arXiv subjects

Ruochi Zhang

Publications and source records attributed to Ruochi Zhang.

11 recordsLinked to original sources

arXiv2026

FLaG: Frequency-Domain Latent-attention Gated Pooling for Token Aggregation

Token aggregation converts token-level representations into fixed-dimensional sample representations, but most pooling methods operate only in the original token space. We introduce Frequency-Domain Latent-attention Gated Pooling (FLaG), a plug-in aggregation module that re-expresses encoder outputs in the Fourier domain before final pooling. FLaG represents the nonredundant rFFT spectrum through concatenated real and imaginary components, summarizes spectral tokens with learnable latent queries, derives a sample-conditioned channel gate, and reconstructs modulated token representations for downstream aggregation. We evaluate the same architecture across ESM2-based antimicrobial peptide (AMP) activity prediction, ResNet18 image classification on CIFAR-10 and CIFAR-100, and three RoBERTa-based language tasks. FLaG achieves the best macro-averaged Spearman correlation coefficient, RMSE, and Recall@50 across four AMP backbone-species settings and the highest top-1 accuracy on CIFAR 10. It also achieves the best mean results on five of seven language metrics, although mean pooling remains strongest on STSBenchmark. AMP-side mechanistic analyses reveal low-frequency prediction sensitivity across most encoder layers, with increased relative high-frequency sensitivity in the final layer, and pronounced peptide-specific positional responses. The residual gate broadly amplifies spectral channels while preserving the low-frequency-dominated energy profile, whereas latent cross-attention exhibits sample- and species-specific spectral allocation. Overall, FLaG provides a transferable frequency-domain aggregation bias across protein, visual, and textual representations, with benefits that depend on the backbone and downstream task. Supplementary materials, source code, and data are available at https://www.healthinformaticslab.org/supp/ and https://github.com/Kewei2023/AMPCliff/tree/FLaG.

cs.AI↗

arXiv2026

Frequency-Domain Latent Attention Gating for Cross-Domain Token Aggregation

Token aggregation is a common bottleneck in models that map token representations to sample-level predictions, yet most pooling methods operate only in the original token domain. We propose FLaG, a plug-in aggregation module that transforms token representations with the real FFT, summarizes spectral components with learnable latent queries, applies a channel-wise gate, and reconstructs enhanced time-domain tokens for final pooling. We evaluate FLaG on antimicrobial peptide (AMP) activity prediction with ESM2, image classification with ResNet18 on CIFAR-10 and CIFAR-100, and text classification with RoBERTa on IMDB and GLUE. FLaG achieves its clearest gains on the ESM2-8M antimicrobial peptide tasks and on CIFAR-100, while remaining competitive with strong text baselines on IMDB and GLUE. Then we probe its behavior on the AMP setting with band knockouts, gate summaries, residue perturbations, latent-query readouts, and structure-proxy stratification. We find that low-frequency bands contribute the most overall, and the remaining higher-band pattern is more sample-specific. The gate acts as a broadly shared spectral reweighting stage and the cross-attention patterns are sample-specific with mild query-wise differentiation, and higher-helix peptides exhibit stronger average spectral sensitivity in both bacteria. The supplementary materials, source code and data are released at https://www.healthinformaticslab.org/supp/ and https://github.com/Kewei2023/AMPCliff/tree/FLaG.

cs.LG↗

arXiv2025

HeFS: Helper-Enhanced Feature Selection via Pareto-Optimized Genetic Search

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/.

cs.LG↗

arXiv2025

A transformer-BiGRU-based framework with data augmentation and confident learning for network intrusion detection

In today's fast-paced digital communication, the surge in network traffic data and frequency demands robust and precise network intrusion solutions. Conventional machine learning methods struggle to grapple with complex patterns within the vast network intrusion datasets, which suffer from data scarcity and class imbalance. As a result, we have integrated machine learning and deep learning techniques within the network intrusion detection system to bridge this gap. This study has developed TrailGate, a novel framework that combines machine learning and deep learning techniques. By integrating Transformer and Bidirectional Gated Recurrent Unit (BiGRU) architectures with advanced feature selection strategies and supplemented by data augmentation techniques, TrailGate can identifies common attack types and excels at detecting and mitigating emerging threats. This algorithmic fusion excels at detecting common and well-understood attack types and has the unique ability to swiftly identify and neutralize emerging threats that stem from existing paradigms.

cs.LG↗

arXiv2025

MolProphecy: Bridging Medicinal Chemists' Knowledge and Molecular Pre-Trained Models via a Multi-Modal Framework

MolProphecy is a human-in-the-loop (HITL) multi-modal framework designed to integrate chemists' domain knowledge into molecular property prediction models. While molecular pre-trained models have enabled significant gains in predictive accuracy, they often fail to capture the tacit, interpretive reasoning central to expert-driven molecular design. To address this, MolProphecy employs ChatGPT as a virtual chemist to simulate expert-level reasoning and decision-making. The generated chemist knowledge is embedded by the large language model (LLM) as a dedicated knowledge representation and then fused with graph-based molecular features through a gated cross-attention mechanism, enabling joint reasoning over human-derived and structural features. Evaluated on four benchmark datasets (FreeSolv, BACE, SIDER, and ClinTox), MolProphecy outperforms state-of-the-art (SOTA) models, achieving a 15.0 percent reduction in RMSE on FreeSolv and a 5.39 percent improvement in AUROC on BACE. Analysis reveals that chemist knowledge and structural features provide complementary contributions, improving both accuracy and interpretability. MolProphecy offers a practical and generalizable approach for collaborative drug discovery, with the flexibility to incorporate real chemist input in place of the current simulated proxy--without the need for model retraining. The implementation is publicly available at https://github.com/zhangruochi/MolProphecy.

cs.LG↗

arXiv2025

DeepSelective: Interpretable Prognosis Prediction via Feature Selection and Compression in EHR Data

The rapid accumulation of Electronic Health Records (EHRs) has transformed healthcare by providing valuable data that enhance clinical predictions and diagnoses. While conventional machine learning models have proven effective, they often lack robust representation learning and depend heavily on expert-crafted features. Although deep learning offers powerful solutions, it is often criticized for its lack of interpretability. To address these challenges, we propose DeepSelective, a novel end to end deep learning framework for predicting patient prognosis using EHR data, with a strong emphasis on enhancing model interpretability. DeepSelective combines data compression techniques with an innovative feature selection approach, integrating custom-designed modules that work together to improve both accuracy and interpretability. Our experiments demonstrate that DeepSelective not only enhances predictive accuracy but also significantly improves interpretability, making it a valuable tool for clinical decision-making. The source code is freely available at http://www.healthinformaticslab.org/supp/resources.php .

cs.LG↗

arXiv2025

Information Entropy Invariance: Enhancing Length Extrapolation in Attention Mechanisms

Since the emergence of research on improving the length extrapolation capabilities of large language models in 2021, some studies have made modifications to the scaling factor in the scaled dot-product attention mechanism as part of their proposed methods without rigorous theoretical justifications. To fill this gap, we propose two new scaled temperatures based on information entropy invariance to enhance length extrapolation. First, a training-free method InfoScale is designed for dotproduct attention, and preserves focus on original tokens during length extrapolation by ensuring consistent entropy. Second, we theoretically analyze the impact of scaling (CosScale) on cosine attention. Experimental data demonstrates that combining InfoScale and CosScale achieves state-ofthe-art performance on the GAU-α model with a context window extended to 64 times the training length, and outperforms seven existing methods. Our analysis reveals that significantly increasing CosScale approximates the Windowed Attention, and highlights the significance of attention score dilution as a key challenge in long-range context handling. The code and data are available at https://github.com/HT-NEKO/ Information-Entropy-Invariance.

cs.CL↗

arXiv2024

AMPCliff: quantitative definition and benchmarking of activity cliffs in antimicrobial peptides

Since the mechanism of action of drug molecules in the human body is difficult to reproduce in the in vitro environment, it becomes difficult to reveal the causes of the activity cliff phenomenon of drug molecules. We found out the AC of small molecules has been extensively investigated but limited knowledge is accumulated about the AC phenomenon in peptides with canonical amino acids. Understanding the mechanism of AC in canonical amino acids might help understand the one in drug molecules. This study introduces a quantitative definition and benchmarking framework AMPCliff for the AC phenomenon in antimicrobial peptides (AMPs) composed by canonical amino acids. A comprehensive analysis of the existing AMP dataset reveals a significant prevalence of AC within AMPs. AMPCliff quantifies the activities of AMPs by the MIC, and defines 0.9 as the minimum threshold for the normalized BLOSUM62 similarity score between a pair of aligned peptides with at least two-fold MIC changes. This study establishes a benchmark dataset of paired AMPs in Staphylococcus aureus from the publicly available AMP dataset GRAMPA, and conducts a rigorous procedure to evaluate various AMP AC prediction models, including nine machine learning, four deep learning algorithms, four masked language models, and four generative language models. Our analysis reveals that these models are capable of detecting AMP AC events and the pre-trained protein language model ESM2 demonstrates superior performance across the evaluations. The predictive performance of AMP activity cliffs remains to be further improved, considering that ESM2 with 33 layers only achieves the Spearman correlation coefficient 0.4669 for the regression task of the MIC values on the benchmark dataset. Source code and additional resources are available at https://www.healthinformaticslab.org/supp/ or https://github.com/Kewei2023/AMPCliff-generation.

q-bio.BM↗

arXiv2024

PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding

Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely unaddressed due to the difficulty in capturing the complex and sometimes unstable structures of peptides. This study introduces a novel multi-view contrastive learning framework PepHarmony for the sequence-based peptide encoding task. PepHarmony innovatively combines both sequence- and structure-level information into a sequence-level encoding module through contrastive learning. We carefully select datasets from the Protein Data Bank (PDB) and AlphaFold database to encompass a broad spectrum of peptide sequences and structures. The experimental data highlights PepHarmony's exceptional capability in capturing the intricate relationship between peptide sequences and structures compared with the baseline and fine-tuned models. The robustness of our model is confirmed through extensive ablation studies, which emphasize the crucial roles of contrastive loss and strategic data sorting in enhancing predictive performance. The proposed PepHarmony framework serves as a notable contribution to peptide representations, and offers valuable insights for future applications in peptide drug discovery and peptide engineering. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/PepHarmony or http://www.healthinformaticslab.org/supp/.

cs.LG↗

arXiv2023

PepLand: a large-scale pre-trained peptide representation model for a comprehensive landscape of both canonical and non-canonical amino acids

In recent years, the scientific community has become increasingly interested on peptides with non-canonical amino acids due to their superior stability and resistance to proteolytic degradation. These peptides present promising modifications to biological, pharmacological, and physiochemical attributes in both endogenous and engineered peptides. Notwithstanding their considerable advantages, the scientific community exhibits a conspicuous absence of an effective pre-trained model adept at distilling feature representations from such complex peptide sequences. We herein propose PepLand, a novel pre-training architecture for representation and property analysis of peptides spanning both canonical and non-canonical amino acids. In essence, PepLand leverages a comprehensive multi-view heterogeneous graph neural network tailored to unveil the subtle structural representations of peptides. Empirical validations underscore PepLand's effectiveness across an array of peptide property predictions, encompassing protein-protein interactions, permeability, solubility, and synthesizability. The rigorous evaluation confirms PepLand's unparalleled capability in capturing salient synthetic peptide features, thereby laying a robust foundation for transformative advances in peptide-centric research domains. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/pepland

q-bio.BM↗

arXiv2019

Hyper-SAGNN: a self-attention based graph neural network for hypergraphs

Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.

cs.LG↗