tFold-TR: Combining Deep Learning Enhanced Hybrid Potential Energy for Template-Based Modelling Structure Refinement

Proteins structure prediction has long been a grand challenge over the past 50 years, owing to its broad scientific and application interests. There are two major types of modelling algorithms, template-free modelling and template-based modelling. The latter one is suitable for easy prediction tasks and is widely adopted in computer-aided drug discoveries for drug design and screening. Although it has been several decades since its first edition, the current template-based modeling approach suffers from two important problems: 1) there are many missing regions in the template-query sequence alignment, and 2) the accuracy of the distance pairs from different regions of the template varies, and this information is not well introduced into the modeling. To solve the two problems, we propose a structural optimization process based on template modelling, introducing two neural network models to predict the distance information of the missing regions and the accuracy of the distance pairs of different regions in the template modeling structure. The predicted distances and residue pairwise-specific deviations are incorporated into the potential energy function for structural optimization, which significantly improves the qualities of the original template modelling decoys.

EBM-Fold: Fully-Differentiable Protein Folding Powered by Energy-based Models

Accurate protein structure prediction from amino-acid sequences is critical to better understanding the protein function. Recent advances in this area largely benefit from more precise inter-residue distance and orientation predictions, powered by deep neural networks. However, the structure optimization procedure is still dominated by traditional tools, e.g. Rosetta, where the structure is solved via minimizing a pre-defined statistical energy function (with optional prediction-based restraints). Such energy function may not be optimal in formulating the whole conformation space of proteins. In this paper, we propose a fully-differentiable approach for protein structure optimization, guided by a data-driven generative network. This network is trained in a denoising manner, attempting to predict the correction signal from corrupted distance matrices between Ca atoms. Once the network is well trained, Langevin dynamics based sampling is adopted to gradually optimize structures from random initialization. Extensive experiments demonstrate that our EBM-Fold approach can efficiently produce high-quality decoys, compared against traditional Rosetta-based structure optimization routines.

Federated Unsupervised Representation Learning

To leverage enormous unlabeled data on distributed edge devices, we formulate a new problem in federated learning called Federated Unsupervised Representation Learning (FURL) to learn a common representation model without supervision while preserving data privacy. FURL poses two new challenges: (1) data distribution shift (Non-IID distribution) among clients would make local models focus on different categories, leading to the inconsistency of representation spaces. (2) without the unified information among clients in FURL, the representations across clients would be misaligned. To address these challenges, we propose Federated Constrastive Averaging with dictionary and alignment (FedCA) algorithm. FedCA is composed of two key modules: (1) dictionary module to aggregate the representations of samples from each client and share with all clients for consistency of representation space and (2) alignment module to align the representation of each client on a base model trained on a public data. We adopt the contrastive loss for local model training. Through extensive experiments with three evaluation protocols in IID and Non-IID settings, we demonstrate that FedCA outperforms all baselines with significant margins.

RatE: Relation-Adaptive Translating Embedding for Knowledge Graph Completion

Many graph embedding approaches have been proposed for knowledge graph completion via link prediction. Among those, translating embedding approaches enjoy the advantages of light-weight structure, high efficiency and great interpretability. Especially when extended to complex vector space, they show the capability in handling various relation patterns including symmetry, antisymmetry, inversion and composition. However, previous translating embedding approaches defined in complex vector space suffer from two main issues: 1) representing and modeling capacities of the model are limited by the translation function with rigorous multiplication of two complex numbers; and 2) embedding ambiguity caused by one-to-many relations is not explicitly alleviated. In this paper, we propose a relation-adaptive translation function built upon a novel weighted product in complex space, where the weights are learnable, relation-specific and independent to embedding size. The translation function only requires eight more scalar parameters each relation, but improves expressive power and alleviates embedding ambiguity problem. Based on the function, we then present our Relation-adaptive translating Embedding (RatE) approach to score each graph triple. Moreover, a novel negative sampling method is proposed to utilize both prior knowledge and self-adversarial learning for effective optimization. Experiments verify RatE achieves state-of-the-art performance on four link prediction benchmarks.

Improving Long-Tail Relation Extraction with Collaborating Relation-Augmented Attention

Wrong labeling problem and long-tail relations are two main challenges caused by distant supervision in relation extraction. Recent works alleviate the wrong labeling by selective attention via multi-instance learning, but cannot well handle long-tail relations even if hierarchies of the relations are introduced to share knowledge. In this work, we propose a novel neural network, Collaborating Relation-augmented Attention (CoRA), to handle both the wrong labeling and long-tail relations. Particularly, we first propose relation-augmented attention network as base model. It operates on sentence bag with a sentence-to-relation attention to minimize the effect of wrong labeling. Then, facilitated by the proposed base model, we introduce collaborating relation features shared among relations in the hierarchies to promote the relation-augmenting process and balance the training data for long-tail relations. Besides the main training objective to predict the relation of a sentence bag, an auxiliary objective is utilized to guide the relation-augmenting process for a more accurate bag-level representation. In the experiments on the popular benchmark dataset NYT, the proposed CoRA improves the prior state-of-the-art performance by a large margin in terms of Precision@N, AUC and Hits@K. Further analyses verify its superior capability in handling long-tail relations in contrast to the competitors.

BiteNet: Bidirectional Temporal Encoder Network to Predict Medical Outcomes

Electronic health records (EHRs) are longitudinal records of a patient's interactions with healthcare systems. A patient's EHR data is organized as a three-level hierarchy from top to bottom: patient journey - all the experiences of diagnoses and treatments over a period of time; individual visit - a set of medical codes in a particular visit; and medical code - a specific record in the form of medical codes. As EHRs begin to amass in millions, the potential benefits, which these data might hold for medical research and medical outcome prediction, are staggering - including, for example, predicting future admissions to hospitals, diagnosing illnesses or determining the efficacy of medical treatments. Each of these analytics tasks requires a domain knowledge extraction method to transform the hierarchical patient journey into a vector representation for further prediction procedure. The representations should embed a sequence of visits and a set of medical codes with a specific timestamp, which are crucial to any downstream prediction tasks. Hence, expressively powerful representations are appealing to boost learning performance. To this end, we propose a novel self-attention mechanism that captures the contextual dependency and temporal relationships within a patient's healthcare journey. An end-to-end bidirectional temporal encoder network (BiteNet) then learns representations of the patient's journeys, based solely on the proposed attention mechanism. We have evaluated the effectiveness of our methods on two supervised prediction and two unsupervised clustering tasks with a real-world EHR dataset. The empirical results demonstrate the proposed BiteNet model produces higher-quality representations than state-of-the-art baseline methods.

Federated Mutual Learning

Federated learning enables collaboratively training machine learning models on decentralized data. The three types of heterogeneous natures that is data, model, and objective bring about unique challenges to the canonical federated learning algorithm (FederatedAveraging), where one shared model is produced by and for all clients. First, due to the Non-IIDness of data, the global shared model may perform worse than local models that solely trained on their private data; Second, clients may need to design their own model because of different communication and computing abilities of devices, which is also private property that should be protected; Third, the objective of achieving consensus throughout the training process will compromise the personalities of clients. In this work, we present a novel federated learning paradigm, named Federated Mutual Leaning (FML), dealing with the three heterogeneities. FML allows clients designing their customized models and training independently, thus the Non-IIDness of data is no longer a bug but a feature that clients can be personally served better. Local customized models can benefit from collaboratively training without compromising personalities. Global model does not have to be an out-of-the-box (OOTB) product but a meta-learner which requires local adaptation for new participants. The experiments show that FML can achieve better performance, robustness and communication efficiency than alternatives.

Self-Attention Enhanced Patient Journey Understanding in Healthcare System

Understanding patients' journeys in healthcare system is a fundamental prepositive task for a broad range of AI-based healthcare applications. This task aims to learn an informative representation that can comprehensively encode hidden dependencies among medical events and its inner entities, and then the use of encoding outputs can greatly benefit the downstream application-driven tasks. A patient journey is a sequence of electronic health records (EHRs) over time that is organized at multiple levels: patient, visits and medical codes. The key challenge of patient journey understanding is to design an effective encoding mechanism which can properly tackle the aforementioned multi-level structured patient journey data with temporal sequential visits and a set of medical codes. This paper proposes a novel self-attention mechanism that can simultaneously capture the contextual and temporal relationships hidden in patient journeys. A multi-level self-attention network (MusaNet) is specifically designed to learn the representations of patient journeys that is used to be a long sequence of activities. The MusaNet is trained in end-to-end manner using the training data derived from EHRs. We evaluated the efficacy of our method on two medical application tasks with real-world benchmark datasets. The results have demonstrated the proposed MusaNet produces higher-quality representations than state-of-the-art baseline methods. The source code is available in https://github.com/xueping/MusaNet.