Zihan Liu

Samuel Cahyawijaya, Tiezheng Yu, Zihan Liu et al.

Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they focus only on understanding haploid sequences, which hinders their applicability towards understanding genetic variations, also known as single nucleotide polymorphisms (SNPs), which is crucial for genome-wide association study. In this paper, we introduce SNP2Vec, a scalable self-supervised pre-training approach for understanding SNP. We apply SNP2Vec to perform long-sequence genomics modeling, and we evaluate the effectiveness of our approach on predicting Alzheimer's disease risk in a Chinese cohort. Our approach significantly outperforms existing polygenic risk score methods and all other baselines, including the model that is trained entirely with haploid sequences. We release our code and dataset on https://github.com/HLTCHKUST/snp2vec.

Zihan Liu, Jiaqi Wang, Yun Luo et al.

In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has enabled the efficient collection of large peptide datasets, providing reliable training data for deep learning. However, the lack of systematic analysis of the peptide encoding, which is essential for AI-assisted peptide-related tasks, makes it an urgent problem to be solved for the improvement of prediction accuracy. To address this issue, we first collect a high-quality, colossal simulation dataset of peptide self-assembly containing over 62,000 samples generated by coarse-grained molecular dynamics (CGMD). Then, we systematically investigate the effect of peptide encoding of amino acids into sequences and molecular graphs using state-of-the-art sequential (i.e., RNN, LSTM, and Transformer) and structural deep learning models (i.e., GCN, GAT, and GraphSAGE), on the accuracy of peptide self-assembly prediction, an essential physiochemical process prior to any peptide-related applications. Extensive benchmarking studies have proven Transformer to be the most powerful sequence-encoding-based deep learning model, pushing the limit of peptide self-assembly prediction to decapeptides. In summary, this work provides a comprehensive benchmark analysis of peptide encoding with advanced deep learning models, serving as a guide for a wide range of peptide-related predictions such as isoelectric points, hydration free energy, etc.

Zihan Liu, Ge Wang, Jiaqi Wang et al.

Peptides are formed by the dehydration condensation of multiple amino acids. The primary structure of a peptide can be represented either as an amino acid sequence or as a molecular graph consisting of atoms and chemical bonds. Previous studies have indicated that deep learning routes specific to sequential and graphical peptide forms exhibit comparable performance on downstream tasks. Despite the fact that these models learn representations of the same modality of peptides, we find that they explain their predictions differently. Considering sequential and graphical models as two experts making inferences from different perspectives, we work on fusing expert knowledge to enrich the learned representations for improving the discriminative performance. To achieve this, we propose a peptide co-modeling method, RepCon, which employs a contrastive learning-based framework to enhance the mutual information of representations from decoupled sequential and graphical end-to-end models. It considers representations from the sequential encoder and the graphical encoder for the same peptide sample as a positive pair and learns to enhance the consistency of representations between positive sample pairs and to repel representations between negative pairs. Empirical studies of RepCon and other co-modeling methods are conducted on open-source discriminative datasets, including aggregation propensity, retention time, antimicrobial peptide prediction, and family classification from Peptide Database. Our results demonstrate the superiority of the co-modeling approach over independent modeling, as well as the superiority of RepCon over other methods under the co-modeling framework. In addition, the attribution on RepCon further corroborates the validity of the approach at the level of model explanation.

Yufei Huang, Siyuan Li, Jin Su et al.

Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein structure data and fail in scenarios where these data are unavailable. Predicted protein structures from AI tools (e.g., AlphaFold2) were utilized as alternatives. However, we observed that current practices, which simply employ accurately predicted structures during inference, suffer from notable degradation in prediction accuracy. While similar phenomena have been extensively studied in general fields (e.g., Computer Vision) as model robustness, their impact on protein property prediction remains unexplored. In this paper, we first investigate the reason behind the performance decrease when utilizing predicted structures, attributing it to the structure embedding bias from the perspective of structure representation learning. To study this problem, we identify a Protein 3D Graph Structure Learning Problem for Robust Protein Property Prediction (PGSL-RP3), collect benchmark datasets, and present a protein Structure embedding Alignment Optimization framework (SAO) to mitigate the problem of structure embedding bias between the predicted and experimental protein structures. Extensive experiments have shown that our framework is model-agnostic and effective in improving the property prediction of both predicted structures and experimental structures. The benchmark datasets and codes will be released to benefit the community.

Zihan Liu, Prashant N. Kambali, C. Nataraj

Accurate models are essential for design, performance prediction, control, and diagnostics in complex engineering systems. Physics-based models excel during the design phase but often become outdated during system deployment due to changing operational conditions, unknown interactions, excitations, and parametric drift. While data-based models can capture the current state of complex systems, they face significant challenges, including excessive data dependence, limited generalizability to changing conditions, and inability to predict parametric dependence. This has led to combining physics and data in modeling, termed physics-infused machine learning, often using numerical simulations from physics-based models. This paper introduces a novel approach that departs from standard techniques by uncovering information from nonlinear dynamical modeling and embedding it in data-based models. The goal is to create a hybrid adaptive modeling framework that integrates data-based modeling with newly measured data and analytical nonlinear dynamical models for enhanced accuracy, parametric dependence, and improved generalizability. By explicitly incorporating nonlinear dynamic phenomena through perturbation methods, the predictive capabilities are more realistic and insightful compared to knowledge obtained from brute-force numerical simulations. In particular, perturbation methods are utilized to derive asymptotic solutions which are parameterized to generate frequency responses. Frequency responses provide comprehensive insights into dynamics and nonlinearity which are quantified and extracted as high-quality features. A machine-learning model, trained by these features, tracks parameter variations and updates the mismatched model. The results demonstrate that this adaptive modeling method outperforms numerical gray box models in prediction accuracy and computational efficiency.