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Register a new userEBIC.JL -- an Efficient Implementation of Evolutionary Biclustering Algorithm in Julia
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Added by
Patryk Orzechowski
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Biclustering is a data mining technique which searches for local patterns in numeric tabular data with main application in bioinformatics. This technique has shown promise in multiple areas, including development of biomarkers for cancer, disease subtype identification, or gene-drug interactions among others. In this paper we introduce EBIC.JL - an implementation of one of the most accurate biclustering algorithms in Julia, a modern highly parallelizable programming language for data science. We show that the new version maintains comparable accuracy to its predecessor EBIC while converging faster for the majority of the problems. We hope that this open source software in a high-level programming language will foster research in this promising field of bioinformatics and expedite development of new biclustering methods for big data.
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In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably the first one capable of discovering with accuracy exceeding 50% multiple complex patterns in real gene expression datasets. It is also one of the very few biclustering methods designed for parallel environments with multiple graphics processing units (GPUs). We demonstrate that EBIC outperforms state-of-the-art biclustering methods, in terms of recovery and relevance, on both synthetic and genetic datasets. EBIC also yields results over 12 times faster than the most accurate reference algorithms. The proposed algorithm is anticipated to be added to the repertoire of unsupervised machine learning algorithms for the analysis of datasets, including those from large-scale genomic studies.
Manachers algorithm has been shown to be optimal to the longest palindromic substring problem. Many of the existing implementations of this algorithm, however, unanimously required in-memory construction of an augmented string that is twice as long as the original string. Although it has found widespread use, we found that this preprocessing is neither economic nor necessary. We present a more efficient implementation of Manachers algorithm based on index mapping that makes the string augmentation process obsolete.
Algorithm NCL is designed for general smooth optimization problems where first and second derivatives are available, including problems whose constraints may not be linearly independent at a solution (i.e., do not satisfy the LICQ). It is equivalent to the LANCELOT augmented Lagrangian method, reformulated as a short sequence of nonlinearly constrained subproblems that can be solved efficiently by IPOPT and KNITRO, with warm starts on each subproblem. We give numerical results from a Julia implementation of Algorithm NCL on tax policy models that do not satisfy the LICQ, and on nonlinear least-squares problems and general problems from the CUTEst test set.
We consider a contextual version of multi-armed bandit problem with global knapsack constraints. In each round, the outcome of pulling an arm is a scalar reward and a resource consumption vector, both dependent on the context, and the global knapsack constraints require the total consumption for each resource to be below some pre-fixed budget. The learning agent competes with an arbitrary set of context-dependent policies. This problem was introduced by Badanidiyuru et al. (2014), who gave a computationally inefficient algorithm with near-optimal regret bounds for it. We give a computationally efficient algorithm for this problem with slightly better regret bounds, by generalizing the approach of Agarwal et al. (2014) for the non-constrained version of the problem. The computational time of our algorithm scales logarithmically in the size of the policy space. This answers the main open question of Badanidiyuru et al. (2014). We also extend our results to a variant where there are no knapsack constraints but the objective is an arbitrary Lipschitz concave function of the sum of outcome vectors.
Many cooperative multiagent reinforcement learning environments provide agents with a sparse team-based reward, as well as a dense agent-specific reward that incentivizes learning basic skills. Training policies solely on the team-based reward is often difficult due to its sparsity. Furthermore, relying solely on the agent-specific reward is sub-optimal because it usually does not capture the team coordination objective. A common approach is to use reward shaping to construct a proxy reward by combining the individual rewards. However, this requires manual tuning for each environment. We introduce Multiagent Evolutionary Reinforcement Learning (MERL), a split-level training platform that handles the two objectives separately through two optimization processes. An evolutionary algorithm maximizes the sparse team-based objective through neuroevolution on a population of teams. Concurrently, a gradient-based optimizer trains policies to only maximize the dense agent-specific rewards. The gradient-based policies are periodically added to the evolutionary population as a way of information transfer between the two optimization processes. This enables the evolutionary algorithm to use skills learned via the agent-specific rewards toward optimizing the global objective. Results demonstrate that MERL significantly outperforms state-of-the-art methods, such as MADDPG, on a number of difficult coordination benchmarks.
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