Machine Learning for QFT and String Theory
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												Improving Model-Based Reinforcement Learning with Internal State Representations Through Self-Supervision
1 Improving Model-Based Reinforcement Learning with Internal State Representations through Self-Supervision Julien Scholz, Cornelius Weber, Muhammad Burhan Hafez and Stefan Wermter Knowledge Technology, Department of Informatics, University of Hamburg, Germany [email protected], fweber, hafez, [email protected] Abstract—Using a model of the environment, reinforcement the design decisions made for MuZero, namely, how uncon- learning agents can plan their future moves and achieve super- strained its learning process is. After explaining all necessary human performance in board games like Chess, Shogi, and Go, fundamentals, we propose two individual augmentations to while remaining relatively sample-efficient. As demonstrated by the MuZero Algorithm, the environment model can even be the algorithm that work fully unsupervised in an attempt to learned dynamically, generalizing the agent to many more tasks improve its performance and make it more reliable. After- while at the same time achieving state-of-the-art performance. ward, we evaluate our proposals by benchmarking the regular Notably, MuZero uses internal state representations derived from MuZero algorithm against the newly augmented creation. real environment states for its predictions. In this paper, we bind the model’s predicted internal state representation to the environ- II. BACKGROUND ment state via two additional terms: a reconstruction model loss and a simpler consistency loss, both of which work independently A. MuZero Algorithm and unsupervised, acting as constraints to stabilize the learning process. Our experiments show that this new integration of The MuZero algorithm [1] is a model-based reinforcement reconstruction model loss and simpler consistency loss provide a learning algorithm that builds upon the success of its prede- significant performance increase in OpenAI Gym environments. - 
												
												Survey on Reinforcement Learning for Language Processing
Survey on reinforcement learning for language processing V´ıctorUc-Cetina1, Nicol´asNavarro-Guerrero2, Anabel Martin-Gonzalez1, Cornelius Weber3, Stefan Wermter3 1 Universidad Aut´onomade Yucat´an- fuccetina, [email protected] 2 Aarhus University - [email protected] 3 Universit¨atHamburg - fweber, [email protected] February 2021 Abstract In recent years some researchers have explored the use of reinforcement learning (RL) algorithms as key components in the solution of various natural language process- ing tasks. For instance, some of these algorithms leveraging deep neural learning have found their way into conversational systems. This paper reviews the state of the art of RL methods for their possible use for different problems of natural language processing, focusing primarily on conversational systems, mainly due to their growing relevance. We provide detailed descriptions of the problems as well as discussions of why RL is well-suited to solve them. Also, we analyze the advantages and limitations of these methods. Finally, we elaborate on promising research directions in natural language processing that might benefit from reinforcement learning. Keywords| reinforcement learning, natural language processing, conversational systems, pars- ing, translation, text generation 1 Introduction Machine learning algorithms have been very successful to solve problems in the natural language pro- arXiv:2104.05565v1 [cs.CL] 12 Apr 2021 cessing (NLP) domain for many years, especially supervised and unsupervised methods. However, this is not the case with reinforcement learning (RL), which is somewhat surprising since in other domains, reinforcement learning methods have experienced an increased level of success with some impressive results, for instance in board games such as AlphaGo Zero [106]. - 
												
												AI for Health Examples from Industry, Government, and Academia Table of Contents
guidehouse.com AI for Health Examples from industry, government, and academia Table of Contents Abstract 3 Introduction to artificial intelligence 4 Introduction to health data 7 Molecules: AI for understanding biology and developing therapies 10 Fundamental research 10 Drug development 11 Patients: AI for predicting disease and improving care 13 Diagnostics and outcome risks 13 Personalized medicine 14 Groups: AI for optimizing clinical trials and safeguarding public health 15 Clinical trials 15 Public health 17 Conclusion and outlook 18 2 Guidehouse Abstract This paper is directed toward a health-informed reader who is curious about the developments and potential of artificial intelligence (AI) in the health space, but could equally be read by AI practitioners curious about how their knowledge and methods are being used to advance human health. We present a brief, equation-free introduction to AI and its major subfields in order to provide a framework for understanding the technical context of the examples that follow. We discuss the various data sources available for questions of health and life sciences, as well as the unique challenges inherent to these fields. We then consider recent (past five years) applications of AI that have already had tangible, measurable impact to the advancement of biomedical knowledge and the development of new and improved treatments. These examples are organized by scale, ranging from the molecule (fundamental research and drug development) to the patient (diagnostics, risk-scoring, and personalized medicine) to the group (clinical trials and public health). Finally, we conclude with a brief summary and our outlook for the future of AI for health. - 
												
												Pre-Training of Deep Bidirectional Protein Sequence Representations with Structural Information
Date of publication xxxx 00, 0000, date of current version xxxx 00, 0000. Digital Object Identifier 10.1109/ACCESS.2017.DOI Pre-training of Deep Bidirectional Protein Sequence Representations with Structural Information SEONWOO MIN1,2, SEUNGHYUN PARK3, SIWON KIM1, HYUN-SOO CHOI4, BYUNGHAN LEE5 (Member, IEEE), and SUNGROH YOON1,6 (Senior Member, IEEE) 1Department of Electrical and Computer engineering, Seoul National University, Seoul 08826, South Korea 2LG AI Research, Seoul 07796, South Korea 3Clova AI Research, NAVER Corp., Seongnam 13561, South Korea 4Department of Computer Science and Engineering, Kangwon National University, Chuncheon 24341, South Korea 5Department of Electronic and IT Media Engineering, Seoul National University of Science and Technology, Seoul 01811, South Korea 6Interdisciplinary Program in Artificial Intelligence, ASRI, INMC, and Institute of Engineering Research, Seoul National University, Seoul 08826, South Korea Corresponding author: Byunghan Lee ([email protected]) or Sungroh Yoon ([email protected]) This research was supported by the National Research Foundation (NRF) of Korea grants funded by the Ministry of Science and ICT (2018R1A2B3001628 (S.Y.), 2014M3C9A3063541 (S.Y.), 2019R1G1A1003253 (B.L.)), the Ministry of Agriculture, Food and Rural Affairs (918013-4 (S.Y.)), and the Brain Korea 21 Plus Project in 2021 (S.Y.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ABSTRACT Bridging the exponentially growing gap between the numbers of unlabeled and labeled protein sequences, several studies adopted semi-supervised learning for protein sequence modeling. In these studies, models were pre-trained with a substantial amount of unlabeled data, and the representations were transferred to various downstream tasks. - 
												
												Multi-Agent Reinforcement Learning: a Review of Challenges and Applications
applied sciences Review Multi-Agent Reinforcement Learning: A Review of Challenges and Applications Lorenzo Canese †, Gian Carlo Cardarilli, Luca Di Nunzio †, Rocco Fazzolari † , Daniele Giardino †, Marco Re † and Sergio Spanò *,† Department of Electronic Engineering, University of Rome “Tor Vergata”, Via del Politecnico 1, 00133 Rome, Italy; [email protected] (L.C.); [email protected] (G.C.C.); [email protected] (L.D.N.); [email protected] (R.F.); [email protected] (D.G.); [email protected] (M.R.) * Correspondence: [email protected]; Tel.: +39-06-7259-7273 † These authors contributed equally to this work. Abstract: In this review, we present an analysis of the most used multi-agent reinforcement learn- ing algorithms. Starting with the single-agent reinforcement learning algorithms, we focus on the most critical issues that must be taken into account in their extension to multi-agent scenarios. The analyzed algorithms were grouped according to their features. We present a detailed taxonomy of the main multi-agent approaches proposed in the literature, focusing on their related mathematical models. For each algorithm, we describe the possible application fields, while pointing out its pros and cons. The described multi-agent algorithms are compared in terms of the most important char- acteristics for multi-agent reinforcement learning applications—namely, nonstationarity, scalability, and observability. We also describe the most common benchmark environments used to evaluate the Citation: Canese, L.; Cardarilli, G.C.; performances of the considered methods. Di Nunzio, L.; Fazzolari, R.; Giardino, D.; Re, M.; Spanò, S. Multi-Agent Keywords: machine learning; reinforcement learning; multi-agent; swarm Reinforcement Learning: A Review of Challenges and Applications. - 
												
												Biological Structure and Function Emerge from Scaling Unsupervised Learning to 250 Million Protein Sequences
bioRxiv preprint doi: https://doi.org/10.1101/622803; this version posted May 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. BIOLOGICAL STRUCTURE AND FUNCTION EMERGE FROM SCALING UNSUPERVISED LEARNING TO 250 MILLION PROTEIN SEQUENCES Alexander Rives ∗y z Siddharth Goyal ∗x Joshua Meier ∗x Demi Guo ∗x Myle Ott x C. Lawrence Zitnick x Jerry Ma y x Rob Fergus y z x ABSTRACT In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. In biology, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. Learning the natural distribution of evolutionary protein sequence variation is a logical step toward predictive and generative modeling for biology. To this end we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million sequences spanning evolutionary diversity. The resulting model maps raw sequences to representations of biological properties without labels or prior domain knowledge. The learned representation space organizes sequences at multiple levels of biological granularity from the biochemical to proteomic levels. Unsupervised learning recovers information about protein structure: secondary structure and residue-residue contacts can be identified by linear projections from the learned representations. Training language models on full sequence diversity rather than individual protein families increases recoverable information about secondary structure. - 
												
												Combining Off and On-Policy Training in Model-Based Reinforcement Learning
Combining Off and On-Policy Training in Model-Based Reinforcement Learning Alexandre Borges Arlindo L. Oliveira INESC-ID / Instituto Superior Técnico INESC-ID / Instituto Superior Técnico University of Lisbon University of Lisbon Lisbon, Portugal Lisbon, Portugal ABSTRACT factor and game length. AlphaGo [1] was the first computer pro- The combination of deep learning and Monte Carlo Tree Search gram to beat a professional human player in the game of Go by (MCTS) has shown to be effective in various domains, such as combining deep neural networks with tree search. In the first train- board and video games. AlphaGo [1] represented a significant step ing phase, the system learned from expert games, but a second forward in our ability to learn complex board games, and it was training phase enabled the system to improve its performance by rapidly followed by significant advances, such as AlphaGo Zero self-play using reinforcement learning. AlphaGoZero [2] learned [2] and AlphaZero [3]. Recently, MuZero [4] demonstrated that only through self-play and was able to beat AlphaGo soundly. Alp- it is possible to master both Atari games and board games by di- haZero [3] improved on AlphaGoZero by generalizing the model rectly learning a model of the environment, which is then used to any board game. However, these methods were designed only with Monte Carlo Tree Search (MCTS) [5] to decide what move for board games, specifically for two-player zero-sum games. to play in each position. During tree search, the algorithm simu- Recently, MuZero [4] improved on AlphaZero by generalizing lates games by exploring several possible moves and then picks the it even more, so that it can learn to play singe-agent games while, action that corresponds to the most promising trajectory. - 
												
												Machine Learning for Speech Recognition by Alice Coucke, Head of Machine Learning Research
Machine Learning for Speech Recognition by Alice Coucke, Head of Machine Learning Research @alicecoucke [email protected] Outline: 1. Recent advances in machine learning 2. From physics to machine learning IA en général Speech & NLP Startup 3. Working at Snips (now Sonos) Snips A lot of applications in the real world, quite a difference from theoretical work Un des rares domaines scientifiques où la théorie et la pratique sont très emmêlées Recent Advances in Applied Machine Learning A lot of applications in the real world, quite a difference from theoretical work Reinforcement learning Learning goal-oriented behavior within simulated environments Go Starcraft II Dota 2 AlphaGo (Deepmind, 2016) AlphaStar (Deepmind) OpenAI Five (OpenAI) Play-driven learning for robots Sim-to-real dexterity learning (Google Brain) Project BLUE (UC Berkeley) Machine Learning for Life Sciences Deep learning applied to biology and medicine Protein folding & structure Cardiac arrhythmia prediction Eye disease diagnosis prediction (NHS, UCL, Deepmind) from ECGs AlphaFold (Deepmind) (Stanford) Reconstruct speech from neural activity Limb control restoration (UCSF) (Batelle, Ohio State Univ) Computer vision High-level understanding of digital images or videos GANs for image generation (Heriot Watt Univ, DeepMind) « Common sense » understanding of actions in videos (TwentyBn, DeepMind, MIT, IBM…) GANs for artificial video dubbing GAN for full body synthesis (Synthesia) (DataGrid) From physics to machine learning and back A surge of interest from the physics community - 
												
												Artificial Intelligence and Cybersecurity
CEPS Task Force Report Artificial Intelligence and Cybersecurity Technology, Governance and Policy Challenges R a p p o r t e u r s L o r e n z o P u p i l l o S t e f a n o F a n t i n A f o n s o F e r r e i r a C a r o l i n a P o l i t o Artificial Intelligence and Cybersecurity Technology, Governance and Policy Challenges Final Report of a CEPS Task Force Rapporteurs: Lorenzo Pupillo Stefano Fantin Afonso Ferreira Carolina Polito Centre for European Policy Studies (CEPS) Brussels May 2021 The Centre for European Policy Studies (CEPS) is an independent policy research institute based in Brussels. Its mission is to produce sound analytical research leading to constructive solutions to the challenges facing Europe today. Lorenzo Pupillo is CEPS Associate Senior Research Fellow and Head of the Cybersecurity@CEPS Initiative. Stefano Fantin is Legal Researcher at Center for IT and IP Law, KU Leuven. Afonso Ferreira is Directeur of Research at CNRS. Carolina Polito is CEPS Research Assistant at GRID unit, Cybersecurity@CEPS Initiative. ISBN 978-94-6138-785-1 © Copyright 2021, CEPS All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise – without the prior permission of the Centre for European Policy Studies. CEPS Place du Congrès 1, B-1000 Brussels Tel: 32 (0) 2 229.39.11 e-mail: [email protected] internet: www.ceps.eu Contents Preface ........................................................................................................................................................... - 
												
												Overview of Current State of Research on the Application of Artificial Intelligence Techniques for COVID-19
Overview of current state of research on the application of artificial intelligence techniques for COVID-19 Vijay Kumar1, Dilbag Singh2, Manjit Kaur2 and Robertas Damaševičius3,4 1 Computer Science and Engineering Department, National Institute of Technology, Hamirpur, Himachal Pradesh, India 2 School of Engineering and Applied Sciences, Bennett University, Greater Noida, India 3 Faculty of Applied Mathematics, Silesian University of Technology, Gliwice, Poland 4 Department of Applied Informatics, Vytautas Magnus University, Kaunas, Lithuania ABSTRACT Background: Until now, there are still a limited number of resources available to predict and diagnose COVID-19 disease. The design of novel drug-drug interaction for COVID-19 patients is an open area of research. Also, the development of the COVID-19 rapid testing kits is still a challenging task. Methodology: This review focuses on two prime challenges caused by urgent needs to effectively address the challenges of the COVID-19 pandemic, i.e., the development of COVID-19 classification tools and drug discovery models for COVID-19 infected patients with the help of artificial intelligence (AI) based techniques such as machine learning and deep learning models. Results: In this paper, various AI-based techniques are studied and evaluated by the means of applying these techniques for the prediction and diagnosis of COVID-19 disease. This study provides recommendations for future research and facilitates knowledge collection and formation on the application of the AI techniques for dealing with the COVID-19 epidemic and its consequences. Conclusions: The AI techniques can be an effective tool to tackle the epidemic caused by COVID-19. These may be utilized in four main fields such as prediction, diagnosis, drug design, and analyzing social implications for COVID-19 infected patients. - 
												
												A Reinforcement Learning Approach to Sequential Conformer Search
TorsionNet: A Reinforcement Learning Approach to Sequential Conformer Search Tarun Gogineni1, Ziping Xu2, Exequiel Punzalan3, Runxuan Jiang1, Joshua Kammeraad2;3, Ambuj Tewari2, Paul Zimmerman3 1Department of EECS, University of Michigan 2Department of Statistics, University of Michigan 3Department of Chemistry, University of Michigan {tgog,zipingxu,epunzal,runxuanj,joshkamm,tewaria,paulzim}@umich.edu Abstract Molecular geometry prediction of flexible molecules, or conformer search, is a long- standing challenge in computational chemistry. This task is of great importance for predicting structure-activity relationships for a wide variety of substances ranging from biomolecules to ubiquitous materials. Substantial computational resources are invested in Monte Carlo and Molecular Dynamics methods to generate diverse and representative conformer sets for medium to large molecules, which are yet intractable to chemoinformatic conformer search methods. We present TorsionNet, an efficient sequential conformer search technique based on reinforcement learning under the rigid rotor approximation. The model is trained via curriculum learning, whose theoretical benefit is explored in detail, to maximize a novel metric grounded in thermodynamics called the Gibbs Score. Our experimental results show that TorsionNet outperforms the highest scoring chemoinformatics method by 4x on large branched alkanes, and by several orders of magnitude on the previously unexplored biopolymer lignin, with applications in renewable energy. TorsionNet also outperforms the far more exhaustive but computationally intensive Self-Guided Molecular Dynamics sampling method. 1 Introduction Accurate prediction of likely 3D geometries of flexible molecules is a long standing goal of com- putational chemistry, with broad implications for drug design, biopolymer research, and QSAR analysis. However, this is a very difficult problem due to the exponential growth of possible stable physical structures, or conformers, as a function of the size of a molecule. - 
												
												Arxiv:1911.05531V1 [Q-Bio.BM] 9 Nov 2019 1 Introduction
Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations Iddo Drori1;2, Darshan Thaker1, Arjun Srivatsa1, Daniel Jeong1, Yueqi Wang1, Linyong Nan1, Fan Wu1, Dimitri Leggas1, Jinhao Lei1, Weiyi Lu1, Weilong Fu1, Yuan Gao1, Sashank Karri1, Anand Kannan1, Antonio Moretti1, Mohammed AlQuraishi3, Chen Keasar4, and Itsik Pe’er1 1 Columbia University, Department of Computer Science, New York, NY, 10027 2 Cornell University, School of Operations Research and Information Engineering, Ithaca, NY 14853 3 Harvard University, Department of Systems Biology, Harvard Medical School, Boston, MA 02115 4 Ben-Gurion University, Department of Computer Science, Israel, 8410501 Abstract. Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fun- damental role in drug design. This motivates predicting the structure of a protein from its sequence of amino acids, a fundamental problem in com- putational biology. In this work, we demonstrate state-of-the-art protein structure prediction (PSP) results using embeddings and deep learning models for prediction of backbone atom distance matrices and torsion angles. We recover 3D coordinates of backbone atoms and reconstruct full atom protein by optimization. We create a new gold standard dataset of proteins which is comprehensive and easy to use. Our dataset consists of amino acid sequences, Q8 secondary structures, position specific scoring matrices, multiple sequence alignment co-evolutionary features, backbone atom distance matrices, torsion angles, and 3D coordinates. We evaluate the quality of our structure prediction by RMSD on the latest Critical Assessment of Techniques for Protein Structure Prediction (CASP) test data and demonstrate competitive results with the winning teams and AlphaFold in CASP13 and supersede the results of the winning teams in CASP12.