Automatic Machine Learning by Pipeline Synthesis using Model-Based Reinforcement Learning and a Grammar

Automatic machine learning is an important problem in the forefront of machine learning. The strongest AutoML systems are based on neural networks, evolutionary algorithms, and Bayesian optimization. Recently AlphaD3M reached state-of-the-art results with an order of magnitude speedup using reinforcement learning with self-play. In this work we extend AlphaD3M by using a pipeline grammar and a pre-trained model which generalizes from many different datasets and similar tasks. Our results demonstrate improved performance compared with our earlier work and existing methods on AutoML benchmark datasets for classification and regression tasks. In the spirit of reproducible research we make our data, models, and code publicly available.Comment: ICML Workshop on Automated Machine Learnin

The EM Algorithm and the Rise of Computational Biology

In the past decade computational biology has grown from a cottage industry with a handful of researchers to an attractive interdisciplinary field, catching the attention and imagination of many quantitatively-minded scientists. Of interest to us is the key role played by the EM algorithm during this transformation. We survey the use of the EM algorithm in a few important computational biology problems surrounding the "central dogma"; of molecular biology: from DNA to RNA and then to proteins. Topics of this article include sequence motif discovery, protein sequence alignment, population genetics, evolutionary models and mRNA expression microarray data analysis.Comment: Published in at http://dx.doi.org/10.1214/09-STS312 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

An Ontological Approach to Constraint-Based Design Case Adaptation

Designing tasks in case-based reasoning requires for the use of case adaptation due to its novelty characteristic. In this paper, constraint satisfaction is used to generate potential solutions for design case adaptation. An ontological approach is proposed to perform the inference process to satisfy the multiple design constraints. Domain application is the dietary menu planning for diabetics. Results show that the dietary menu planning designed by the proposed approach is better than the conventional approach. Both the physical and aesthetic constraints were satisfied by the proposed approach

Automatic Curriculum Learning For Deep RL: A Short Survey

Automatic Curriculum Learning (ACL) has become a cornerstone of recent successes in Deep Reinforcement Learning (DRL).These methods shape the learning trajectories of agents by challenging them with tasks adapted to their capacities. In recent years, they have been used to improve sample efficiency and asymptotic performance, to organize exploration, to encourage generalization or to solve sparse reward problems, among others. The ambition of this work is dual: 1) to present a compact and accessible introduction to the Automatic Curriculum Learning literature and 2) to draw a bigger picture of the current state of the art in ACL to encourage the cross-breeding of existing concepts and the emergence of new ideas.Comment: Accepted at IJCAI202

PyCogent: a toolkit for making sense from sequence

The COmparative GENomic Toolkit, a framework for probabilistic analyses of biological sequences, devising workflows and generating publication quality graphics, has been implemented in Python