Siqi Sun

Bio: Siqi Sun is an academic researcher from Microsoft. The author has contributed to research in topics: Language model & Computer science. The author has an hindex of 16, co-authored 41 publications receiving 2218 citations. Previous affiliations of Siqi Sun include Toyota Technological Institute at Chicago & Fudan University.

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

Abstract: Motivation Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. Method 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 neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. Results Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one 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 but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact-assisted models also have much better quality than template-based models especially for membrane proteins. The 3D models built from our contact prediction have TMscore>0.5 for 208 of the 398 membrane proteins, while those from homology modeling have TMscore>0.5 for only 10 of them. Further, even if trained mostly by soluble proteins, our deep learning method works very well on membrane proteins. In the recent blind CAMEO benchmark, our fully-automated web server implementing this method successfully folded 6 targets with a new fold and only 0.3L-2.3L effective sequence homologs, including one β protein of 182 residues, one α+β protein of 125 residues, one α protein of 140 residues, one α protein of 217 residues, one α/β of 260 residues and one α protein of 462 residues. Our method also achieved the highest F1 score on free-modeling targets in the latest CASP (Critical Assessment of Structure Prediction), although it was not fully implemented back then. Availability http://raptorx.uchicago.edu/ContactMap/

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

Abstract: 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

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

Abstract: 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.

Patient Knowledge Distillation for BERT Model Compression

Abstract: 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.

Patient Knowledge Distillation for BERT Model Compression

Abstract: 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 a significant gain in training efficiency, without sacrificing model accuracy.

Highly accurate protein structure prediction with AlphaFold

Abstract: Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort1–4, the structures of around 100,000 unique proteins have been determined5, but this represents a small fraction of the billions of known protein sequences6,7. Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence—the structure prediction component of the ‘protein folding problem’8—has been an important open research problem for more than 50 years9. Despite recent progress10–14, existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14)15, demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm. AlphaFold predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture.

Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer

Abstract: Transfer learning, where a model is first pre-trained on a data-rich task before being fine-tuned on a downstream task, has emerged as a powerful technique in natural language processing (NLP). The effectiveness of transfer learning has given rise to a diversity of approaches, methodology, and practice. In this paper, we explore the landscape of transfer learning techniques for NLP by introducing a unified framework that converts all text-based language problems into a text-to-text format. Our systematic study compares pre-training objectives, architectures, unlabeled data sets, transfer approaches, and other factors on dozens of language understanding tasks. By combining the insights from our exploration with scale and our new ``Colossal Clean Crawled Corpus'', we achieve state-of-the-art results on many benchmarks covering summarization, question answering, text classification, and more. To facilitate future work on transfer learning for NLP, we release our data set, pre-trained models, and code.

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

ALBERT: A Lite BERT for Self-supervised Learning of Language Representations

Abstract: Increasing model size when pretraining natural language representations often results in improved performance on downstream tasks. However, at some point further model increases become harder due to GPU/TPU memory limitations, longer training times, and unexpected model degradation. To address these problems, we present two parameter-reduction techniques to lower memory consumption and increase the training speed of BERT. Comprehensive empirical evidence shows that our proposed methods lead to models that scale much better compared to the original BERT. We also use a self-supervised loss that focuses on modeling inter-sentence coherence, and show it consistently helps downstream tasks with multi-sentence inputs. As a result, our best model establishes new state-of-the-art results on the GLUE, RACE, and SQuAD benchmarks while having fewer parameters compared to BERT-large.

ALBERT: A Lite BERT for Self-supervised Learning of Language Representations

Abstract: Increasing model size when pretraining natural language representations often results in improved performance on downstream tasks. However, at some point further model increases become harder due to GPU/TPU memory limitations and longer training times. To address these problems, we present two parameter-reduction techniques to lower memory consumption and increase the training speed of BERT. Comprehensive empirical evidence shows that our proposed methods lead to models that scale much better compared to the original BERT. We also use a self-supervised loss that focuses on modeling inter-sentence coherence, and show it consistently helps downstream tasks with multi-sentence inputs. As a result, our best model establishes new state-of-the-art results on the GLUE, RACE, and \squad benchmarks while having fewer parameters compared to BERT-large. The code and the pretrained models are available at this https URL.