Unsupervised and Supervised Structure Learning for Protein Contact Prediction

Protein contacts provide key information for the understanding of protein structure and function, and therefore contact prediction from sequences is an important problem. Recent research shows that some correctly predicted long-range contacts could help topology-level structure modeling. Thus, contact prediction and contact-assisted protein folding also proves the importance of this problem. In this thesis, I will briefly introduce the extant related work, then show how to establish the contact prediction through unsupervised graphical models with topology constraints. Further, I will explain how to use the supervised deep learning methods to further boost the accuracy of contact prediction. Finally, I will propose a scoring system called diversity score to measure the novelty of contact predictions, as well as an algorithm that predicts contacts with respect to the new scoring system.

Hierarchical Graph Network for Multi-hop Question Answering

In this paper, we present Hierarchical Graph Network (HGN) for multi-hop question answering. To aggregate clues from scattered texts across multiple paragraphs, a hierarchical graph is created by constructing nodes from different levels of granularity (i.e., questions, paragraphs, sentences, and entities), the representations of which are initialized with BERT-based context encoders. By weaving heterogeneous nodes in an integral unified graph, this characteristic hierarchical differentiation of node granularity enables HGN to support different question answering sub-tasks simultaneously (e.g., paragraph selection, supporting facts extraction, and answer prediction). Given a constructed hierarchical graph for each question, the initial node representations are updated through graph propagation; and for each sub-task, multi-hop reasoning is performed by traversing through graph edges. Extensive experiments on the HotpotQA benchmark demonstrate that the proposed HGN approach significantly outperforms prior state-of-the-art methods by a large margin in both Distractor and Fullwiki settings.

DialoGPT: Large-Scale Generative Pre-training for Conversational Response Generation

We present a large, tunable neural conversational response generation model, DialoGPT (dialogue generative pre-trained transformer). Trained on 147M conversation-like exchanges extracted from Reddit comment chains over a period spanning from 2005 through 2017, DialoGPT extends the Hugging Face PyTorch transformer to attain a performance close to human both in terms of automatic and human evaluation in single-turn dialogue settings. We show that conversational systems that leverage DialoGPT generate more relevant, contentful and context-consistent responses than strong baseline systems. The pre-trained model and training pipeline are publicly released to facilitate research into neural response generation and the development of more intelligent open-domain dialogue systems.

FreeLB: Enhanced Adversarial Training for Language Understanding

Adversarial training, which minimizes the maximal risk for label-preserving input perturbations, has proved to be effective for improving the generalization of language models. In this work, we propose a novel adversarial training algorithm - FreeLB, that promotes higher robustness and invariance in the embedding space, by adding adversarial perturbations to word embeddings and minimizing the resultant adversarial risk inside different regions around input samples. To validate the effectiveness of the proposed approach, we apply it to Transformer-based models for natural language understanding and commonsense reasoning tasks. Experiments on the GLUE benchmark show that when applied only to the finetuning stage, it is able to improve the overall test scores of BERT-based model from 78.3 to 79.4, and RoBERTa-large model from 88.5 to 88.8. In addition, the proposed approach achieves state-of-the-art single-model test accuracies of 85.44% and 67.75% on ARC-Easy and ARC-Challenge. Experiments on CommonsenseQA benchmark further demonstrate that FreeLB can be generalized and boost the performance of RoBERTa-large model on other tasks as well.

Patient Knowledge Distillation for BERT Model Compression

Pre-trained language models such as BERT have proven to be highly effective for natural language processing (NLP) tasks. However, the high demand for computing resources in training such models hinders their application in practice. In order to alleviate this resource hunger in large-scale model training, we propose a Patient Knowledge Distillation approach to compress an original large model (teacher) into an equally-effective lightweight shallow network (student). Different from previous knowledge distillation methods, which only use the output from the last layer of the teacher network for distillation, our student model patiently learns from multiple intermediate layers of the teacher model for incremental knowledge extraction, following two strategies: ($i$) PKD-Last: learning from the last $k$ layers; and ($ii$) PKD-Skip: learning from every $k$ layers. These two patient distillation schemes enable the exploitation of rich information in the teacher's hidden layers, and encourage the student model to patiently learn from and imitate the teacher through a multi-layer distillation process. Empirically, this translates into improved results on multiple NLP tasks with significant gain in training efficiency, without sacrificing model accuracy.

Microsoft Dialogue Challenge: Building End-to-End Task-Completion Dialogue Systems

This proposal introduces a Dialogue Challenge for building end-to-end task-completion dialogue systems, with the goal of encouraging the dialogue research community to collaborate and benchmark on standard datasets and unified experimental environment. In this special session, we will release human-annotated conversational data in three domains (movie-ticket booking, restaurant reservation, and taxi booking), as well as an experiment platform with built-in simulators in each domain, for training and evaluation purposes. The final submitted systems will be evaluated both in simulated setting and by human judges.

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

Recently exciting progress has been made on protein contact prediction, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual networks. This deep neural network allows us to model very complex sequence-contact relationship as well as long-range inter-contact correlation. Our method greatly outperforms existing contact prediction methods and leads to much more accurate contact-assisted protein folding. Tested on three datasets of 579 proteins, the average top L long-range prediction accuracy obtained our method, the representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints can yield correct folds (i.e., TMscore>0.6) for 203 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 proteins, respectively. Further, our contact-assisted models have much better quality than template-based models. Using our predicted contacts as restraints, we can (ab initio) fold 208 of the 398 membrane proteins with TMscore>0.5. By contrast, when the training proteins of our method are used as templates, homology modeling can only do so for 10 of them. One interesting finding is that even if we do not train our prediction models with any membrane proteins, our method works very well on membrane protein prediction. Finally, in recent blind CAMEO benchmark our method successfully folded 5 test proteins with a novel fold.

Graphical Model Sketch

Structured high-cardinality data arises in many domains, and poses a major challenge for both modeling and inference. Graphical models are a popular approach to modeling structured data but they are unsuitable for high-cardinality variables. The count-min (CM) sketch is a popular approach to estimating probabilities in high-cardinality data but it does not scale well beyond a few variables. In this work, we bring together the ideas of graphical models and count sketches; and propose and analyze several approaches to estimating probabilities in structured high-cardinality streams of data. The key idea of our approximations is to use the structure of a graphical model and approximately estimate its factors by "sketches", which hash high-cardinality variables using random projections. Our approximations are computationally efficient and their space complexity is independent of the cardinality of variables. Our error bounds are multiplicative and significantly improve upon those of the CM sketch, a state-of-the-art approach to estimating probabilities in streams. We evaluate our approximations on synthetic and real-world problems, and report an order of magnitude improvements over the CM sketch.