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Proteins, often represented as multi-modal data of 1D sequences and 2D/3D structures, provide a motivating example for the communities of machine learning and computational biology to advance multi-modal representation learning. Protein language models over sequences and geometric deep learning over structures learn excellent single-modality representations for downstream tasks. It is thus desirable to fuse the single-modality models for better representation learning, but it remains an open question on how to fuse them effectively into multi-modal representation learning with a modest computational cost yet significant downstream performance gain. To answer the question, we propose to make use of separately pretrained single-modality models, integrate them in parallel connections, and continuously pretrain them end-to-end under the framework of multimodal contrastive learning. The technical challenge is to construct views for both intra- and inter-modality contrasts while addressing the heterogeneity of various modalities, particularly various levels of semantic robustness. We address the challenge by using domain knowledge of protein homology to inform the design of positive views, specifically protein classifications of families (based on similarities in sequences) and superfamilies (based on similarities in structures). We also assess the use of such views compared to, together with, and composed to other positive views such as identity and cropping. Extensive experiments on enzyme classification and protein function prediction benchmarks demonstrate the potential of domain-informed view construction and combination in multi-modal contrastive learning 

Abstract MotivationComputational methods for compound–protein affinity and contact (CPAC) prediction aim at facilitating rational drug discovery by simultaneous prediction of the strength and the pattern of compound–protein interactions. Although the desired outputs are highly structure-dependent, the lack of protein structures often makes structure-free methods rely on protein sequence inputs alone. The scarcity of compound–protein pairs with affinity and contact labels further limits the accuracy and the generalizability of CPAC models. ResultsTo overcome the aforementioned challenges of structure naivety and labeled-data scarcity, we introduce cross-modality and self-supervised learning, respectively, for structure-aware and task-relevant protein embedding. Specifically, protein data are available in both modalities of 1D amino-acid sequences and predicted 2D contact maps that are separately embedded with recurrent and graph neural networks, respectively, as well as jointly embedded with two cross-modality schemes. Furthermore, both protein modalities are pre-trained under various self-supervised learning strategies, by leveraging massive amount of unlabeled protein data. Our results indicate that individual protein modalities differ in their strengths of predicting affinities or contacts. Proper cross-modality protein embedding combined with self-supervised learning improves model generalizability when predicting both affinities and contacts for unseen proteins. Availability and implementationData and source codes are available at https://github.com/Shen-Lab/CPAC. Supplementary informationSupplementary data are available at Bioinformatics online. 

Optimizing an objective function with uncertainty awareness is well-known to improve the accuracy and confidence of optimization solutions. Meanwhile, another relevant but very different question remains yet open: how to model and quantify the uncertainty of an optimization algorithm (aka, optimizer) itself? To close such a gap, the prerequisite is to consider the optimizers as sampled from a distribution, rather than a few prefabricated and fixed update rules. We first take the novel angle to consider the algorithmic space of optimizers, and provide definitions for the optimizer prior and likelihood, that intrinsically determine the posterior and therefore uncertainty. We then leverage the recent advance of learning to optimize (L2O) for the space parameterization, with the end-to-end training pipeline built via variational inference, referred to as uncertainty-aware L2O (UA-L2O). Our study represents the first effort to recognize and quantify the uncertainty of the optimization algorithm. The extensive numerical results show that, UA-L2O achieves superior uncertainty calibration with accurate confidence estimation and tight confidence intervals, suggesting the improved posterior estimation thanks to considering optimizer uncertainty. Intriguingly, UA-L2O even improves optimization performances for two out of three test functions, the loss function in data privacy attack, and four of five cases of the energy function in protein docking. Our codes are released at https://github. com/Shen-Lab/Bayesian-L2O. 

Optimizing an objective function with uncertainty awareness is well-known to improve the accuracy and confidence of optimization solutions. Meanwhile, another relevant but very different question remains yet open: how to model and quantify the uncertainty of an optimization algorithm (a.k.a., optimizer) itself? To close such a gap, the prerequisite is to consider the optimizers as sampled from a distribution, rather than a few prefabricated and fixed update rules. We first take the novel angle to consider the algorithmic space of optimizers, and provide definitions for the optimizer prior and likelihood, that intrinsically determine the posterior and therefore uncertainty. We then leverage the recent advance of learning to optimize (L2O) for the space parameterization, with the end-to-end training pipeline built via variational inference, referred to as uncertainty-aware L2O (UA-L2O). Our study represents the first effort to recognize and quantify the uncertainty of the optimization algorithm. The extensive numerical results show that, UA-L2O achieves superior uncertainty calibration with accurate confidence estimation and tight confidence intervals, suggesting the improved posterior estimation thanks to considering optimizer uncertainty. Intriguingly, UA-L2O even improves optimization performances for two out of three test functions, the loss function in data privacy attack, and four of five cases of the energy function in protein docking. Our codes are released at https://github.com/Shen-Lab/Bayesian-L2O. 

This paper targets at improving the generalizability of hypergraph neural networks in the low-label regime, through applying the contrastive learning approach from images/graphs (we refer to it as HyperGCL). We focus on the following question: How to construct contrastive views for hypergraphs via augmentations? We provide the solutions in two folds. First, guided by domain knowledge, we fabricate two schemes to augment hyperedges with higher-order relations encoded, and adopt three vertex augmentation strategies from graph-structured data. Second, in search of more effective views in a data-driven manner, we for the first time propose a hypergraph generative model to generate augmented views, and then an end-to-end differentiable pipeline to jointly learn hypergraph augmentations and model parameters. Our technical innovations are reflected in designing both fabricated and generative augmentations of hypergraphs. The experimental findings include: (i) Among fabricated augmentations in HyperGCL, augmenting hyperedges provides the most numerical gains, implying that higher-order information in structures is usually more downstream-relevant; (ii) Generative augmentations do better in preserving higher-order information to further benefit generalizability; (iii) HyperGCL also boosts robustness and fairness in hypergraph representation learning. Codes are released at https://github.com/weitianxin/HyperGCL. 

Compound-protein pairs dominate FDA-approved drug-target pairs and the prediction of compound-protein affinity and contact (CPAC) could help accelerate drug discovery. In this study we consider proteins as multi-modal data including 1D amino-acid sequences and (sequence-predicted) 2D residue-pair contact maps. We empirically evaluate the embeddings of the two single modalities in their accuracyand generalizability of CPAC prediction (i.e. structure-free interpretable compound-protein affinity prediction). And we rationalize their performances in both challenges of embedding individual modalities and learning generalizable embedding-label relationship. We further propose two models involving cross-modality protein embedding and establish that the one with cross interaction (thus capturing correlations among modalities) outperforms SOTAs and our single modality models in affinity, contact, and binding-site predictions for proteins never seen in the training set.