPT-4o (45\% accuracy), achieving nearly 100\% accuracy on 6- and 10-qubit datasets when trained on 4-qubit or larger datasets. It also demonstrated strong generalization, surpassing 95\% accuracy for systems with over 20 qubits when trained on 3- to 6-qubit data. Analysis indicates GroverGPT captures quantum features of Grover's search rather than classical patterns, supported by novel prompting strategies to enhance performance. Although accuracy declines with increasing system size, these findings offer insights into the practical boundaries of classical simulatability. This work suggests task-specific LLMs can surpass general-purpose models like GPT-4o in quantum algorithm learning and serve as powerful tools for advancing quantum research.

quant-ph↗

arXiv2025

LucidAtlas: Learning Uncertainty-Aware, Covariate-Disentangled, Individualized Atlas Representations

The goal of this work is to develop principled techniques to extract information from high dimensional data sets with complex dependencies in areas such as medicine that can provide insight into individual as well as population level variation. We develop $\texttt{LucidAtlas}$, an approach that can represent spatially varying information, and can capture the influence of covariates as well as population uncertainty. As a versatile atlas representation, $\texttt{LucidAtlas}$ offers robust capabilities for covariate interpretation, individualized prediction, population trend analysis, and uncertainty estimation, with the flexibility to incorporate prior knowledge. Additionally, we discuss the trustworthiness and potential risks of neural additive models for analyzing dependent covariates and then introduce a marginalization approach to explain the dependence of an individual predictor on the models' response (the atlas). To validate our method, we demonstrate its generalizability on two medical datasets. Our findings underscore the critical role of by-construction interpretable models in advancing scientific discovery. Our code will be publicly available upon acceptance.

cs.LG↗

arXiv2025

Layer-Level Self-Exposure and Patch: Affirmative Token Mitigation for Jailbreak Attack Defense

As large language models (LLMs) are increasingly deployed in diverse applications, including chatbot assistants and code generation, aligning their behavior with safety and ethical standards has become paramount. However, jailbreak attacks, which exploit vulnerabilities to elicit unintended or harmful outputs, threaten LLMs' safety significantly. In this paper, we introduce Layer-AdvPatcher, a novel methodology designed to defend against jailbreak attacks by utilizing an unlearning strategy to patch specific layers within LLMs through self-augmented datasets. Our insight is that certain layer(s), tend to produce affirmative tokens when faced with harmful prompts. By identifying these layers and adversarially exposing them to generate more harmful data, one can understand their inherent and diverse vulnerabilities to attacks. With these exposures, we then "unlearn" these issues, reducing the impact of affirmative tokens and hence minimizing jailbreak risks while keeping the model's responses to safe queries intact. We conduct extensive experiments on two models, four benchmark datasets, and multiple state-of-the-art jailbreak attacks to demonstrate the efficacy of our approach. Results indicate that our framework reduces the harmfulness and attack success rate of jailbreak attacks without compromising utility for benign queries compared to recent defense methods. Our code is publicly available at: https://github.com/oyy2000/LayerAdvPatcher

cs.CR↗

arXiv2025

GuideLLM: Exploring LLM-Guided Conversation with Applications in Autobiography Interviewing

Although Large Language Models (LLMs) succeed in human-guided conversations such as instruction following and question answering, the potential of LLM-guided conversations-where LLMs direct the discourse and steer the conversation's objectives-remains under-explored. In this study, we first characterize LLM-guided conversation into three fundamental components: (i) Goal Navigation; (ii) Context Management; (iii) Empathetic Engagement, and propose GuideLLM as an installation. We then implement an interviewing environment for the evaluation of LLM-guided conversation. Specifically, various topics are involved in this environment for comprehensive interviewing evaluation, resulting in around 1.4k turns of utterances, 184k tokens, and over 200 events mentioned during the interviewing for each chatbot evaluation. We compare GuideLLM with 6 state-of-the-art LLMs such as GPT-4o and Llama-3-70b-Instruct, from the perspective of interviewing quality, and autobiography generation quality. For automatic evaluation, we derive user proxies from multiple autobiographies and employ LLM-as-a-judge to score LLM behaviors. We further conduct a human-involved experiment by employing 45 human participants to chat with GuideLLM and baselines. We then collect human feedback, preferences, and ratings regarding the qualities of conversation and autobiography. Experimental results indicate that GuideLLM significantly outperforms baseline LLMs in automatic evaluation and achieves consistent leading performances in human ratings.

cs.CL↗

arXiv2025

FlowTS: Time Series Generation via Rectified Flow

Diffusion-based models have significant achievements in time series generation but suffer from inefficient computation: solving high-dimensional ODEs/SDEs via iterative numerical solvers demands hundreds to thousands of drift function evaluations per sample, incurring prohibitive costs. To resolve this, we propose FlowTS, an ODE-based model that leverages rectified flow with straight-line transport in probability space. By learning geodesic paths between distributions, FlowTS achieves computational efficiency through exact linear trajectory simulation, accelerating training and generation while improving performances. We further introduce an adaptive sampling strategy inspired by the exploration-exploitation trade-off, balancing noise adaptation and precision. Notably, FlowTS enables seamless adaptation from unconditional to conditional generation without retraining, ensuring efficient real-world deployment. Also, to enhance generation authenticity, FlowTS integrates trend and seasonality decomposition, attention registers (for global context aggregation), and Rotary Position Embedding (RoPE) (for position information). For unconditional setting, extensive experiments demonstrate that FlowTS achieves state-of-the-art performance, with context FID scores of 0.019 and 0.011 on Stock and ETTh datasets (prev. best: 0.067, 0.061). For conditional setting, we have achieved superior performance in solar forecasting (MSE 213, prev. best: 375) and MuJoCo imputation tasks (MSE 7e-5, prev. best 2.7e-4). The code is available at https://github.com/UNITES-Lab/FlowTS.

cs.LG↗

arXiv2025

G-Designer: Architecting Multi-agent Communication Topologies via Graph Neural Networks

Recent advancements in large language model (LLM)-based agents have demonstrated that collective intelligence can significantly surpass the capabilities of individual agents, primarily due to well-crafted inter-agent communication topologies. Despite the diverse and high-performing designs available, practitioners often face confusion when selecting the most effective pipeline for their specific task: \textit{Which topology is the best choice for my task, avoiding unnecessary communication token overhead while ensuring high-quality solution?} In response to this dilemma, we introduce G-Designer, an adaptive, efficient, and robust solution for multi-agent deployment, which dynamically designs task-aware, customized communication topologies. Specifically, G-Designer models the multi-agent system as a multi-agent network, leveraging a variational graph auto-encoder to encode both the nodes (agents) and a task-specific virtual node, and decodes a task-adaptive and high-performing communication topology. Extensive experiments on six benchmarks showcase that G-Designer is: \textbf{(1) high-performing}, achieving superior results on MMLU with accuracy at $84.50\%$ and on HumanEval with pass@1 at $89.90\%$; \textbf{(2) task-adaptive}, architecting communication protocols tailored to task difficulty, reducing token consumption by up to $95.33\%$ on HumanEval; and \textbf{(3) adversarially robust}, defending against agent adversarial attacks with merely $0.3\%$ accuracy drop.

cs.MA↗

arXiv2025

BrainMAP: Learning Multiple Activation Pathways in Brain Networks

Functional Magnetic Resonance Image (fMRI) is commonly employed to study human brain activity, since it offers insight into the relationship between functional fluctuations and human behavior. To enhance analysis and comprehension of brain activity, Graph Neural Networks (GNNs) have been widely applied to the analysis of functional connectivities (FC) derived from fMRI data, due to their ability to capture the synergistic interactions among brain regions. However, in the human brain, performing complex tasks typically involves the activation of certain pathways, which could be represented as paths across graphs. As such, conventional GNNs struggle to learn from these pathways due to the long-range dependencies of multiple pathways. To address these challenges, we introduce a novel framework BrainMAP to learn Multiple Activation Pathways in Brain networks. BrainMAP leverages sequential models to identify long-range correlations among sequentialized brain regions and incorporates an aggregation module based on Mixture of Experts (MoE) to learn from multiple pathways. Our comprehensive experiments highlight BrainMAP's superior performance. Furthermore, our framework enables explanatory analyses of crucial brain regions involved in tasks. Our code is provided at https://github.com/LzyFischer/Graph-Mamba.

cs.AI↗

arXiv2025

Continually Evolved Multimodal Foundation Models for Cancer Prognosis

Cancer prognosis is a critical task that involves predicting patient outcomes and survival rates. To enhance prediction accuracy, previous studies have integrated diverse data modalities, such as clinical notes, medical images, and genomic data, leveraging their complementary information. However, existing approaches face two major limitations. First, they struggle to incorporate newly arrived data with varying distributions into training, such as patient records from different hospitals, thus rendering sub-optimal generalizability and limited utility in real-world applications. Second, most multimodal integration methods rely on simplistic concatenation or task-specific pipelines, which fail to capture the complex interdependencies across modalities. To address these, we propose a continually evolving multi-modal foundation model. Extensive experiments on the TCGA dataset demonstrate the effectiveness of our approach, highlighting its potential to advance cancer prognosis by enabling robust and adaptive multimodal integration.

cs.LG↗

arXiv2025

Accessing the topological properties of human brain functional sub-circuits in Echo State Networks

Recent years have witnessed an emerging trend in neuromorphic computing that centers around the use of brain connectomics as a blueprint for artificial neural networks. Connectomics-based neuromorphic computing has primarily focused on embedding human brain large-scale structural connectomes (SCs), as estimated from diffusion Magnetic Resonance Imaging (dMRI) modality, to echo-state networks (ESNs). A critical step in ESN embedding requires pre-determined read-in and read-out layers constructed by the induced subgraphs of the embedded reservoir. As \textit{a priori} set of functional sub-circuits are derived from functional MRI (fMRI) modality, it is unknown, till this point, whether the embedding of fMRI-induced sub-circuits/networks onto SCs is well justified from the neuro-physiological perspective and ESN performance across a variety of tasks. This paper proposes a pipeline to implement and evaluate ESNs with various embedded topologies and processing/memorization tasks. To this end, we showed that different performance optimums highly depend on the neuro-physiological characteristics of these pre-determined fMRI-induced sub-circuits. In general, fMRI-induced sub-circuit-embedded ESN outperforms simple bipartite and various null models with feed-forward properties commonly seen in MLP for different tasks and reservoir criticality conditions. We provided a thorough analysis of the topological properties of pre-determined fMRI-induced sub-circuits and highlighted their graph-theoretical properties that play significant roles in determining ESN performance.

q-bio.NC↗

arXiv2024

Aurora-M: Open Source Continual Pre-training for Multilingual Language and Code

Pretrained language models are an integral part of AI applications, but their high computational cost for training limits accessibility. Initiatives such as Bloom and StarCoder aim to democratize access to pretrained models for collaborative community development. Despite these efforts, such models encounter challenges such as limited multilingual capabilities, risks of catastrophic forgetting during continual pretraining, and the high costs of training models from scratch, alongside the need to align with AI safety standards and regulatory frameworks. This paper presents Aurora-M, a 15B parameter multilingual open-source model trained on English, Finnish, Hindi, Japanese, Vietnamese, and code. Continually pretrained from StarCoderPlus on 435B additional tokens, Aurora-M surpasses 2T tokens in total training token count. It is the first open-source multilingual model fine-tuned on human-reviewed safety instructions, thus aligning its development not only with conventional red-teaming considerations, but also with the specific concerns articulated in the Biden-Harris Executive Order on the Safe, Secure, and Trustworthy Development and Use of Artificial Intelligence. We evaluate Aurora-M across a wide range of tasks and languages, showcasing its robustness against catastrophic forgetting and its superior performance in multilingual settings, particularly in safety evaluations. We open-source Aurora-M and its variants to encourage responsible open-source development of large language models at https://huggingface.co/aurora-m.

cs.CL↗

arXiv2024

Political-LLM: Large Language Models in Political Science

In recent years, large language models (LLMs) have been widely adopted in political science tasks such as election prediction, sentiment analysis, policy impact assessment, and misinformation detection. Meanwhile, the need to systematically understand how LLMs can further revolutionize the field also becomes urgent. In this work, we--a multidisciplinary team of researchers spanning computer science and political science--present the first principled framework termed Political-LLM to advance the comprehensive understanding of integrating LLMs into computational political science. Specifically, we first introduce a fundamental taxonomy classifying the existing explorations into two perspectives: political science and computational methodologies. In particular, from the political science perspective, we highlight the role of LLMs in automating predictive and generative tasks, simulating behavior dynamics, and improving causal inference through tools like counterfactual generation; from a computational perspective, we introduce advancements in data preparation, fine-tuning, and evaluation methods for LLMs that are tailored to political contexts. We identify key challenges and future directions, emphasizing the development of domain-specific datasets, addressing issues of bias and fairness, incorporating human expertise, and redefining evaluation criteria to align with the unique requirements of computational political science. Political-LLM seeks to serve as a guidebook for researchers to foster an informed, ethical, and impactful use of Artificial Intelligence in political science. Our online resource is available at: http://political-llm.org/.

cs.CL↗

arXiv2024

Model-GLUE: Democratized LLM Scaling for A Large Model Zoo in the Wild

As Large Language Models (LLMs) excel across tasks and specialized domains, scaling LLMs based on existing models has garnered significant attention, which faces the challenge of decreasing performance when combining disparate models. Various techniques have been proposed for the aggregation of pre-trained LLMs, including model merging, Mixture-of-Experts, and stacking. Despite their merits, a comprehensive comparison and synergistic application of them to a diverse model zoo is yet to be adequately addressed. In light of this research gap, this paper introduces Model-GLUE, a holistic LLM scaling guideline. First, our work starts with a benchmarking of existing LLM scaling techniques, especially selective merging, and variants of mixture. Utilizing the insights from the benchmark results, we formulate an optimal strategy for the selection and aggregation of a heterogeneous model zoo characterizing different architectures and initialization.Our methodology involves the clustering of mergeable models and optimal merging strategy selection, and the integration of clusters through a model mixture. Finally, evidenced by our experiments on a diverse Llama-2-based model zoo, Model-GLUE shows an average performance enhancement of 5.61%, achieved without additional training. Codes are available at: https://github.com/Model-GLUE/Model-GLUE.

cs.LG↗