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Truong-Son Hy

Publications and source records attributed to Truong-Son Hy.

At least 19 recordsLinked to original sources
arXiv2026

Q-BIOLAT: Binary Latent Protein Fitness Landscapes for QUBO-Based Optimization

Protein fitness optimization is a discrete search problem, and the representation used for prediction also determines the neighborhood graph traversed by an optimizer. We introduce Q-BioLat, a framework that maps pretrained protein-language-model embeddings to compact binary codes and fits a quadratic unconstrained binary optimization (QUBO) surrogate with unary and pairwise latent interactions. Our central contribution is an optimization-aware view of representation: binary encodings that are similar in pointwise predictive accuracy can induce different Hamming neighborhoods, local optima, and search trajectories. We formalize when a recoding is only a Hamming-isometric reparameterization and give a constructive example showing that exact pointwise agreement does not imply optimization equivalence. We study experimentally measured GFP and AAV fitness landscapes from ProteinGym. The internal QUBO surrogate is evaluated against labels withheld from QUBO fitting. A conservative retrieval analysis maps optimized codes to measured variants and reports their experimental fitness, while neural decoding of potentially unmeasured sequences is evaluated separately with an experiment-trained sequence surrogate and is interpreted only as model-based candidate prioritization. Across the reported comparisons, PCA followed by per-coordinate median thresholding yields a more balanced and decodable binary space than the post-hoc-zero-threshold AE/VAE baselines, despite the latter's low continuous reconstruction error. In the measured-library retrieval analysis, simulated annealing, genetic algorithms, and greedy hill climbing frequently return high-percentile variants; decoded candidates are reported separately using surrogate-predicted scores.

cs.LG↗
arXiv2026

Evaluating Agentic Bioinformatics through Function, Evidence, and Validation

Large language model agents increasingly plan, execute, and interpret biological analyses, yet fluent responses, successful tool calls, and benchmark performance alone do not establish scientific credibility. Existing reviews primarily organize biological agents by application, architecture, and agentic capability, but do not jointly operationalize the accountability of agent-generated workflows. We address this gap by treating the inspectable workflow trajectory, rather than architecture or final output alone, as the primary unit of analysis. We introduce the Function--Evidence--Validation (FEV) framework, which separates demonstrated workflow operations, traceable support for actions and claims, and use-case-specific validation. Using FEV, we map 109 agentic or agent-adjacent systems and 28 benchmark or evaluation resources, representing 128 unique publications across genomics, single-cell and spatial omics, protein science, drug discovery, computational pathology, and general bioinformatics automation. Across domains, planning and tool-mediated execution have advanced more rapidly than replayability, provenance, robust scientific assessment, external validation, and prospective empirical testing. We therefore argue that agentic bioinformatics should be assessed through workflow correctness rather than final-answer correctness alone. FEV provides a practical basis for comparing systems and designing transparent, auditable, and scientifically accountable bioinformatics workflows.

cs.AI↗
arXiv2026

PRIME: Protein Representation via Physics-Informed Multiscale Equivariant Hierarchies

Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology. However, existing protein representation learning methods typically operate at a single structural level or treat different sources of structural information as parallel modalities, without explicitly modeling their hierarchical relationships. We introduce PRIME (Protein Representation via Physics-Informed Multiscale Equivariant Hierarchies), a unified framework that models proteins as a nested family of five physically grounded structural graphs spanning surface, atomic, residue, secondary-structure, and protein levels. Adjacent levels are connected through deterministic, physics-informed assignment operators, enabling bidirectional information exchange via bottom-up aggregation and top-down contextual refinement. Experiments on standard protein representation learning benchmarks demonstrate strong and competitive performance across diverse tasks, with particularly notable gains on the Fold Classification benchmark, where PRIME outperforms the strongest geometric GNN baseline by margins of 13.80 and 18.30 points on the harder Superfamily and Fold splits, and achieves a state-of-the-art accuracy of 84.10\% on Reaction Class prediction, surpassing all baseline methods, including ESM. Ablation studies confirm that each structural level contributes complementary and non-redundant information, and adaptive cross-attention analysis reveals that PRIME autonomously identifies the most task-relevant structural resolutions at prediction time. Our source code is publicly available at https://github.com/HySonLab/PRIME

cs.LG↗
arXiv2026

A Wearable Device Dataset for Mental Health Assessment Using Laser Doppler Flowmetry and Fluorescence Spectroscopy Sensors

Mental health problems such as stress, anxiety, and depression affect millions of people worldwide. These conditions are usually assessed using questionnaires, which rely on how people describe their own feelings. In this study, we explore whether a wearable device can help measure mental health using physical signals from the body. The device records small changes in blood flow and tissue activity from the fingertip. We collected data from 132 adults across 19 countries and compared these signals with mental health questionnaire results. We found that patterns in blood flow and tissue activity are linked to stress-related symptoms. This approach may help develop new tools for simple, non-invasive mental health monitoring in everyday life. Code and datasets are publicly available: https://github.com/leduckhai/Wearable_LDF-FS

cs.LG↗
arXiv2026

DiFlow-TTS: Compact and Low-Latency Zero-Shot Text-to-Speech with Discrete Flow Matching

Zero-shot text-to-speech (TTS) has made significant progress in replicating unseen voices, yet balancing generation quality and inference efficiency remains challenging. Autoregressive models suffer from high latency, while diffusion-based approaches are constrained by training-time configurations. Moreover, most flow-based methods operate in continuous space, which introduces optimization challenges because continuous token spaces are inherently more complex than discrete ones. To address these limitations, we propose DiFlow-TTS, a novel zero-shot TTS framework based on discrete flow matching. The model consists of a deterministic Phoneme-Content Mapper for linguistic modeling and a Factorized Discrete Flow Denoiser that simultaneously generates prosody and acoustic token streams. Experimental results demonstrate the effectiveness of our approach across multiple evaluation metrics.

cs.SD↗
arXiv2026

From SQL to Knowledge Graphs: An LLM-Driven Multi-Agent Approach with Data Schema Improvement

RDBMS (Relational Database Management System) databases face several limitations, including slow execution with multi-hop queries and a lack of explainability by graphical interpretations. In contrast, Graph database offers a more intuitive and efficient data schema that performs faster execution on large datasets. Most existing RDBMS conversion pipelines focus on running traditional loading commands and relying on Cypher queries. However, the efficiency of using an LLM to generate an effective graph data schema, significantly reducing the ambiguity of the graph database, remains underexplored in the current research literature. This paper presents a novel algorithm that bridges RDBMS and graph database by using a novel LLM-powered ETL agent to standardize table and column names before saving them to the Data Mart. A Multi-Agent System generates a looping discussion between ETL, Analyzer, and Graph agents to optimize the final design through an iterative process of suggesting and scoring the graph database schema. We ensure that the final graph database meets three criteria before being accepted for data conversion: Accuracy, Groundedness, and Faithfulness. This system demonstrates an effective pipeline to automatically convert a tabular database into a graph database through a comprehensive end-to-end process. Our study highlights notable efficiency in using the converted graph database, which is measured on 1,081 samples of the BFSI dataset across three levels of complexity (easy, medium, and hard). Specifically, CypherAgent achieves an 85.6% accuracy for Q&A tasks using a Graph database, which is 12.12% higher than the accuracy achieved by an SQLAgent on the RDBMS database type PostgreSQL, for all queries. Additionally, the Graph database demonstrates faster performance, reducing latency by approximately 3 times.

cs.DB↗
arXiv2026

A Hybrid Matheuristic Framework for the Chinese Postman Problem with Load-Dependent Costs

The Chinese Postman Problem with load-dependent costs (CPP-LC) arises in real-world logistics and transportation systems where travel costs depend on vehicle load and energy consumption. In this work, we propose a hybrid optimization framework that integrates metaheuristic search with mathematical programming to efficiently solve CPP-LC. The proposed method combines local search procedures with reduced mixed-integer linear programming (MILP) models to balance exploration and intensification. In addition, we develop an Ant Colony Optimization (ACO) algorithm to enhance scalability on large instances. Extensive experiments on benchmark datasets demonstrate that the proposed framework consistently achieves high-quality solutions and outperforms existing approaches in solution quality, while maintaining competitive computational efficiency. These results highlight the effectiveness of hybrid optimization strategies for complex, load-dependent routing problems in practical applications. Our implementation is publicly available at https://github.com/HySonLab/MatCPP

math.OC↗
arXiv2026

Spectral Embeddings Leak Graph Topology: Theory, Benchmark, and Adaptive Reconstruction

Graph Neural Networks (GNNs) excel on relational data, but standard benchmarks unrealistically assume the graph is centrally available. In practice, settings such as Federated Graph Learning, distributed systems, and privacy-sensitive applications involve graph data that are localized, fragmented, noisy, and privacy-leaking. We present a unified framework for this setting. We introduce LoGraB (Local Graph Benchmark), which decomposes standard datasets into fragmented benchmarks using three strategies and four controls: neighborhood radius $d$, spectral quality $k$, noise level $σ$, and coverage ratio $p$. LoGraB supports graph reconstruction, localized node classification, and inter-fragment link prediction, with Island Cohesion. We propose AFR (Adaptive Fidelity-driven Reconstruction), a method for noisy spectral fragments. AFR scores patch quality via a fidelity measure combining a gap-to-truncation stability ratio and structural entropy, then assembles fragments using RANSAC-Procrustes alignment, adaptive stitching, and Bundle Adjustment. Rather than forcing a single global graph, AFR recovers large faithful islands. We prove heat-kernel edge recovery under a separation condition, Davis--Kahan perturbation stability, and bounded alignment error. We establish a Spectral Leakage Proposition: under a spectral-gap assumption, polynomial-time Bayesian recovery is feasible once enough eigenvectors are shared, complementing AFR's deterministic guarantees. Experiments on nine benchmarks show that LoGraB reveals model strengths and weaknesses under fragmentation, AFR achieves the best F1 on 7/9 datasets, and under per-embedding $(ε,δ)$-Gaussian differential privacy, AFR retains 75% of its undefended F1 at $ε=2$. Our anonymous code is available at https://anonymous.4open.science/r/JMLR_submission

cs.LG↗
arXiv2026

RedBench: A Universal Dataset for Comprehensive Red Teaming of Large Language Models

As large language models (LLMs) become integral to safety-critical applications, ensuring their robustness against adversarial prompts is paramount. However, existing red teaming datasets suffer from inconsistent risk categorizations, limited domain coverage, and outdated evaluations, hindering systematic vulnerability assessments. To address these challenges, we introduce RedBench, a universal dataset aggregating 37 benchmark datasets from leading conferences and repositories, comprising 29,362 samples across attack and refusal prompts. RedBench employs a standardized taxonomy with 22 risk categories and 19 domains, enabling consistent and comprehensive evaluations of LLM vulnerabilities. We provide a detailed analysis of existing datasets, establish baselines for modern LLMs, and open-source the dataset and evaluation code. Our contributions facilitate robust comparisons, foster future research, and promote the development of secure and reliable LLMs for real-world deployment. Code: https://github.com/knoveleng/redeval

cs.CL↗
arXiv2026

DiffPlace: A Conditional Diffusion Framework for Simultaneous VLSI Placement Beyond Sequential Paradigms

Chip placement, a critical step in the VLSI physical design flow, directly impacts performance, power, and routability. Traditional chip placement methods, relying on analytical optimization or sequential reinforcement learning (RL), face significant challenges in modern VLSI design, including the inability to consistently satisfy hard placement constraints and the requirement for computationally expensive online training for each new circuit design. Furthermore, existing sequential decision-making paradigms often suffer from compounding errors and extreme wirelength minimization that aggressively compresses modules into dense clusters, leading to severe routing congestion hotspots and failures in downstream design stages. To address these limitations, we introduce DiffPlace, a framework that reformulates chip placement as a conditional denoising diffusion process, enabling transferable policies that generalize to unseen netlists without extensive retraining. Unlike sequential paradigms, DiffPlace simultaneously optimizes all macro positions utilizing a neural backbone equipped with vector-wise message passing to capture geometric dependencies. By prioritizing a more balanced spatial distribution of macros, our framework adopts a routability-first perspective to effectively prevent routing hotspots while maintaining competitive wirelength. To effectively handle the multi-objective nature of placement, we propose a decoupled guidance mechanism: global objectives are optimized via energy-based conditioning, while local physical constraints are actively mitigated through explicit manifold gradient injection during the reverse sampling process. Extensive experiments demonstrate that DiffPlace achieves competitive placement quality while offering superior generalization efficiency compared to state-of-the-art learning-based baselines.

cs.AR↗
arXiv2026

DiFlowDubber: Discrete Flow Matching for Automated Video Dubbing via Cross-Modal Alignment and Synchronization

Video dubbing requires content accuracy, expressive prosody, high-quality acoustics, and precise lip synchronization, yet existing approaches struggle on all four fronts. To address these issues, we propose DiFlowDubber, the first video dubbing framework built upon a discrete flow matching backbone with a novel two-stage training strategy. In the first stage, a zero-shot text-to-speech (TTS) system is pre-trained on large-scale corpora, where a deterministic architecture captures linguistic structures, and the Discrete Flow-based Prosody-Acoustic (DFPA) module models expressive prosody and realistic acoustic characteristics. In the second stage, we propose the Content-Consistent Temporal Adaptation (CCTA) to transfer TTS knowledge to the dubbing domain: its Synchronizer enforces cross-modal alignment for lip-synchronized speech. Complementarily, the Face-to-Prosody Mapper (FaPro) conditions prosody on facial expressions, whose outputs are then fused with those of the Synchronizer to construct rich, fine-grained multimodal embeddings that capture prosody-content correlations, guiding the DFPA to generate expressive prosody and acoustic tokens for content-consistent speech. Experiments on two benchmark datasets demonstrate that DiFlowDubber outperforms prior methods across multiple evaluation metrics.

cs.CV↗
arXiv2026

Multimodal Machine Learning for Soft High-k Elastomers under Data Scarcity

Dielectric materials are critical building blocks for modern electronics such as sensors, actuators, and transistors. With rapid advances in soft and stretchable electronics for emerging human- and robot-interfacing applications, there is a growing need for high-performance dielectric elastomers. However, developing soft elastomers that simultaneously exhibit high dielectric constants (k) and low Young's moduli (E) remains a major challenge. Although individual elastomer designs have been reported, structured datasets that systematically integrate molecular sequence, dielectric, and mechanical properties are largely unavailable. To address this gap, we curate a compact, high-quality dataset of acrylate-based dielectric elastomers by aggregating experimental results from the past decade. Building on this dataset, we propose a multimodal learning framework leveraging large-scale pretrained polymer representations. These pretrained embeddings transfer chemical and structural knowledge from vast polymer corpora, enabling accurate few-shot prediction of dielectric and mechanical properties and accelerating data-efficient discovery of soft high-$k$ dielectric elastomers. Our data and implementation are publicly available at: https://github.com/HySonLab/Polymers

cs.LG↗
arXiv2026

Halfway to 3D: Ensembling 2.5D and 3D Models for Robust COVID-19 CT Diagnosis

We propose a deep learning framework for COVID-19 detection and disease classification from chest CT scans that integrates both 2.5D and 3D representations to capture complementary slice-level and volumetric information. The 2.5D branch processes multi-view CT slices (axial, coronal, sagittal) using a DINOv3 vision transformer to extract robust visual features, while the 3D branch employs a ResNet-18 architecture to model volumetric context and is pretrained with Variance Risk Extrapolation (VREx) followed by supervised contrastive learning to improve cross-source robustness. Predictions from both branches are combined through logit-level ensemble inference. Experiments on the PHAROS-AIF-MIH benchmark demonstrate the effectiveness of the proposed approach: for binary COVID-19 detection, the ensemble achieves 94.48% accuracy and a 0.9426 Macro F1-score, outperforming both individual models, while for multi-class disease classification the 2.5D DINOv3 model achieves the best performance with 79.35% accuracy and a 0.7497 Macro F1-score. These results highlight the benefit of combining pretrained slice-based representations with volumetric modeling for robust multi-source medical imaging analysis. Code is available at https://github.com/HySonLab/PHAROS-AIF-MIH

eess.IV↗
arXiv2026

Binary Latent Protein Fitness Landscapes for Quantum Annealing Optimization

We propose Q-BIOLAT, a framework for modeling and optimizing protein fitness landscapes in binary latent spaces. Starting from protein sequences, we leverage pretrained protein language models to obtain continuous embeddings, which are then transformed into compact binary latent representations. In this space, protein fitness is approximated using a quadratic unconstrained binary optimization (QUBO) model, enabling efficient combinatorial search via classical heuristics such as simulated annealing and genetic algorithms. On the ProteinGym benchmark, we demonstrate that Q-BIOLAT captures meaningful structure in protein fitness landscapes and enables the identification of high-fitness variants. Despite using a simple binarization scheme, our method consistently retrieves sequences whose nearest neighbors lie within the top fraction of the training fitness distribution, particularly under the strongest configurations. We further show that different optimization strategies exhibit distinct behaviors, with evolutionary search performing better in higher-dimensional latent spaces and local search remaining competitive in preserving realistic sequences. Beyond its empirical performance, Q-BIOLAT provides a natural bridge between protein representation learning and combinatorial optimization. By formulating protein fitness as a QUBO problem, our framework is directly compatible with emerging quantum annealing hardware, opening new directions for quantum-assisted protein engineering. Our implementation is publicly available at: https://github.com/HySonLab/Q-BIOLAT

cs.LG↗
arXiv2026

Self-Evolving Multi-Agent Network for Industrial IoT Predictive Maintenance

Industrial IoT predictive maintenance requires systems capable of real-time anomaly detection without sacrificing interpretability or demanding excessive computational resources. Traditional approaches rely on static, offline-trained models that cannot adapt to evolving operational conditions, while LLM-based monolithic systems demand prohibitive memory and latency, rendering them impractical for on-site edge deployment. We introduce SEMAS, a self-evolving hierarchical multi-agent system that distributes specialized agents across Edge, Fog, and Cloud computational tiers. Edge agents perform lightweight feature extraction and pre-filtering; Fog agents execute diversified ensemble detection with dynamic consensus voting; and Cloud agents continuously optimize system policies via Proximal Policy Optimization (PPO) while maintaining asynchronous, non-blocking inference. The framework incorporates LLM-based response generation for explainability and federated knowledge aggregation for adaptive policy distribution. This architecture enables resource-aware specialization without sacrificing real-time performance or model interpretability. Empirical evaluation on two industrial benchmarks (Boiler Emulator and Wind Turbine) demonstrates that SEMAS achieves superior anomaly detection performance with exceptional stability under adaptation, sustains prediction accuracy across evolving operational contexts, and delivers substantial latency improvements enabling genuine real-time deployment. Ablation studies confirm that PPO-driven policy evolution, consensus voting, and federated aggregation each contribute materially to system effectiveness. These findings indicate that resource-aware, self-evolving 1multi-agent coordination is essential for production-ready industrial IoT predictive maintenance under strict latency and explainability constraints.

cs.MA↗
arXiv2026

Efficient Deep Learning for Medical Imaging: Bridging the Gap Between High-Performance AI and Clinical Deployment

Deep learning has revolutionized medical image analysis, playing a vital role in modern clinical applications. However, the deployment of large-scale models in real-world clinical settings remains challenging due to high computational costs, latency constraints, and patient data privacy concerns associated with cloud-based processing. To address these bottlenecks, this review provides a comprehensive synthesis of efficient and lightweight deep learning architectures specifically tailored for the medical domain. We categorize the landscape of modern efficient models into three primary streams: Convolutional Neural Networks (CNNs), Lightweight Transformers, and emerging Linear Complexity Models. Furthermore, we examine key model compression strategies (including pruning, quantization, knowledge distillation, and low-rank factorization) and evaluate their efficacy in maintaining diagnostic performance while reducing hardware requirements. By identifying current limitations and discussing the transition toward on-device intelligence, this review serves as a roadmap for researchers and practitioners aiming to bridge the gap between high-performance AI and resource-constrained clinical environments.

cs.LG↗
arXiv2026

RainbowPlus: Enhancing Adversarial Prompt Generation via Evolutionary Quality-Diversity Search

Large Language Models (LLMs) exhibit remarkable capabilities but are susceptible to adversarial prompts that exploit vulnerabilities to produce unsafe or biased outputs. Existing red-teaming methods often face scalability challenges, resource-intensive requirements, or limited diversity in attack strategies. We propose RainbowPlus, a novel red-teaming framework rooted in evolutionary computation, enhancing adversarial prompt generation through an adaptive quality-diversity (QD) search that extends classical evolutionary algorithms like MAP-Elites with innovations tailored for language models. By employing a multi-element archive to store diverse high-quality prompts and a comprehensive fitness function to evaluate multiple prompts concurrently, RainbowPlus overcomes the constraints of single-prompt archives and pairwise comparisons in prior QD methods like Rainbow Teaming. Experiments comparing RainbowPlus to QD methods across six benchmark datasets and four open-source LLMs demonstrate superior attack success rate (ASR) and diversity (Diverse-Score $\approx 0.84$), generating up to 100 times more unique prompts (e.g., 10,418 vs. 100 for Ministral-8B-Instruct-2410). Against nine state-of-the-art methods on the HarmBench dataset with twelve LLMs (ten open-source, two closed-source), RainbowPlus achieves an average ASR of 81.1%, surpassing AutoDAN-Turbo by 3.9%, and is 9 times faster (1.45 vs. 13.50 hours). Our open-source implementation fosters further advancements in LLM safety, offering a scalable tool for vulnerability assessment. Code and resources are publicly available at https://github.com/knoveleng/rainbowplus, supporting reproducibility and future research in LLM red-teaming.

cs.CL↗
arXiv2025

TESGNN: Temporal Equivariant Scene Graph Neural Networks for Efficient and Robust Multi-View 3D Scene Understanding

Scene graphs have proven to be highly effective for various scene understanding tasks due to their compact and explicit representation of relational information. However, current methods often overlook the critical importance of preserving symmetry when generating scene graphs from 3D point clouds, which can lead to reduced accuracy and robustness, particularly when dealing with noisy, multi-view data. Furthermore, a major limitation of prior approaches is the lack of temporal modeling to capture time-dependent relationships among dynamically evolving entities in a scene. To address these challenges, we propose Temporal Equivariant Scene Graph Neural Network (TESGNN), consisting of two key components: (1) an Equivariant Scene Graph Neural Network (ESGNN), which extracts information from 3D point clouds to generate scene graph while preserving crucial symmetry properties, and (2) a Temporal Graph Matching Network, which fuses scene graphs generated by ESGNN across multiple time sequences into a unified global representation using an approximate graph-matching algorithm. Our combined architecture TESGNN shown to be effective compared to existing methods in scene graph generation, achieving higher accuracy and faster training convergence. Moreover, we show that leveraging the symmetry-preserving property produces a more stable and accurate global scene representation compared to existing approaches. Finally, it is computationally efficient and easily implementable using existing frameworks, making it well-suited for real-time applications in robotics and computer vision. This approach paves the way for more robust and scalable solutions to complex multi-view scene understanding challenges. Our source code is publicly available at: https://github.com/HySonLab/TESGraph

cs.CV↗