Hongzong Li

Fengrui Zhang, Yujia Yin, Hongzong Li et al.

Despite significant advancements in causal research on graphs and its application to cracking label imbalance, the role of edge features in detecting the causal effects within graphs has been largely overlooked, leaving existing methods with untapped potential for further performance gains. In this paper, we enhance the causal attention mechanism through effectively leveraging edge information to disentangle the causal subgraph from the original graph, as well as further utilizing edge features to reshape graph representations. Capturing more comprehensive causal signals, our design leads to improved performance on graph classification tasks with label imbalance issues. We evaluate our approach on real-word datasets PTC, Tox21, and ogbg-molhiv, observing improvements over baselines. Overall, we highlight the importance of edge features in graph causal detection and provide a promising direction for addressing label imbalance challenges in graph-level tasks. The model implementation details and the codes are available on https://github.com/fengrui-z/ECAL

Zhang-Yu You, Jiahao Ma, Hongzong Li et al.

Accurate prediction of antibody-antigen (Ab-Ag) interfaces is critical for vaccine design, immunodiagnostics, and therapeutic antibody development. However, achieving reliable predictions from sequences alone remains a challenge. In this paper, we present ABCONFORMER, a model based on the Conformer backbone that captures both local and global features of a biosequence. To accurately capture Ab-Ag interactions, we introduced the physics-inspired sliding attention, enabling residue-level contact recovery without relying on three-dimensional structural data. ABConformer can accurately predict paratopes and epitopes given the antibody and antigen sequence, and predict pan-epitopes on the antigen without antibody information. In comparison experiments, ABCONFORMER achieves state-of-the-art performance on a recent SARS-CoV-2 Ab-Ag dataset, and surpasses widely used sequence-based methods for antibody-agnostic epitope prediction. Ablation studies further quantify the contribution of each component, demonstrating that, compared to conventional cross-attention, sliding attention significantly enhances the precision of epitope prediction. To facilitate reproducibility, we will release the code under an open-source license upon acceptance.

Ao Ding, Hongzong Li, Zi Liang et al.

Large language models (LLMs) are increasingly deployed on edge devices under strict computation and quantization constraints, yet their security implications remain unclear. We study query-based knowledge extraction from quantized edge-deployed LLMs under realistic query budgets and show that, although quantization introduces noise, it does not remove the underlying semantic knowledge, allowing substantial behavioral recovery through carefully designed queries. To systematically analyze this risk, we propose \textbf{CLIQ} (\textbf{Cl}ustered \textbf{I}nstruction \textbf{Q}uerying), a structured query construction framework that improves semantic coverage while reducing redundancy. Experiments on quantized Qwen models (INT8/INT4) demonstrate that CLIQ consistently outperforms original queries across BERTScore, BLEU, and ROUGE, enabling more efficient extraction under limited budgets. These results indicate that quantization alone does not provide effective protection against query-based extraction, highlighting a previously underexplored security risk in edge-deployed LLMs.

Shiqin Tang, Rong Feng, Shuxin Zhuang et al.

We study counterfactual prediction under assignment bias and propose a mathematically grounded, information-theoretic approach that removes treatment-covariate dependence without adversarial training. Starting from a bound that links the counterfactual-factual risk gap to mutual information, we learn a stochastic representation Z that is predictive of outcomes while minimizing I(Z; T). We derive a tractable variational objective that upper-bounds the information term and couples it with a supervised decoder, yielding a stable, provably motivated training criterion. The framework extends naturally to dynamic settings by applying the information penalty to sequential representations at each decision time. We evaluate the method on controlled numerical simulations and a real-world clinical dataset, comparing against recent state-of-the-art balancing, reweighting, and adversarial baselines. Across metrics of likelihood, counterfactual error, and policy evaluation, our approach performs favorably while avoiding the training instabilities and tuning burden of adversarial schemes.

Shiqin Tang, Shuxin Zhuang, Rong Feng et al.

Latent-variable energy-based models (LVEBMs) assign a single normalized energy to joint pairs of observed data and latent variables, offering expressive generative modeling while capturing hidden structure. We recast maximum-likelihood training as a saddle problem over distributions on the latent and joint manifolds and view the inner updates as coupled Wasserstein gradient flows. The resulting algorithm alternates overdamped Langevin updates for a joint negative pool and for conditional latent particles with stochastic parameter ascent, requiring no discriminator or auxiliary networks. We prove existence and convergence under standard smoothness and dissipativity assumptions, with decay rates in KL divergence and Wasserstein-2 distance. The saddle-point view further yields an ELBO strictly tighter than bounds obtained with restricted amortized posteriors. Our method is evaluated on numerical approximations of physical systems and performs competitively against comparable approaches.

Hongzong Li, Jiahao Ma, Zhanpeng Shi et al.

Antibody binding site prediction plays a pivotal role in computational immunology and therapeutic antibody design. Existing sequence or structure methods rely on single-view features and fail to identify antibody-specific binding sites on the antigens. In this paper, we propose \textbf{CAME-AB}, a novel Cross-modality Attention framework with a Mixture-of-Experts (MoE) backbone for robust antibody binding site prediction. CAME-AB integrates five biologically grounded modalities, including raw amino acid encodings, BLOSUM substitution profiles, pretrained language model embeddings, structure-aware features, and GCN-refined biochemical graphs, into a unified multimodal representation. To enhance adaptive cross-modal reasoning, we propose an \emph{adaptive modality fusion} module that learns to dynamically weight each modality based on its global relevance and input-specific contribution. A Transformer encoder combined with an MoE module further promotes feature specialization and capacity expansion. We additionally incorporate a supervised contrastive learning objective to explicitly shape the latent space geometry, encouraging intra-class compactness and inter-class separability. To improve optimization stability and generalization, we apply stochastic weight averaging during training. Extensive experiments on benchmark antibody-antigen datasets demonstrate that CAME-AB consistently outperforms strong baselines on multiple metrics, including Precision, Recall, F1-score, AUC-ROC, and MCC. Ablation studies further validate the effectiveness of each architectural component and the benefit of multimodal feature integration. The model implementation details and the codes are available on https://anonymous.4open.science/r/CAME-AB-C525

Zhangyu You, Jiahao Ma, Hongzong Li et al.

Accurate prediction of antibody-binding sites (epitopes) on antigens is crucial for vaccine design, immunodiagnostics, therapeutic antibody development, antibody engineering, research into autoimmune and allergic diseases, and for advancing our understanding of immune responses. Despite in silico methods that have been proposed to predict both linear (continuous) and conformational (discontinuous) epitopes, they consistently underperform in predicting conformational epitopes. In this work, we propose a conformer-based model trained on antigen sequences derived from 1,080 antigen-antibody complexes, leveraging convolutional neural networks (CNNs) to extract local features and Transformers to capture long-range dependencies within antigen sequences. Ablation studies demonstrate that CNN enhances the prediction of linear epitopes, and the Transformer module improves the prediction of conformational epitopes. Experimental results show that our model outperforms existing baselines in terms of PCC, ROC-AUC, PR-AUC, and F1 scores on both linear and conformational epitopes.