CodeTrans: Towards Cracking the Language of Silicone's Code Through Self-Supervised Deep Learning and High Performance Computing

Currently, a growing number of mature natural language processing applications make people's life more convenient. Such applications are built by source code - the language in software engineering. However, the applications for understanding source code language to ease the software engineering process are under-researched. Simultaneously, the transformer model, especially its combination with transfer learning, has been proven to be a powerful technique for natural language processing tasks. These breakthroughs point out a promising direction for process source code and crack software engineering tasks. This paper describes CodeTrans - an encoder-decoder transformer model for tasks in the software engineering domain, that explores the effectiveness of encoder-decoder transformer models for six software engineering tasks, including thirteen sub-tasks. Moreover, we have investigated the effect of different training strategies, including single-task learning, transfer learning, multi-task learning, and multi-task learning with fine-tuning. CodeTrans outperforms the state-of-the-art models on all the tasks. To expedite future works in the software engineering domain, we have published our pre-trained models of CodeTrans. https://github.com/agemagician/CodeTrans

ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing

Computational biology and bioinformatics provide vast data gold-mines from protein sequences, ideal for Language Models (LMs) taken from Natural Language Processing (NLP). These LMs reach for new prediction frontiers at low inference costs. Here, we trained two auto-regressive language models (Transformer-XL, XLNet) and two auto-encoder models (Bert, Albert) on data from UniRef and BFD containing up to 393 billion amino acids (words) from 2.1 billion protein sequences (22- and 112-times the entire English Wikipedia). The LMs were trained on the Summit supercomputer at Oak Ridge National Laboratory (ORNL), using 936 nodes (total 5616 GPUs) and one TPU Pod (V3-512 or V3-1024). We validated the advantage of up-scaling LMs to larger models supported by bigger data by predicting secondary structure (3-states: Q3=76-84, 8-states: Q8=65-73), sub-cellular localization for 10 cellular compartments (Q10=74) and whether a protein is membrane-bound or water-soluble (Q2=89). Dimensionality reduction revealed that the LM-embeddings from unlabeled data (only protein sequences) captured important biophysical properties governing protein shape. This implied learning some of the grammar of the language of life realized in protein sequences. The successful up-scaling of protein LMs through HPC to larger data sets slightly reduced the gap between models trained on evolutionary information and LMs. The official GitHub repository: https://github.com/agemagician/ProtTrans

Enabling real-time multi-messenger astrophysics discoveries with deep learning

Multi-messenger astrophysics is a fast-growing, interdisciplinary field that combines data, which vary in volume and speed of data processing, from many different instruments that probe the Universe using different cosmic messengers: electromagnetic waves, cosmic rays, gravitational waves and neutrinos. In this Expert Recommendation, we review the key challenges of real-time observations of gravitational wave sources and their electromagnetic and astroparticle counterparts, and make a number of recommendations to maximize their potential for scientific discovery. These recommendations refer to the design of scalable and computationally efficient machine learning algorithms; the cyber-infrastructure to numerically simulate astrophysical sources, and to process and interpret multi-messenger astrophysics data; the management of gravitational wave detections to trigger real-time alerts for electromagnetic and astroparticle follow-ups; a vision to harness future developments of machine learning and cyber-infrastructure resources to cope with the big-data requirements; and the need to build a community of experts to realize the goals of multi-messenger astrophysics.

Deep Learning for Multi-Messenger Astrophysics: A Gateway for Discovery in the Big Data Era

This report provides an overview of recent work that harnesses the Big Data Revolution and Large Scale Computing to address grand computational challenges in Multi-Messenger Astrophysics, with a particular emphasis on real-time discovery campaigns. Acknowledging the transdisciplinary nature of Multi-Messenger Astrophysics, this document has been prepared by members of the physics, astronomy, computer science, data science, software and cyberinfrastructure communities who attended the NSF-, DOE- and NVIDIA-funded "Deep Learning for Multi-Messenger Astrophysics: Real-time Discovery at Scale" workshop, hosted at the National Center for Supercomputing Applications, October 17-19, 2018. Highlights of this report include unanimous agreement that it is critical to accelerate the development and deployment of novel, signal-processing algorithms that use the synergy between artificial intelligence (AI) and high performance computing to maximize the potential for scientific discovery with Multi-Messenger Astrophysics. We discuss key aspects to realize this endeavor, namely (i) the design and exploitation of scalable and computationally efficient AI algorithms for Multi-Messenger Astrophysics; (ii) cyberinfrastructure requirements to numerically simulate astrophysical sources, and to process and interpret Multi-Messenger Astrophysics data; (iii) management of gravitational wave detections and triggers to enable electromagnetic and astro-particle follow-ups; (iv) a vision to harness future developments of machine and deep learning and cyberinfrastructure resources to cope with the scale of discovery in the Big Data Era; (v) and the need to build a community that brings domain experts together with data scientists on equal footing to maximize and accelerate discovery in the nascent field of Multi-Messenger Astrophysics.