arXiv subjects

Ka-Chun Wong

Publications and source records attributed to Ka-Chun Wong.

18 recordsLinked to original sources

arXiv2026

SyncPlan: Long-Horizon LLM Coordination with Explicit Synchronization and Adaptive Correction

LLM-based multi-agent coordination faces a fundamental trade-off between efficiency and adaptivity in dynamic environments. Existing approaches typically rely on repeated LLM invocations or multi-round communication to adapt decisions during execution, introducing substantial latency and making coordination vulnerable to asynchronous progress and environmental changes. Conversely, one-shot planning reduces coordination overhead but produces open-loop plans that can quickly become stale or fail when actions depend on other agents and the environment. We introduce SyncPlan, a plan-execute-correct framework for long-horizon coordination through explicit synchronization and adaptive correction. Given the state and team-level task, a centralized LLM coordinator generates per-agent action chains in a single planning call. During execution, explicit wait primitives and deadlock detection enforce inter-agent and agent-environment dependencies, while a lightweight Plan Staleness Detector continuously assesses the remaining plan and triggers replanning when environmental changes invalidate its assumptions. We further optimize the coordinator through SFT and planning-oriented RL with dense task progress and outcome-level execution feedback. Experiments on the public Overcooked benchmark and the complex Honor of Kings environment show that SyncPlan achieves state-of-the-art task success rates while using less than 0.05% of the wall-clock runtime compared with existing LLM-based coordinators. Code and datasets will be made publicly available.

cs.RO↗

arXiv2026

Physically Real-time Infrared Attack against Optical Flow Estimation Networks

With the promising performance of deep neural networks on image-based tasks, different real-world applications such as autonomous driving and motion detection have become increasingly mature and relevant to human lives. In particular, Optical Flow Estimation Networks (OFENs), as upstream models, play a critical role in different domains. Its outputs are heavily assumed and adopted for different downstream tasks, and it is essential to test its robustness to prevent safety accidents. We present an approach for real-time attacks on OFENs in the physical world, leveraging infrared lights for their stealthiness. By generating a large number of Adversarial Examples in advance, our approach computes AEs in real time and dynamically displays them, which allows our method to facilitate precise and targeted attacks without modifying the victim system. Unlike previous digital-to-physical attack techniques, our method directly attacks victim models within the physical world, thereby overcoming the limitations associated with the ineffectiveness of AEs. Experimental results demonstrate the efficacy of our approach in compromising OFENs across diverse lighting conditions, varying object motion velocities, and different object placements, ultimately impairing the network's ability to accurately estimate optical flow.

cs.CV↗

arXiv2026

AMix-2: Establishing Protein as a Native Modality in Large Language Models

We present AMix-2, a protein-text foundation model that establishes protein as a native modality in large language models (LLMs), unifying protein understanding and sequence design within a single foundation model. AMix-2 is built upon two key ideas: (1) a unified protein-text formulation that embeds natural language and protein sequence in a shared token space, enabling one model to perform biological reasoning and conditional design instead of separate downstream task-specialized models; and (2) a block-wise diffusion language modeling backbone that combines causal generation across blocks with bidirectional context and iterative refinement within blocks. This scheme better matches the intrinsic nature of proteins than a strict left-to-right factorization. To evaluate protein foundation models under realistic generalization settings, we further introduce ProteinArena, a comprehensive benchmark with time-aware and homology-aware protocols across various understanding and design tasks, and with baselines covering classical bioinformatics tools, protein-specialized models and LLMs. On ProteinArena, AMix-2 outperforms frontier LLMs and demonstrates competitive performance to task-specific protein models. Controlled experiments further show that the diffusion-based paradigm generally surpasses its autoregressive counterpart, highlighting the advantage of flexible generation order for protein sequences. We release both AMix-2 and ProteinArena to facilitate open research in protein foundation models.

q-bio.BM↗

arXiv2025

Directed Link Prediction using GNN with Local and Global Feature Fusion

Link prediction is a classical problem in graph analysis with many practical applications. For directed graphs, recently developed deep learning approaches typically analyze node similarities through contrastive learning and aggregate neighborhood information through graph convolutions. In this work, we propose a novel graph neural network (GNN) framework to fuse feature embedding with community information. We theoretically demonstrate that such hybrid features can improve the performance of directed link prediction. To utilize such features efficiently, we also propose an approach to transform input graphs into directed line graphs so that nodes in the transformed graph can aggregate more information during graph convolutions. Experiments on benchmark datasets show that our approach outperforms the state-of-the-art in most cases when 30%, 40%, 50%, and 60% of the connected links are used as training data, respectively.

cs.LG↗

arXiv2024

A versatile informative diffusion model for single-cell ATAC-seq data generation and analysis

The rapid advancement of single-cell ATAC sequencing (scATAC-seq) technologies holds great promise for investigating the heterogeneity of epigenetic landscapes at the cellular level. The amplification process in scATAC-seq experiments often introduces noise due to dropout events, which results in extreme sparsity that hinders accurate analysis. Consequently, there is a significant demand for the generation of high-quality scATAC-seq data in silico. Furthermore, current methodologies are typically task-specific, lacking a versatile framework capable of handling multiple tasks within a single model. In this work, we propose ATAC-Diff, a versatile framework, which is based on a latent diffusion model conditioned on the latent auxiliary variables to adapt for various tasks. ATAC-Diff is the first diffusion model for the scATAC-seq data generation and analysis, composed of auxiliary modules encoding the latent high-level variables to enable the model to learn the semantic information to sample high-quality data. Gaussian Mixture Model (GMM) as the latent prior and auxiliary decoder, the yield variables reserve the refined genomic information beneficial for downstream analyses. Another innovation is the incorporation of mutual information between observed and hidden variables as a regularization term to prevent the model from decoupling from latent variables. Through extensive experiments, we demonstrate that ATAC-Diff achieves high performance in both generation and analysis tasks, outperforming state-of-the-art models.

q-bio.GN↗

arXiv2024

Exhaustive Exploitation of Nature-inspired Computation for Cancer Screening in an Ensemble Manner

Accurate screening of cancer types is crucial for effective cancer detection and precise treatment selection. However, the association between gene expression profiles and tumors is often limited to a small number of biomarker genes. While computational methods using nature-inspired algorithms have shown promise in selecting predictive genes, existing techniques are limited by inefficient search and poor generalization across diverse datasets. This study presents a framework termed Evolutionary Optimized Diverse Ensemble Learning (EODE) to improve ensemble learning for cancer classification from gene expression data. The EODE methodology combines an intelligent grey wolf optimization algorithm for selective feature space reduction, guided random injection modeling for ensemble diversity enhancement, and subset model optimization for synergistic classifier combinations. Extensive experiments were conducted across 35 gene expression benchmark datasets encompassing varied cancer types. Results demonstrated that EODE obtained significantly improved screening accuracy over individual and conventionally aggregated models. The integrated optimization of advanced feature selection, directed specialized modeling, and cooperative classifier ensembles helps address key challenges in current nature-inspired approaches. This provides an effective framework for robust and generalized ensemble learning with gene expression biomarkers. Specifically, we have opened EODE source code on Github at https://github.com/wangxb96/EODE.

cs.NE↗

arXiv2024

Core-periphery Detection Based on Masked Bayesian Non-negative Matrix Factorization

Core-periphery structure is an essential mesoscale feature in complex networks. Previous researches mostly focus on discriminative approaches while in this work, we propose a generative model called masked Bayesian non-negative matrix factorization. We build the model using two pair affiliation matrices to indicate core-periphery pair associations and using a mask matrix to highlight connections to core nodes. We propose an approach to infer the model parameters, and prove the convergence of variables with our approach. Besides the abilities as traditional approaches, it is able to identify core scores with overlapping core-periphery pairs. We verify the effectiveness of our method using randomly generated networks and real-world networks. Experimental results demonstrate that the proposed method outperforms traditional approaches.

cs.SI↗

arXiv2023

DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins

Advances in deep generative models shed light on de novo molecule generation with desired properties. However, molecule generation targeted for dual protein targets still faces formidable challenges including protein 3D structure data requisition for model training, auto-regressive sampling, and model generalization for unseen targets. Here, we proposed DiffDTM, a novel conditional structure-free deep generative model based on a diffusion model for dual targets based molecule generation to address the above issues. Specifically, DiffDTM receives protein sequences and molecular graphs as inputs instead of protein and molecular conformations and incorporates an information fusion module to achieve conditional generation in a one-shot manner. We have conducted comprehensive multi-view experiments to demonstrate that DiffDTM can generate drug-like, synthesis-accessible, novel, and high-binding affinity molecules targeting specific dual proteins, outperforming the state-of-the-art (SOTA) models in terms of multiple evaluation metrics. Furthermore, we utilized DiffDTM to generate molecules towards dopamine receptor D2 and 5-hydroxytryptamine receptor 1A as new antipsychotics. The experimental results indicate that DiffDTM can be easily plugged into unseen dual targets to generate bioactive molecules, addressing the issues of requiring insufficient active molecule data for training as well as the need to retrain when encountering new targets.

cs.LG↗

arXiv2022

MDM: Molecular Diffusion Model for 3D Molecule Generation

Molecule generation, especially generating 3D molecular geometries from scratch (i.e., 3D \textit{de novo} generation), has become a fundamental task in drug designs. Existing diffusion-based 3D molecule generation methods could suffer from unsatisfactory performances, especially when generating large molecules. At the same time, the generated molecules lack enough diversity. This paper proposes a novel diffusion model to address those two challenges. First, interatomic relations are not in molecules' 3D point cloud representations. Thus, it is difficult for existing generative models to capture the potential interatomic forces and abundant local constraints. To tackle this challenge, we propose to augment the potential interatomic forces and further involve dual equivariant encoders to encode interatomic forces of different strengths. Second, existing diffusion-based models essentially shift elements in geometry along the gradient of data density. Such a process lacks enough exploration in the intermediate steps of the Langevin dynamics. To address this issue, we introduce a distributional controlling variable in each diffusion/reverse step to enforce thorough explorations and further improve generation diversity. Extensive experiments on multiple benchmarks demonstrate that the proposed model significantly outperforms existing methods for both unconditional and conditional generation tasks. We also conduct case studies to help understand the physicochemical properties of the generated molecules.

cs.LG↗

arXiv2021

A Self-adaptive Weighted Differential Evolution Approach for Large-scale Feature Selection

Recently, many evolutionary computation methods have been developed to solve the feature selection problem. However, the studies focused mainly on small-scale issues, resulting in stagnation issues in local optima and numerical instability when dealing with large-scale feature selection dilemmas. To address these challenges, this paper proposes a novel weighted differential evolution algorithm based on self-adaptive mechanism, named SaWDE, to solve large-scale feature selection. First, a multi-population mechanism is adopted to enhance the diversity of the population. Then, we propose a new self-adaptive mechanism that selects several strategies from a strategy pool to capture the diverse characteristics of the datasets from the historical information. Finally, a weighted model is designed to identify the important features, which enables our model to generate the most suitable feature-selection solution. We demonstrate the effectiveness of our algorithm on twelve large-scale datasets. The performance of SaWDE is superior compared to six non-EC algorithms and six other EC algorithms, on both training and test datasets and on subset size, indicating that our algorithm is a favorable tool to solve the large-scale feature selection problem. Moreover, we have experimented SaWDE with six EC algorithms on twelve higher-dimensional data, which demonstrates that SaWDE is more robust and efficient compared to those state-of-the-art methods. SaWDE source code is available on Github at https://github.com/wangxb96/SaWDE.

cs.NE↗

arXiv2021

EGFI: Drug-Drug Interaction Extraction and Generation with Fusion of Enriched Entity and Sentence Information

The rapid growth in literature accumulates diverse and yet comprehensive biomedical knowledge hidden to be mined such as drug interactions. However, it is difficult to extract the heterogeneous knowledge to retrieve or even discover the latest and novel knowledge in an efficient manner. To address such a problem, we propose EGFI for extracting and consolidating drug interactions from large-scale medical literature text data. Specifically, EGFI consists of two parts: classification and generation. In the classification part, EGFI encompasses the language model BioBERT which has been comprehensively pre-trained on biomedical corpus. In particular, we propose the multi-head attention mechanism and pack BiGRU to fuse multiple semantic information for rigorous context modeling. In the generation part, EGFI utilizes another pre-trained language model BioGPT-2 where the generation sentences are selected based on filtering rules. We evaluated the classification part on "DDIs 2013" dataset and "DTIs" dataset, achieving the FI score of 0.842 and 0.720 respectively. Moreover, we applied the classification part to distinguish high-quality generated sentences and verified with the exiting growth truth to confirm the filtered sentences. The generated sentences that are not recorded in DrugBank and DDIs 2013 dataset also demonstrate the potential of EGFI to identify novel drug relationships.

cs.CL↗

arXiv2020

Review of Single-cell RNA-seq Data Clustering for Cell Type Identification and Characterization

In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become the central component to identify and characterize novel cell types and gene expression patterns. In this study, we review the existing single-cell RNA-seq data clustering methods with critical insights into the related advantages and limitations. In addition, we also review the upstream single-cell RNA-seq data processing techniques such as quality control, normalization, and dimension reduction. We conduct performance comparison experiments to evaluate several popular single-cell RNA-seq clustering approaches on two single-cell transcriptomic datasets.

q-bio.GN↗

arXiv2019

Context awareness and embedding for biomedical event extraction

Motivation: Biomedical event detection is fundamental for information extraction in molecular biology and biomedical research. The detected events form the central basis for comprehensive biomedical knowledge fusion, facilitating the digestion of massive information influx from literature. Limited by the feature context, the existing event detection models are mostly applicable for a single task. A general and scalable computational model is desiderated for biomedical knowledge management. Results: We consider and propose a bottom-up detection framework to identify the events from recognized arguments. To capture the relations between the arguments, we trained a bi-directional Long Short-Term Memory (LSTM) network to model their context embedding. Leveraging the compositional attributes, we further derived the candidate samples for training event classifiers. We built our models on the datasets from BioNLP Shared Task for evaluations. Our method achieved the average F-scores of 0.81 and 0.92 on BioNLPST-BGI and BioNLPST-BB datasets respectively. Comparing with 7 state-of-the-art methods, our method nearly doubled the existing F-score performance (0.92 vs 0.56) on the BioNLPST-BB dataset. Case studies were conducted to reveal the underlying reasons. Availability: https://github.com/cskyan/evntextrc

cs.CL↗

arXiv2018

Big Data Challenges in Genome Informatics

In recent years, we have witnessed a dramatic data explosion in genomics, thanks to the improvement in sequencing technologies and the drastically decreasing costs. We are entering the era of millions of available genomes. Notably, each genome can be composed of billions of nucleotides stored as plain text files in GigaBytes (GBs). It is undeniable that those genome data impose unprecedented data challenges for us. In this article, we briefly discuss the big data challenges associated with genomics in recent years.

q-bio.OT↗

arXiv2015

A Short Survey on Data Clustering Algorithms

With rapidly increasing data, clustering algorithms are important tools for data analytics in modern research. They have been successfully applied to a wide range of domains; for instance, bioinformatics, speech recognition, and financial analysis. Formally speaking, given a set of data instances, a clustering algorithm is expected to divide the set of data instances into the subsets which maximize the intra-subset similarity and inter-subset dissimilarity, where a similarity measure is defined beforehand. In this work, the state-of-the-arts clustering algorithms are reviewed from design concept to methodology; Different clustering paradigms are discussed. Advanced clustering algorithms are also discussed. After that, the existing clustering evaluation metrics are reviewed. A summary with future insights is provided at the end.

cs.DS↗

arXiv2015

Evolutionary Multimodal Optimization: A Short Survey

Real world problems always have different multiple solutions. For instance, optical engineers need to tune the recording parameters to get as many optimal solutions as possible for multiple trials in the varied-line-spacing holographic grating design problem. Unfortunately, most traditional optimization techniques focus on solving for a single optimal solution. They need to be applied several times; yet all solutions are not guaranteed to be found. Thus the multimodal optimization problem was proposed. In that problem, we are interested in not only a single optimal point, but also the others. With strong parallel search capability, evolutionary algorithms are shown to be particularly effective in solving this type of problem. In particular, the evolutionary algorithms for multimodal optimization usually not only locate multiple optima in a single run, but also preserve their population diversity throughout a run, resulting in their global optimization ability on multimodal functions. In addition, the techniques for multimodal optimization are borrowed as diversity maintenance techniques to other problems. In this chapter, we describe and review the state-of-the-arts evolutionary algorithms for multimodal optimization in terms of methodology, benchmarking, and application.

cs.NE↗

arXiv2015

Unsupervised Learning in Genome Informatics

With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this book chapter, we review the state-of-the-art unsupervised learning algorithms for genome informatics from DNA to MicroRNA. DNA (DeoxyriboNucleic Acid) is the basic component of genomes. A significant fraction of DNA regions (transcription factor binding sites) are bound by proteins (transcription factors) to regulate gene expression at different development stages in different tissues. To fully understand genetics, it is necessary of us to apply unsupervised learning algorithms to learn and infer those DNA regions. Here we review several unsupervised learning methods for deciphering the genome-wide patterns of those DNA regions. MicroRNA (miRNA), a class of small endogenous non-coding RNA (RiboNucleic acid) species, regulate gene expression post-transcriptionally by forming imperfect base-pair with the target sites primarily at the 3$'$ untranslated regions of the messenger RNAs. Since the 1993 discovery of the first miRNA \emph{let-7} in worms, a vast amount of studies have been dedicated to functionally characterizing the functional impacts of miRNA in a network context to understand complex diseases such as cancer. Here we review several representative unsupervised learning frameworks on inferring miRNA regulatory network by exploiting the static sequence-based information pertinent to the prior knowledge of miRNA targeting and the dynamic information of miRNA activities implicated by the recently available large data compendia, which interrogate genome-wide expression profiles of miRNAs and/or mRNAs across various cell conditions.

q-bio.GN↗

arXiv2015

Evolutionary Algorithms: Concepts, Designs, and Applications in Bioinformatics: Evolutionary Algorithms for Bioinformatics

Since genetic algorithm was proposed by John Holland (Holland J. H., 1975) in the early 1970s, the study of evolutionary algorithm has emerged as a popular research field (Civicioglu & Besdok, 2013). Researchers from various scientific and engineering disciplines have been digging into this field, exploring the unique power of evolutionary algorithms (Hadka & Reed, 2013). Many applications have been successfully proposed in the past twenty years. For example, mechanical design (Lampinen & Zelinka, 1999), electromagnetic optimization (Rahmat-Samii & Michielssen, 1999), environmental protection (Bertini, Felice, Moretti, & Pizzuti, 2010), finance (Larkin & Ryan, 2010), musical orchestration (Esling, Carpentier, & Agon, 2010), pipe routing (Furuholmen, Glette, Hovin, & Torresen, 2010), and nuclear reactor core design (Sacco, Henderson, Rios-Coelho, Ali, & Pereira, 2009). In particular, its function optimization capability was highlighted (Goldberg & Richardson, 1987) because of its high adaptability to different function landscapes, to which we cannot apply traditional optimization techniques (Wong, Leung, & Wong, 2009). Here we review the applications of evolutionary algorithms in bioinformatics.

cs.NE↗