Wenyu Zhu

Wenyu Zhu, Hao Wang, Yuchen Zhou et al.

Binary Code Embedding (BCE) has important applications in various reverse engineering tasks such as binary code similarity detection, type recovery, control-flow recovery and data-flow analysis. Recent studies have shown that the Transformer model can comprehend the semantics of binary code to support downstream tasks. However, existing models overlooked the prior knowledge of assembly language. In this paper, we propose a novel Transformer-based approach, namely kTrans, to generate knowledge-aware binary code embedding. By feeding explicit knowledge as additional inputs to the Transformer, and fusing implicit knowledge with a novel pre-training task, kTrans provides a new perspective to incorporating domain knowledge into a Transformer framework. We inspect the generated embeddings with outlier detection and visualization, and also apply kTrans to 3 downstream tasks: Binary Code Similarity Detection (BCSD), Function Type Recovery (FTR) and Indirect Call Recognition (ICR). Evaluation results show that kTrans can generate high-quality binary code embeddings, and outperforms state-of-the-art (SOTA) approaches on downstream tasks by 5.2%, 6.8%, and 12.6% respectively. kTrans is publicly available at: https://github.com/Learner0x5a/kTrans-release

Huanyu Bian, Zhilong Jia, Menghan Dou et al.

With the rapid development of classical and quantum machine learning, a large number of machine learning frameworks have been proposed. However, existing machine learning frameworks usually only focus on classical or quantum, rather than both. Therefore, based on VQNet 1.0, we further propose VQNet 2.0, a new generation of unified classical and quantum machine learning framework that supports hybrid optimization. The core library of the framework is implemented in C++, and the user level is implemented in Python, and it supports deployment on quantum and classical hardware. In this article, we analyze the development trend of the new generation machine learning framework and introduce the design principles of VQNet 2.0 in detail: unity, practicality, efficiency, and compatibility, as well as full particulars of implementation. We illustrate the functions of VQNet 2.0 through several basic applications, including classical convolutional neural networks, quantum autoencoders, hybrid classical-quantum networks, etc. After that, through extensive experiments, we demonstrate that the operation speed of VQNet 2.0 is higher than the comparison method. Finally, through extensive experiments, we demonstrate that VQNet 2.0 can deploy on different hardware platforms, the overall calculation speed is faster than the comparison method. It also can be mixed and optimized with quantum circuits composed of multiple quantum computing libraries.

Zeyu Gao, Hao Wang, Yuchen Zhou et al.

As software becomes increasingly complex and prone to vulnerabilities, automated vulnerability detection is critically important, yet challenging. Given the significant successes of large language models (LLMs) in various tasks, there is growing anticipation of their efficacy in vulnerability detection. However, a quantitative understanding of their potential in vulnerability detection is still missing. To bridge this gap, we introduce a comprehensive vulnerability benchmark VulBench. This benchmark aggregates high-quality data from a wide range of CTF (Capture-the-Flag) challenges and real-world applications, with annotations for each vulnerable function detailing the vulnerability type and its root cause. Through our experiments encompassing 16 LLMs and 6 state-of-the-art (SOTA) deep learning-based models and static analyzers, we find that several LLMs outperform traditional deep learning approaches in vulnerability detection, revealing an untapped potential in LLMs. This work contributes to the understanding and utilization of LLMs for enhanced software security.

Hao Wang, Zeyu Gao, Chao Zhang et al.

Binary code representation learning has shown significant performance in binary analysis tasks. But existing solutions often have poor transferability, particularly in few-shot and zero-shot scenarios where few or no training samples are available for the tasks. To address this problem, we present CLAP (Contrastive Language-Assembly Pre-training), which employs natural language supervision to learn better representations of binary code (i.e., assembly code) and get better transferability. At the core, our approach boosts superior transfer learning capabilities by effectively aligning binary code with their semantics explanations (in natural language), resulting a model able to generate better embeddings for binary code. To enable this alignment training, we then propose an efficient dataset engine that could automatically generate a large and diverse dataset comprising of binary code and corresponding natural language explanations. We have generated 195 million pairs of binary code and explanations and trained a prototype of CLAP. The evaluations of CLAP across various downstream tasks in binary analysis all demonstrate exceptional performance. Notably, without any task-specific training, CLAP is often competitive with a fully supervised baseline, showing excellent transferability. We release our pre-trained model and code at https://github.com/Hustcw/CLAP.

Qian Wang, Zhaoyang Bu, Jiaxuan Mao et al.

Recent advancements in deep learning techniques have sparked performance boosts in various real-world applications including disease diagnosis based on multi-modal medical data. Cough sound data-based respiratory disease (e.g., COVID-19 and Chronic Obstructive Pulmonary Disease) diagnosis has also attracted much attention. However, existing works usually utilise traditional machine learning or deep models of moderate scales. On the other hand, the developed approaches are trained and evaluated on small-scale data due to the difficulty of curating and annotating clinical data on scale. To address these issues in prior works, we create a unified framework to evaluate various deep models from lightweight Convolutional Neural Networks (e.g., ResNet18) to modern vision transformers and compare their performance in respiratory disease classification. Based on the observations from such an extensive empirical study, we propose a novel approach to cough-based disease classification based on both self-supervised and supervised learning on a large-scale cough data set. Experimental results demonstrate our proposed approach outperforms prior arts consistently on two benchmark datasets for COVID-19 diagnosis and a proprietary dataset for COPD/non-COPD classification with an AUROC of 92.5%.

Jianhui Wang, Yangfan He, Yan Zhong et al.

Modern text-to-image generation systems have enabled the creation of remarkably realistic and high-quality visuals, yet they often falter when handling the inherent ambiguities in user prompts. In this work, we present Twin-Co, a framework that leverages synchronized, co-adaptive dialogue to progressively refine image generation. Instead of a static generation process, Twin-Co employs a dynamic, iterative workflow where an intelligent dialogue agent continuously interacts with the user. Initially, a base image is generated from the user's prompt. Then, through a series of synchronized dialogue exchanges, the system adapts and optimizes the image according to evolving user feedback. The co-adaptive process allows the system to progressively narrow down ambiguities and better align with user intent. Experiments demonstrate that Twin-Co not only enhances user experience by reducing trial-and-error iterations but also improves the quality of the generated images, streamlining the creative process across various applications.

Yusi Fan, Tian Wang, Zhiying Yan et al.

Feature selection is a combinatorial optimization problem that is NP-hard. Conventional approaches often employ heuristic or greedy strategies, which are prone to premature convergence and may fail to capture subtle yet informative features. This limitation becomes especially critical in high-dimensional datasets, where complex and interdependent feature relationships prevail. We introduce the HeFS (Helper-Enhanced Feature Selection) framework to refine feature subsets produced by existing algorithms. HeFS systematically searches the residual feature space to identify a Helper Set - features that complement the original subset and improve classification performance. The approach employs a biased initialization scheme and a ratio-guided mutation mechanism within a genetic algorithm, coupled with Pareto-based multi-objective optimization to jointly maximize predictive accuracy and feature complementarity. Experiments on 18 benchmark datasets demonstrate that HeFS consistently identifies overlooked yet informative features and achieves superior performance over state-of-the-art methods, including in challenging domains such as gastric cancer classification, drug toxicity prediction, and computer science applications. The code and datasets are available at https://healthinformaticslab.org/supp/.

Wenyu Zhu, Chengzhu Li, Xiaohe Tian et al.

Molecular optimization is a central task in drug discovery that requires precise structural reasoning and domain knowledge. While large language models (LLMs) have shown promise in generating high-level editing intentions in natural language, they often struggle to faithfully execute these modifications-particularly when operating on non-intuitive representations like SMILES. We introduce MECo, a framework that bridges reasoning and execution by translating editing actions into executable code. MECo reformulates molecular optimization for LLMs as a cascaded framework: generating human-interpretable editing intentions from a molecule and property goal, followed by translating those intentions into executable structural edits via code generation. Our approach achieves over 98% accuracy in reproducing held-out realistic edits derived from chemical reactions and target-specific compound pairs. On downstream optimization benchmarks spanning physicochemical properties and target activities, MECo substantially improves consistency by 38-86 percentage points to 90%+ and achieves higher success rates over SMILES-based baselines while preserving structural similarity. By aligning intention with execution, MECo enables consistent, controllable and interpretable molecular design, laying the foundation for high-fidelity feedback loops and collaborative human-AI workflows in drug discovery.

Jianhui Wang, Wenyu Zhu, Bowen Gao et al.

Protein-ligand binding prediction is central to virtual screening and affinity ranking, two fundamental tasks in drug discovery. While recent retrieval-based methods embed ligands and protein pockets into Euclidean space for similarity-based search, the geometry of Euclidean embeddings often fails to capture the hierarchical structure and fine-grained affinity variations intrinsic to molecular interactions. In this work, we propose HypSeek, a hyperbolic representation learning framework that embeds ligands, protein pockets, and sequences into Lorentz-model hyperbolic space. By leveraging the exponential geometry and negative curvature of hyperbolic space, HypSeek enables expressive, affinity-sensitive embeddings that can effectively model both global activity and subtle functional differences-particularly in challenging cases such as activity cliffs, where structurally similar ligands exhibit large affinity gaps. Our mode unifies virtual screening and affinity ranking in a single framework, introducing a protein-guided three-tower architecture to enhance representational structure. HypSeek improves early enrichment in virtual screening on DUD-E from 42.63 to 51.44 (+20.7%) and affinity ranking correlation on JACS from 0.5774 to 0.7239 (+25.4%), demonstrating the benefits of hyperbolic geometry across both tasks and highlighting its potential as a powerful inductive bias for protein-ligand modeling.

Wenyu Zhu, Zhiyao Feng, Zihan Zhang et al.

Recovering binary programs' call graphs is crucial for inter-procedural analysis tasks and applications based on them.transfer One of the core challenges is recognizing targets of indirect calls (i.e., indirect callees). Existing solutions all have high false positives and negatives, making call graphs inaccurate. In this paper, we propose a new solution Callee combining transfer learning and contrastive learning. The key insight is that, deep neural networks (DNNs) can automatically identify patterns concerning indirect calls, which can be more efficient than designing approximation algorithms or heuristic rules to handle various cases. Inspired by the advances in question-answering applications, we utilize contrastive learning to answer the callsite-callee question. However, one of the toughest challenges is that DNNs need large datasets to achieve high performance, while collecting large-scale indirect-call ground-truths can be computational-expensive. Since direct calls and indirect calls share similar calling conventions, it is possible to transfer knowledge learned from direct calls to indirect ones. Therefore, we leverage transfer learning to pre-train DNNs with easy-to-collect direct calls and further fine-tune the indirect-call DNNs. We evaluate Callee on several groups of targets, and results show that our solution could match callsites to callees with an F1-Measure of 94.6%, much better than state-of-the-art solutions. Further, we apply Callee to binary code similarity detection and hybrid fuzzing, and found it could greatly improve their performance.