arXiv subjects

Zikun Wang

Publications and source records attributed to Zikun Wang.

7 recordsLinked to original sources

arXiv2026

GPU-Accelerated ANNS: Quantized for Speed, Built for Change

Approximate nearest neighbor search (ANNS) is a core problem in machine learning and information retrieval applications. GPUs offer a promising path to high-performance ANNS: they provide massive parallelism for distance computations, are readily available, and can co-locate with downstream applications. Despite these advantages, current GPU-accelerated ANNS systems face three key limitations. First, real-world applications operate on evolving datasets that require fast batch updates, yet most GPU indices must be rebuilt from scratch when new data arrives. Second, high-dimensional vectors strain memory bandwidth, but current GPU systems lack efficient quantization techniques that reduce data movement without introducing costly random memory accesses. Third, the data-dependent memory accesses inherent to greedy search make overlapping compute and memory difficult, leading to reduced performance. We present Jasper, a GPU-native ANNS system with both high query throughput and updatability. Jasper builds on the Vamana graph index and overcomes existing bottlenecks via three contributions: (1) a CUDA batch-parallel construction algorithm that enables lock-free streaming insertions, (2) a GPU-efficient implementation of RaBitQ quantization that reduces memory footprint up to 8x without the random access penalties, and (3) an optimized greedy search kernel that increases compute utilization, resulting in better latency hiding and higher throughput. Our evaluation across five datasets shows that Jasper achieves up to 1.84x higher query throughput than CAGRA and achieves up to 80% peak utilization as measured by the roofline model. Jasper's construction scales efficiently and constructs indices an average of 7x faster than CAGRA while providing updatability that CAGRA lacks. Compared to BANG, the previous fastest GPU Vamana implementation, Jasper delivers 10-74x faster queries.

cs.DB↗

arXiv2025

A general language model for peptide function identification

Accurate identification of bioactive peptides (BPs) and protein post-translational modifications (PTMs) is essential for understanding protein function and advancing therapeutic discovery. However, most computational methods remain limited in their generalizability across diverse peptide functions. Here, we present PDeepPP, a unified deep learning framework that integrates pretrained protein language models with a hybrid transformer-CNN architecture, enabling robust identification across diverse peptide classes and PTM sites. We curated comprehensive benchmark datasets and implemented strategies to address data imbalance, allowing PDeepPP to systematically extract both global and local sequence features. Through extensive analyses including dimensionality reduction and comparison studies, PDeepPP demonstrates strong, interpretable peptide representations and achieves state-of-the-art performance in 25 of the 33 biological identification tasks. Notably, PDeepPP attains high accuracy in antimicrobial (0.9726) and phosphorylation site (0.9984) identification, with 99.5% specificity in glycosylation site prediction and substantial reduction in false negatives in antimalarial tasks. By enabling large-scale, accurate peptide analysis, PDeepPP supports biomedical research and the discovery of novel therapeutic targets for disease treatment. All code, datasets, and pretrained models are publicly available via GitHub (https://github.com/fondress/PDeepPP) and Hugging Face (https://huggingface.co/fondress/PDeppPP)

cs.LG↗

arXiv2025

SCMPPI: Supervised Contrastive Multimodal Framework for Predicting Protein-Protein Interactions

Protein-protein interaction (PPI) prediction plays a pivotal role in deciphering cellular functions and disease mechanisms. To address the limitations of traditional experimental methods and existing computational approaches in cross-modal feature fusion and false-negative suppression, we propose SCMPPI-a novel supervised contrastive multimodal framework. By effectively integrating sequence-based features (AAC, DPC, ESMC-CKSAAP) with network topology (Node2Vec embeddings) and incorporating an enhanced contrastive learning strategy with negative sample filtering, SCMPPI achieves superior prediction performance. Extensive experiments on eight benchmark datasets demonstrate its state-of-the-art accuracy(98.13%) and AUC(99.69%), along with excellent cross-species generalization (AUC>99%). Successful applications in CD9 networks, Wnt pathway analysis, and cancer-specific networks further highlight its potential for disease target discovery, establishing SCMPPI as a powerful tool for multimodal biological data analysis.

cs.LG↗

arXiv2025

Machine learning algorithms to predict stroke in China based on causal inference of time series analysis

Participants: This study employed a combination of Vector Autoregression (VAR) model and Graph Neural Networks (GNN) to systematically construct dynamic causal inference. Multiple classic classification algorithms were compared, including Random Forest, Logistic Regression, XGBoost, Support Vector Machine (SVM), K-Nearest Neighbor (KNN), Gradient Boosting, and Multi Layer Perceptron (MLP). The SMOTE algorithm was used to undersample a small number of samples and employed Stratified K-fold Cross Validation. Results: This study included a total of 11,789 participants, including 6,334 females (53.73%) and 5,455 males (46.27%), with an average age of 65 years. Introduction of dynamic causal inference features has significantly improved the performance of almost all models. The area under the ROC curve of each model ranged from 0.78 to 0.83, indicating significant difference (P < 0.01). Among all the models, the Gradient Boosting model demonstrated the highest performance and stability. Model explanation and feature importance analysis generated model interpretation that illustrated significant contributors associated with risks of stroke. Conclusions and Relevance: This study proposes a stroke risk prediction method that combines dynamic causal inference with machine learning models, significantly improving prediction accuracy and revealing key health factors that affect stroke. The research results indicate that dynamic causal inference features have important value in predicting stroke risk, especially in capturing the impact of changes in health status over time on stroke risk. By further optimizing the model and introducing more variables, this study provides theoretical basis and practical guidance for future stroke prevention and intervention strategies.

q-bio.QM↗

arXiv2024

WENDY: Covariance Dynamics Based Gene Regulatory Network Inference

Determining gene regulatory network (GRN) structure is a central problem in biology, with a variety of inference methods available for different types of data. For a widely prevalent and challenging use case, namely single-cell gene expression data measured after intervention at multiple time points with unknown joint distributions, there is only one known specifically developed method, which does not fully utilize the rich information contained in this data type. We develop an inference method for the GRN in this case, netWork infErence by covariaNce DYnamics, dubbed WENDY. The core idea of WENDY is to model the dynamics of the covariance matrix, and solve this dynamics as an optimization problem to determine the regulatory relationships. To evaluate its effectiveness, we compare WENDY with other inference methods using synthetic data and experimental data. Our results demonstrate that WENDY performs well across different data sets.

q-bio.MN↗

arXiv2023

CAB: Empathetic Dialogue Generation with Cognition, Affection and Behavior

Empathy is an important characteristic to be considered when building a more intelligent and humanized dialogue agent. However, existing methods did not fully comprehend empathy as a complex process involving three aspects: cognition, affection and behavior. In this paper, we propose CAB, a novel framework that takes a comprehensive perspective of cognition, affection and behavior to generate empathetic responses. For cognition, we build paths between critical keywords in the dialogue by leveraging external knowledge. This is because keywords in a dialogue are the core of sentences. Building the logic relationship between keywords, which is overlooked by the majority of existing works, can improve the understanding of keywords and contextual logic, thus enhance the cognitive ability. For affection, we capture the emotional dependencies with dual latent variables that contain both interlocutors' emotions. The reason is that considering both interlocutors' emotions simultaneously helps to learn the emotional dependencies. For behavior, we use appropriate dialogue acts to guide the dialogue generation to enhance the empathy expression. Extensive experiments demonstrate that our multi-perspective model outperforms the state-of-the-art models in both automatic and manual evaluation.

cs.CL↗

arXiv2022

Inference on the structure of gene regulatory networks

In this paper, we conduct theoretical analyses on inferring the structure of gene regulatory networks. Depending on the experimental method and data type, the inference problem is classified into 20 different scenarios. For each scenario, we discuss the problem that with enough data, under what assumptions, what can be inferred about the structure. For scenarios that have been covered in the literature, we provide a brief review. For scenarios that have not been covered in literature, if the structure can be inferred, we propose new mathematical inference methods and evaluate them on simulated data. Otherwise, we prove that the structure cannot be inferred.

q-bio.MN↗