Recent progress in engineering highly promising biocatalysts has increasingly involved machine learning methods. These methods leverage existing experimental and simulation data to aid in the discovery and annotation of promising enzymes, as well as in suggesting beneficial mutations for improving known targets. The field of machine learning for protein engineering is gathering steam, driven by recent success stories and notable progress in other areas. It already encompasses ambitious tasks such as understanding and predicting protein structure and function, catalytic efficiency, enantioselectivity, protein dynamics, stability, solubility, aggregation, and more. Nonetheless, the field is still evolving, with many challenges to overcome and questions to address. In this Perspective, we provide an overview of ongoing trends in this domain, highlight recent case studies, and examine the current limitations of machine learning-based methods. We emphasize the crucial importance of thorough experimental validation of emerging models before their use for rational protein design. We present our opinions on the fundamental problems and outline the potential directions for future research.

Machine Learning-Guided Protein Engineering

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology. 

Current and future directions in network biology

Graph neural networks (GNNs) have achieved impressive impressions for graph-related tasks. However, most GNNs are primarily studied under the cases of signal domain with supervised training, which requires abundant task-specific labels and is difficult to transfer to other domains. There are few works focused on domain adaptation for graph node classification. They mainly focused on aligning the feature space of the source and target domains, without considering the feature alignment between different categories, which may lead to confusion of classification in the target domain. However, due to the scarcity of labels of the target domain, we cannot directly perform effective alignment of categories from different domains, which makes the problem more challenging. In this paper, we present the Spectral Augmentation for Graph Domain Adaptation (SA-GDA) for graph node classification. First, we observe that nodes with the same category in different domains exhibit similar characteristics in the spectral domain, while different classes are quite different. Following the observation, we align the category feature space of different domains in the spectral domain instead of aligning the whole features space, and we theoretical proof the stability of proposed SA-GDA. Then, we develop a dual graph convolutional network to jointly exploits local and global consistency for feature aggregation. Last, we utilize a domain classifier with an adversarial learning submodule to facilitate knowledge transfer between different domain graphs. Experimental results on a variety of publicly available datasets reveal the effectiveness of our SA-GDA.

SA-GDA: Spectral Augmentation for Graph Domain Adaptation

In this work, we focus on robust time series representation learning. Our assumption is that real-world time series is noisy and complementary information from different views of the same time series plays an important role while analyzing noisy input. Based on this, we create two views for the input time series through two different encoders. We conduct co-training based contrastive learning iteratively to learn the encoders. Our experiments demonstrate that this co-training approach leads to a significant improvement in performance. Especially, by leveraging the complementary information from different views, our proposed TS-CoT method can mitigate the impact of data noise and corruption. Empirical evaluations on four time series benchmarks in unsupervised and semi-supervised settings reveal that TS-CoT outperforms existing methods. Furthermore, the representations learned by TS-CoT can transfer well to downstream tasks through fine-tuning1.

pdf/a-co-training-approach-for-noisy-time-series-learning-2a3bwaxb0o.pdf

A Co-training Approach for Noisy Time Series Learning

Preservatives are added as antimicrobial agents to extend the shelf life of meat. Adding preservatives to meat products can affect their flavor and nutrition. This review clarifies the effects of preservatives on metabolic pathways and network molecular transformations in meat products based on lipidomics, metabolomics and proteomics analyses. Preservatives change the nutrient content of meat products via altering ionic strength and pH to influence enzyme activity. Ionic strength in salt triggers muscle triglyceride hydrolysis by causing phosphorylation and lipid droplet splitting in adipose tissue hormone-sensitive lipase and triglyceride lipase. DisoLipPred exploiting deep recurrent networks and transfer learning can predict the lipid binding trend of each amino acid in the disordered region of input protein sequences, which could provide omics analyses of biomarkers metabolic pathways in meat products. While conventional meat quality assessment tools are unable to elucidate the intrinsic mechanisms and pathways of variables in the influences of preservatives on the quality of meat products, the promising application of omics techniques in food analysis and discovery through multimodal learning prediction algorithms of neural networks (e.g., deep neural network, convolutional neural network, artificial neural network) will drive the meat industry to develop new strategies for food spoilage prevention and control.

Integrative deep learning framework predicts lipidomics-based investigation of preservatives on meat nutritional biomarkers and metabolic pathways.

Protein-Protein Interactions (PPIs) are fundamental means of functions and signalings in biological systems. The massive growth in demand and cost associated with experimental PPI studies calls for computational tools for automated prediction and understanding of PPIs. Despite recent progress, in silico methods remain inadequate in modeling the natural PPI hierarchy. Here we present a double-viewed hierarchical graph learning model, HIGH-PPI, to predict PPIs and extrapolate the molecular details involved. In this model, we create a hierarchical graph, in which a node in the PPI network (top outside-of-protein view) is a protein graph (bottom inside-of-protein view). In the bottom view, a group of chemically relevant descriptors, instead of the protein sequences, are used to better capture the structure-function relationship of the protein. HIGH-PPI examines both outside-of-protein and inside-of-protein of the human interactome to establish a robust machine understanding of PPIs. This model demonstrates high accuracy and robustness in predicting PPIs. Moreover, HIGH-PPI can interpret the modes of action of PPIs by identifying important binding and catalytic sites precisely. Overall, "HIGH-PPI [ https://github.com/zqgao22/HIGH-PPI ]" is a domain-knowledge-driven and interpretable framework for PPI prediction studies. 

/pdf/hierarchical-graph-learning-for-protein-protein-interaction-2qw86ao5.pdf

Hierarchical graph learning for protein–protein interaction

Irregularly sampled multivariate time series are ubiquitous in various fields, particularly in healthcare, and exhibit two key characteristics: intra-series irregularity and inter-series discrepancy. Intra-series irregularity refers to the fact that time-series signals are often recorded at irregular intervals, while inter-series discrepancy refers to the significant variability in sampling rates among diverse series. However, recent advances in irregular time series have primarily focused on addressing intra-series irregularity, overlooking the issue of inter-series discrepancy. To bridge this gap, we present Warpformer, a novel approach that fully considers these two characteristics. In a nutshell, Warpformer has several crucial designs, including a specific input representation that explicitly characterizes both intra-series irregularity and inter-series discrepancy, a warping module that adaptively unifies irregular time series in a given scale, and a customized attention module for representation learning. Additionally, we stack multiple warping and attention modules to learn at different scales, producing multi-scale representations that balance coarse-grained and fine-grained signals for downstream tasks. We conduct extensive experiments on widely used datasets and a new large-scale benchmark built from clinical databases. The results demonstrate the superiority of Warpformer over existing state-of-the-art approaches.

/pdf/warpformer-a-multi-scale-modeling-approach-for-irregular-2m149trx.pdf

Warpformer: A Multi-scale Modeling Approach for Irregular Clinical Time Series

Time-series forecasting serves as a linchpin in a myriad of applications, spanning various domains. With the growth of deep learning, this arena has bifurcated into two salient branches: one focuses on crafting specific neural architectures tailored for time series, and the other harnesses advanced deep generative models for probabilistic forecasting. While both branches have made significant progress, their differences across data scenarios, methodological focuses, and decoding schemes pose profound, yet unexplored, research questions. To bridge this knowledge chasm, we introduce ProbTS, a pioneering toolkit developed to synergize and compare these two distinct branches. Endowed with a unified data module, a modularized model module, and a comprehensive evaluator module, ProbTS allows us to revisit and benchmark leading methods from both branches. The scrutiny with ProbTS highlights their distinct characteristics, relative strengths and weaknesses, and areas that need further exploration. Our analyses point to new avenues for research, aiming for more effective time-series forecasting.

pdf/probts-a-unified-toolkit-to-probe-deep-time-series-43nsuqdwzu.pdf

ProbTS: A Unified Toolkit to Probe Deep Time-series Forecasting

pdf/unify-and-anchor-a-context-aware-transformer-for-cross-b3n9mf38hqwi.pdf

Unify and Anchor: A Context-Aware Transformer for Cross-Domain Time Series Forecasting

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Hierarchical graph learning for protein–protein interaction

Warpformer: A Multi-scale Modeling Approach for Irregular Clinical Time Series

ProbTS: A Unified Toolkit to Probe Deep Time-series Forecasting

Unify and Anchor: A Context-Aware Transformer for Cross-Domain Time Series Forecasting