Zebin Ma

Zebin Ma, Yonglin Zou, Xiaobin Huang et al.

Functional peptides have the potential to treat a variety of diseases. Their good therapeutic efficacy and low toxicity make them ideal therapeutic agents. Artificial intelligence-based computational strategies can help quickly identify new functional peptides from collections of protein sequences and discover their different functions.Using protein language model-based embeddings (ESM-2), we developed a tool called pLMFPPred (Protein Language Model-based Functional Peptide Predictor) for predicting functional peptides and identifying toxic peptides. We also introduced SMOTE-TOMEK data synthesis sampling and Shapley value-based feature selection techniques to relieve data imbalance issues and reduce computational costs. On a validated independent test set, pLMFPPred achieved accuracy, Area under the curve - Receiver Operating Characteristics, and F1-Score values of 0.974, 0.99, and 0.974, respectively. Comparative experiments show that pLMFPPred outperforms current methods for predicting functional peptides.The experimental results suggest that the proposed method (pLMFPPred) can provide better performance in terms of Accuracy, Area under the curve - Receiver Operating Characteristics, and F1-Score than existing methods. pLMFPPred has achieved good performance in predicting functional peptides and represents a new computational method for predicting functional peptides.

Difei Xu, Meng Ding, Zebin Ma et al.

Real-world deployments routinely face distribution shifts, group imbalances, and adversarial perturbations, under which the traditional Empirical Risk Minimization (ERM) framework can degrade severely. Distributionally Robust Optimization (DRO) addresses this issue by optimizing the worst-case expected loss over an uncertainty set of distributions, offering a principled approach to robustness. Meanwhile, as training data in DRO always involves sensitive information, safeguarding it against leakage under Differential Privacy (DP) is essential. In contrast to classical DP-ERM, DP-DRO has received much less attention due to its minimax optimization structure with uncertainty constraint. To bridge the gap, we provide a comprehensive study of DP-(finite-sum)-DRO with $ψ$-divergence and non-convex loss. First, we study DRO with general $ψ$-divergence by reformulating it as a minimization problem, and develop a novel $(\varepsilon, δ)$-DP optimization method, called DP Double-Spider, tailored to this structure. Under mild assumptions, we show that it achieves a utility bound of $\mathcal{O}(\frac{1}{\sqrt{n}}+ (\frac{\sqrt{d \log (1/δ)}}{n \varepsilon})^{2/3})$ in terms of the gradient norm, where $n$ denotes the data size and $d$ denotes the model dimension. We further improve the utility rate for specific divergences. In particular, for DP-DRO with KL-divergence, by transforming the problem into a compositional finite-sum optimization problem, we develop a DP Recursive-Spider method and show that it achieves a utility bound of $\mathcal{O}((\frac{\sqrt{d \log(1/δ)}}{n\varepsilon})^{2/3} )$, matching the best-known result for non-convex DP-ERM. Experimentally, we demonstrate that our proposed methods outperform existing approaches for DP minimax optimization.

Changwen Xing, SamZaak Wong, Xinlai Wan et al.

While Large Language Models (LLMs) demonstrate immense potential for automating integrated circuit (IC) development, their practical deployment is fundamentally limited by restricted context windows. Existing context-extension methods struggle to achieve effective semantic modeling and thorough multi-hop reasoning over extensive, intricate circuit specifications. To address this, we introduce ChipMind, a novel knowledge graph-augmented reasoning framework specifically designed for lengthy IC specifications. ChipMind first transforms circuit specifications into a domain-specific knowledge graph ChipKG through the Circuit Semantic-Aware Knowledge Graph Construction methodology. It then leverages the ChipKG-Augmented Reasoning mechanism, combining information-theoretic adaptive retrieval to dynamically trace logical dependencies with intent-aware semantic filtering to prune irrelevant noise, effectively balancing retrieval completeness and precision. Evaluated on an industrial-scale specification reasoning benchmark, ChipMind significantly outperforms state-of-the-art baselines, achieving an average improvement of 34.59% (up to 72.73%). Our framework bridges a critical gap between academic research and practical industrial deployment of LLM-aided Hardware Design (LAD).