Literature DB >> 32508484

Learning to Optimize in Swarms.

Yue Cao1, Tianlong Chen1, Zhangyang Wang1, Yang Shen1.   

Abstract

Learning to optimize has emerged as a powerful framework for various optimization and machine learning tasks. Current such "meta-optimizers" often learn in the space of continuous optimization algorithms that are point-based and uncertainty-unaware. To overcome the limitations, we propose a meta-optimizer that learns in the algorithmic space of both point-based and population-based optimization algorithms. The meta-optimizer targets at a meta-loss function consisting of both cumulative regret and entropy. Specifically, we learn and interpret the update formula through a population of LSTMs embedded with sample- and feature-level attentions. Meanwhile, we estimate the posterior directly over the global optimum and use an uncertainty measure to help guide the learning process. Empirical results over non-convex test functions and the protein-docking application demonstrate that this new meta-optimizer outperforms existing competitors. The codes are publicly available at: https://github.com/Shen-Lab/LOIS.

Entities:  

Year:  2019        PMID: 32508484      PMCID: PMC7274747     

Source DB:  PubMed          Journal:  Adv Neural Inf Process Syst        ISSN: 1049-5258


  8 in total

Review 1.  Prediction of protein-protein interactions by docking methods.

Authors:  Graham R Smith; Michael J E Sternberg
Journal:  Curr Opin Struct Biol       Date:  2002-02       Impact factor: 6.809

2.  Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.

Authors:  Jeffrey J Gray; Stewart Moughon; Chu Wang; Ora Schueler-Furman; Brian Kuhlman; Carol A Rohl; David Baker
Journal:  J Mol Biol       Date:  2003-08-01       Impact factor: 5.469

3.  Protein-protein docking benchmark version 4.0.

Authors:  Howook Hwang; Thom Vreven; Joël Janin; Zhiping Weng
Journal:  Proteins       Date:  2010-11-15

4.  Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking.

Authors:  Yue Cao; Yang Shen
Journal:  J Chem Theory Comput       Date:  2020-07-06       Impact factor: 6.006

5.  The formation of learning sets.

Authors:  H F HARLOW
Journal:  Psychol Rev       Date:  1949-01       Impact factor: 8.934

6.  Interactome3D: adding structural details to protein networks.

Authors:  Roberto Mosca; Arnaud Céol; Patrick Aloy
Journal:  Nat Methods       Date:  2012-12-16       Impact factor: 28.547

7.  ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers.

Authors:  Brian G Pierce; Kevin Wiehe; Howook Hwang; Bong-Hyun Kim; Thom Vreven; Zhiping Weng
Journal:  Bioinformatics       Date:  2014-02-14       Impact factor: 6.937

8.  SwarmDock and the use of normal modes in protein-protein docking.

Authors:  Iain H Moal; Paul A Bates
Journal:  Int J Mol Sci       Date:  2010-09-28       Impact factor: 5.923

  8 in total
  1 in total

1.  Exploring Parameter and Hyper-Parameter Spaces of Neuroscience Models on High Performance Computers With Learning to Learn.

Authors:  Alper Yegenoglu; Anand Subramoney; Thorsten Hater; Cristian Jimenez-Romero; Wouter Klijn; Aarón Pérez Martín; Michiel van der Vlag; Michael Herty; Abigail Morrison; Sandra Diaz-Pier
Journal:  Front Comput Neurosci       Date:  2022-05-27       Impact factor: 3.387

  1 in total

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