arXiv subjects

Tong Chen

Publications and source records attributed to Tong Chen.

At least 91 records · Page 5Linked to original sources

arXiv2025

The Multivariate SEM-PGS Model: Using Polygenic Scores to Investigate Cross-Trait Genetic Nurture and Assortative Mating

Genetic nurture effects and assortative mating (AM) occur across many human behaviors and can bias estimates from traditional genetic models. These influences are typically studied univariately, within the same trait. However, estimation of cross-trait genetic nurture effects and cross-trait AM remains underexplored due to the absence of suitable approaches. To address this, we developed a multivariate extension of the SEM-PGS model for datasets with genotyped and phenotyped parents and offspring, enabling joint estimation of within-trait and cross-trait genetic and environmental influences. By integrating haplotypic polygenic scores (PGS) into a structural equation modeling framework, the model simultaneously estimates same-trait and cross-trait direct effects, genetic nurture, vertical transmission, and assortative mating. We also provide the first formal description of how copaths can be used to model multivariate assortative mating and derive the corresponding parameter expectations in matrix form. Forward-time Monte Carlo simulations under varying conditions of r^2_PGS and N_trio demonstrate that the model yields unbiased estimates of both within-trait and cross-trait effects when assumptions are met. The precision of estimates was adequate with large sample sizes (N_trio > 16k) and improved as PGS predictive power increased. In addition, our simulation results show that failing to model cross-trait effects biases within-trait estimates, underscoring the importance of incorporating cross-trait effects. The multivariate SEM-PGS model offers a powerful and flexible tool for disentangling gene-environment interplay and advancing the understanding of familial influences on human traits.

q-bio.QM↗

arXiv2025

AReUReDi: Annealed Rectified Updates for Refining Discrete Flows with Multi-Objective Guidance

Designing sequences that satisfy multiple, often conflicting, objectives is a central challenge in therapeutic and biomolecular engineering. Existing generative frameworks largely operate in continuous spaces with single-objective guidance, while discrete approaches lack guarantees for multi-objective Pareto optimality. We introduce AReUReDi (Annealed Rectified Updates for Refining Discrete Flows), a discrete optimization algorithm with theoretical guarantees of convergence to the Pareto front. Building on Rectified Discrete Flows (ReDi), AReUReDi combines Tchebycheff scalarization, locally balanced proposals, and annealed Metropolis-Hastings updates to bias sampling toward Pareto-optimal states while preserving distributional invariance. Applied to peptide and SMILES sequence design, AReUReDi simultaneously optimizes up to five therapeutic properties (including affinity, solubility, hemolysis, half-life, and non-fouling) and outperforms both evolutionary and diffusion-based baselines. These results establish AReUReDi as a powerful, sequence-based framework for multi-property biomolecule generation.

cs.LG↗

arXiv2025

MedFact: A Large-scale Chinese Dataset for Evidence-based Medical Fact-checking of LLM Responses

Medical fact-checking has become increasingly critical as more individuals seek medical information online. However, existing datasets predominantly focus on human-generated content, leaving the verification of content generated by large language models (LLMs) relatively unexplored. To address this gap, we introduce MedFact, the first evidence-based Chinese medical fact-checking dataset of LLM-generated medical content. It consists of 1,321 questions and 7,409 claims, mirroring the complexities of real-world medical scenarios. We conduct comprehensive experiments in both in-context learning (ICL) and fine-tuning settings, showcasing the capability and challenges of current LLMs on this task, accompanied by an in-depth error analysis to point out key directions for future research. Our dataset is publicly available at https://github.com/AshleyChenNLP/MedFact.

cs.CL↗

arXiv2025

Trading-R1: Financial Trading with LLM Reasoning via Reinforcement Learning

Developing professional, structured reasoning on par with human financial analysts and traders remains a central challenge in AI for finance, where markets demand interpretability and trust. Traditional time-series models lack explainability, while LLMs face challenges in turning natural-language analysis into disciplined, executable trades. Although reasoning LLMs have advanced in step-by-step planning and verification, their application to risk-sensitive financial decisions is underexplored. We present Trading-R1, a financially-aware model that incorporates strategic thinking and planning for comprehensive thesis composition, facts-grounded analysis, and volatility-adjusted decision making. Trading-R1 aligns reasoning with trading principles through supervised fine-tuning and reinforcement learning with a three-stage easy-to-hard curriculum. Training uses Tauric-TR1-DB, a 100k-sample corpus spanning 18 months, 14 equities, and five heterogeneous financial data sources. Evaluated on six major equities and ETFs, Trading-R1 demonstrates improved risk-adjusted returns and lower drawdowns compared to both open-source and proprietary instruction-following models as well as reasoning models. The system generates structured, evidence-based investment theses that support disciplined and interpretable trading decisions. Trading-R1 Terminal will be released at https://github.com/TauricResearch/Trading-R1.

q-fin.TR↗

arXiv2025

Is Adversarial Training with Compressed Datasets Effective?

Dataset Condensation (DC) refers to the recent class of dataset compression methods that generate a smaller, synthetic, dataset from a larger dataset. This synthetic dataset aims to retain the essential information of the original dataset, enabling models trained on it to achieve performance levels comparable to those trained on the full dataset. Most current DC methods have mainly concerned with achieving high test performance with limited data budget, and have not directly addressed the question of adversarial robustness. In this work, we investigate the impact of adversarial robustness on models trained with compressed datasets. We show that the compressed datasets obtained from DC methods are not effective in transferring adversarial robustness to models. As a solution to improve dataset compression efficiency and adversarial robustness simultaneously, we present a robustness-aware dataset compression method based on finding the Minimal Finite Covering (MFC) of the dataset. The proposed method is (1) provably robust by minimizing the generalized adversarial loss, (2) more effective than DC methods when applying adversarial training over MFC, (3) obtained by a one-time computation and is applicable for any model.

cs.LG↗

arXiv2025

Beyond Sequential Reranking: Reranker-Guided Search Improves Reasoning Intensive Retrieval

The widely used retrieve-and-rerank pipeline faces two critical limitations: they are constrained by the initial retrieval quality of the top-k documents, and the growing computational demands of LLM-based rerankers restrict the number of documents that can be effectively processed. We introduce Reranker-Guided-Search (RGS), a novel approach that bypasses these limitations by directly retrieving documents according to reranker preferences rather than following the traditional sequential reranking method. Our method uses a greedy search on proximity graphs generated by approximate nearest neighbor algorithms, strategically prioritizing promising documents for reranking based on document similarity. Experimental results demonstrate substantial performance improvements across multiple benchmarks: 3.5 points on BRIGHT, 2.9 on FollowIR, and 5.1 on M-BEIR, all within a constrained reranker budget of 100 documents. Our analysis suggests that, given a fixed pair of embedding and reranker models, strategically selecting documents to rerank can significantly improve retrieval accuracy under limited reranker budget.

cs.IR↗

arXiv2025

The Ramon Llull's Thinking Machine for Automated Ideation

This paper revisits Ramon Llull's Ars combinatoria - a medieval framework for generating knowledge through symbolic recombination - as a conceptual foundation for building a modern Llull's thinking machine for research ideation. Our approach defines three compositional axes: Theme (e.g., efficiency, adaptivity), Domain (e.g., question answering, machine translation), and Method (e.g., adversarial training, linear attention). These elements represent high-level abstractions common in scientific work - motivations, problem settings, and technical approaches - and serve as building blocks for LLM-driven exploration. We mine elements from human experts or conference papers and show that prompting LLMs with curated combinations produces research ideas that are diverse, relevant, and grounded in current literature. This modern thinking machine offers a lightweight, interpretable tool for augmenting scientific creativity and suggests a path toward collaborative ideation between humans and AI.

cs.AI↗

arXiv2025

Towards Propagation-aware Representation Learning for Supervised Social Media Graph Analytics

Social media platforms generate vast, complex graph-structured data, facilitating diverse tasks such as rumor detection, bot identification, and influence modeling. Real-world applications like public opinion monitoring and stock trading -- which have a strong attachment to social media -- demand models that are performant across diverse tasks and datasets. However, most existing solutions are purely data-driven, exhibiting vulnerability to the inherent noise within social media data. Moreover, the reliance on task-specific model design challenges efficient reuse of the same model architecture on different tasks, incurring repetitive engineering efforts. To address these challenges in social media graph analytics, we propose a general representation learning framework that integrates a dual-encoder structure with a kinetic-guided propagation module. In addition to jointly modeling structural and contextual information with two encoders, our framework innovatively captures the information propagation dynamics within social media graphs by integrating principled kinetic knowledge. By deriving a propagation-aware encoder and corresponding optimization objective from a Markov chain-based transmission model, the representation learning pipeline receives a boost in its robustness to noisy data and versatility in diverse tasks. Extensive experiments verify that our approach achieves state-of-the-art performance with a unified architecture on a variety of social media graph mining tasks spanning graph classification, node classification, and link prediction. Besides, our solution exhibits strong zero-shot and few-shot transferability across datasets, demonstrating practicality when handling data-scarce tasks.

cs.SI↗

arXiv2025

Cloud-Device Collaborative Agents for Sequential Recommendation

Recent advances in large language models (LLMs) have enabled agent-based recommendation systems with strong semantic understanding and flexible reasoning capabilities. While LLM-based agents deployed in the cloud offer powerful personalization, they often suffer from privacy concerns, limited access to real-time signals, and scalability bottlenecks. Conversely, on-device agents ensure privacy and responsiveness but lack the computational power for global modeling and large-scale retrieval. To bridge these complementary limitations, we propose CDA4Rec, a novel Cloud-Device collaborative framework for sequential Recommendation, powered by dual agents: a cloud-side LLM and a device-side small language model (SLM). CDA4Rec tackles the core challenge of cloud-device coordination by decomposing the recommendation task into modular sub-tasks including semantic modeling, candidate retrieval, structured user modeling, and final ranking, which are allocated to cloud or device based on computational demands and privacy sensitivity. A strategy planning mechanism leverages the cloud agent's reasoning ability to generate personalized execution plans, enabling context-aware task assignment and partial parallel execution across agents. This design ensures real-time responsiveness, improved efficiency, and fine-grained personalization, even under diverse user states and behavioral sparsity. Extensive experiments across multiple real-world datasets demonstrate that CDA4Rec consistently outperforms competitive baselines in both accuracy and efficiency, validating its effectiveness in heterogeneous and resource-constrained environments.

cs.IR↗

arXiv2025

Bridging Brain Connectomes and Clinical Reports for Early Alzheimer's Disease Diagnosis

Integrating brain imaging data with clinical reports offers a valuable opportunity to leverage complementary multimodal information for more effective and timely diagnosis in practical clinical settings. This approach has gained significant attention in brain disorder research, yet a key challenge remains: how to effectively link objective imaging data with subjective text-based reports, such as doctors' notes. In this work, we propose a novel framework that aligns brain connectomes with clinical reports in a shared cross-modal latent space at both the subject and connectome levels, thereby enhancing representation learning. The key innovation of our approach is that we treat brain subnetworks as tokens of imaging data, rather than raw image patches, to align with word tokens in clinical reports. This enables a more efficient identification of system-level associations between neuroimaging findings and clinical observations, which is critical since brain disorders often manifest as network-level abnormalities rather than isolated regional alterations. We applied our method to mild cognitive impairment (MCI) using the ADNI dataset. Our approach not only achieves state-of-the-art predictive performance but also identifies clinically meaningful connectome-text pairs, offering new insights into the early mechanisms of Alzheimer's disease and supporting the development of clinically useful multimodal biomarkers.

cs.CV↗

arXiv2025

On-Device Recommender Systems: A Comprehensive Survey

Recommender systems have been widely deployed in various real-world applications to help users identify content of interest from massive amounts of information. Traditional recommender systems work by collecting user-item interaction data in a cloud-based data center and training a centralized model to perform the recommendation service. However, such cloud-based recommender systems (CloudRSs) inevitably suffer from excessive resource consumption, response latency, as well as privacy and security risks concerning both data and models. Recently, driven by the advances in storage, communication, and computation capabilities of edge devices, there has been a shift of focus from CloudRSs to on-device recommender systems (DeviceRSs), which leverage the capabilities of edge devices to minimize centralized data storage requirements, reduce the response latency caused by communication overheads, and enhance user privacy and security by localizing data processing and model training. Despite the rapid rise of DeviceRSs, there is a clear absence of timely literature reviews that systematically introduce, categorize and contrast these methods. To bridge this gap, we aim to provide a comprehensive survey of DeviceRSs, covering three main aspects: (1) the deployment and inference of DeviceRSs (2) the training and update of DeviceRSs (3) the security and privacy of DeviceRSs. Furthermore, we provide a fine-grained and systematic taxonomy of the methods involved in each aspect, followed by a discussion regarding challenges and future research directions. This is the first comprehensive survey on DeviceRSs that covers a spectrum of tasks to fit various needs. We believe this survey will help readers effectively grasp the current research status in this field, equip them with relevant technical foundations, and stimulate new research ideas for developing DeviceRSs.

cs.IR↗

arXiv2025

Harnessing Large Language Models for Group POI Recommendations

The rapid proliferation of Location-Based Social Networks (LBSNs) has underscored the importance of Point-of-Interest (POI) recommendation systems in enhancing user experiences. While individual POI recommendation methods leverage users' check-in histories to provide personalized suggestions, they struggle to address scenarios requiring group decision-making. Group POI recommendation systems aim to satisfy the collective preferences of multiple users, but existing approaches face two major challenges: diverse group preferences and extreme data sparsity in group check-in data. To overcome these challenges, we propose LLMGPR, a novel framework that leverages large language models (LLMs) for group POI recommendations. LLMGPR introduces semantic-enhanced POI tokens and incorporates rich contextual information to model the diverse and complex dynamics of group decision-making. To further enhance its capabilities, we developed a sequencing adapter using Quantized Low-Rank Adaptation (QLoRA), which aligns LLMs with group POI recommendation tasks. To address the issue of sparse group check-in data, LLMGPR employs an aggregation adapter that integrates individual representations into meaningful group representations. Additionally, a self-supervised learning (SSL) task is designed to predict the purposes of check-in sequences (e.g., business trips and family vacations), thereby enriching group representations with deeper semantic insights. Extensive experiments demonstrate the effectiveness of LLMGPR, showcasing its ability to significantly enhance the accuracy and robustness of group POI recommendations.

cs.IR↗

arXiv2025

Controllable and Stealthy Shilling Attacks via Dispersive Latent Diffusion

Recommender systems (RSs) are now fundamental to various online platforms, but their dependence on user-contributed data leaves them vulnerable to shilling attacks that can manipulate item rankings by injecting fake users. Although widely studied, most existing attack models fail to meet two critical objectives simultaneously: achieving strong adversarial promotion of target items while maintaining realistic behavior to evade detection. As a result, the true severity of shilling threats that manage to reconcile the two objectives remains underappreciated. To expose this overlooked vulnerability, we present DLDA, a diffusion-based attack framework that can generate highly effective yet indistinguishable fake users by enabling fine-grained control over target promotion. Specifically, DLDA operates in a pre-aligned collaborative embedding space, where it employs a conditional latent diffusion process to iteratively synthesize fake user profiles with precise target item control. To evade detection, DLDA introduces a dispersive regularization mechanism that promotes variability and realism in generated behavioral patterns. Extensive experiments on three real-world datasets and five popular RS models demonstrate that, compared to prior attacks, DLDA consistently achieves stronger item promotion while remaining harder to detect. These results highlight that modern RSs are more vulnerable than previously recognized, underscoring the urgent need for more robust defenses.

cs.LG↗

arXiv2025

Thinker-DDM: Modeling Deliberation for Machine Translation with a Drift-Diffusion Process

Large language models (LLMs) have demonstrated promising potential in various downstream tasks, including machine translation. However, prior work on LLM-based machine translation has mainly focused on better utilizing training data, demonstrations, or pre-defined and universal knowledge to improve performance, with a lack of consideration of decision-making like human translators. In this paper, we incorporate Thinker with the Drift-Diffusion Model (Thinker-DDM) to address this issue. We then redefine the Drift-Diffusion process to emulate human translators' dynamic decision-making under constrained resources. We conduct extensive experiments under the high-resource, low-resource, and commonsense translation settings using the WMT22 and CommonMT datasets, in which Thinker-DDM outperforms baselines in the first two scenarios. We also perform additional analysis and evaluation on commonsense translation to illustrate the high effectiveness and efficacy of the proposed method.

cs.CL↗

arXiv2025

Watermarking Large Language Model-based Time Series Forecasting

Large Language Model-based Time Series Forecasting (LLMTS) has shown remarkable promise in handling complex and diverse temporal data, representing a significant step toward foundation models for time series analysis. However, this emerging paradigm introduces two critical challenges. First, the substantial commercial potential and resource-intensive development raise urgent concerns about intellectual property (IP) protection. Second, their powerful time series forecasting capabilities may be misused to produce misleading or fabricated deepfake time series data. To address these concerns, we explore watermarking the outputs of LLMTS models, that is, embedding imperceptible signals into the generated time series data that remain detectable by specialized algorithms. We propose a novel post-hoc watermarking framework, Waltz, which is broadly compatible with existing LLMTS models. Waltz is inspired by the empirical observation that time series patch embeddings are rarely aligned with a specific set of LLM tokens, which we term ``cold tokens''. Leveraging this insight, Waltz embeds watermarks by rewiring the similarity statistics between patch embeddings and cold token embeddings, and detects watermarks using similarity z-scores. To minimize potential side effects, we introduce a similarity-based embedding position identification strategy and employ projected gradient descent to constrain the watermark noise within a defined boundary. Extensive experiments using two popular LLMTS models across seven benchmark datasets demonstrate that Waltz achieves high watermark detection accuracy with minimal impact on the quality of the generated time series.

cs.IR↗

arXiv2025

Epidemiology-informed Network for Robust Rumor Detection

The rapid spread of rumors on social media has posed significant challenges to maintaining public trust and information integrity. Since an information cascade process is essentially a propagation tree, recent rumor detection models leverage graph neural networks to additionally capture information propagation patterns, thus outperforming text-only solutions. Given the variations in topics and social impact of the root node, different source information naturally has distinct outreach capabilities, resulting in different heights of propagation trees. This variation, however, impedes the data-driven design of existing graph-based rumor detectors. Given a shallow propagation tree with limited interactions, it is unlikely for graph-based approaches to capture sufficient cascading patterns, questioning their ability to handle less popular news or early detection needs. In contrast, a deep propagation tree is prone to noisy user responses, and this can in turn obfuscate the predictions. In this paper, we propose a novel Epidemiology-informed Network (EIN) that integrates epidemiological knowledge to enhance performance by overcoming data-driven methods sensitivity to data quality. Meanwhile, to adapt epidemiology theory to rumor detection, it is expected that each users stance toward the source information will be annotated. To bypass the costly and time-consuming human labeling process, we take advantage of large language models to generate stance labels, facilitating optimization objectives for learning epidemiology-informed representations. Our experimental results demonstrate that the proposed EIN not only outperforms state-of-the-art methods on real-world datasets but also exhibits enhanced robustness across varying tree depths.

cs.SI↗

arXiv2025

ParaPO: Aligning Language Models to Reduce Verbatim Reproduction of Pre-training Data

Language models (LMs) can memorize and reproduce segments from their pretraining data verbatim even in non-adversarial settings, raising concerns about copyright, plagiarism, privacy, and creativity. We introduce Paraphrase Preference Optimization (ParaPO), a post-training method that fine-tunes LMs to reduce unintentional regurgitation while preserving their overall utility. ParaPO trains LMs to prefer paraphrased versions of memorized segments over the original verbatim content from the pretraining data. To maintain the ability to recall famous quotations when appropriate, we develop a variant of ParaPO that uses system prompts to control regurgitation behavior. In our evaluation on Llama3.1-8B, ParaPO consistently reduces regurgitation across all tested datasets (e.g., reducing the regurgitation metric from 17.3 to 12.9 in creative writing), whereas unlearning methods used in prior work to mitigate regurgitation are less effective outside their targeted unlearned domain (from 17.3 to 16.9). When applied to the instruction-tuned Tulu3-8B model, ParaPO with system prompting successfully preserves famous quotation recall while reducing unintentional regurgitation (from 8.7 to 6.3 in creative writing) when prompted not to regurgitate. In contrast, without ParaPO tuning, prompting the model not to regurgitate produces only a marginal reduction (8.7 to 8.4).

cs.CL↗

arXiv2025

Quenched Disorder in the Triangular Lattice Antiferromagnet YbZn$_2$GaO$_5$

We investigate the crystal electric field (CEF) excitations of Yb$^{3+}$ ions in powder samples of the triangular-lattice rare-earth-based antiferromagnet YbZn$_2$GaO$_5$ using inelastic neutron scattering (INS). Three CEF excitations from the ground-state Kramers doublet were observed, each exhibiting significant broadening beyond instrumental resolution. Combining temperature-dependent INS and neutron powder diffraction, we identify a significant static contribution to this broadening and attribute it to heterogeneous coordination of Yb$^{3+}$ ions due to Ga$^{3+}$/Zn$^{2+}$ site mixing. Rietveld refinement of neutron powder diffraction indicates that 35% of Ga occupies the Zn site and 60% of Zn occupies the Ga site. We show with a point charge model for the CEF Hamiltonian that heterogeneous coordination of Yb$^{3+}$ ions leads to broadened CEF peaks. First-principles calculations demonstrate that the random Ga$^{3+}$/Zn$^{2+}$ distribution can produce the distortions of the YbO$_6$ octahedra observed from neutron diffraction. Because the documented heterogeneity will extend to exchange interactions, our results suggest that disorder is a significant factor in the unusual magnetism previously reported in YbZn$_2$GaO$_5$, including broad low-energy magnetic excitations and the absence of magnetic ordering down to 0.3K.

cond-mat.str-el↗