Regular Language Induction with Grammar-based Classifier System

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Use of a novel grammatical inference approach in classification of amyloidogenic hexapeptides

The present paper is a novel contribution to the field of bioinformatics by using grammatical inference in the analysis of data. We developed an algorithm for generating star-free regular expressions which turned out to be good recommendation tools, as they are characterized by a relatively high correlation coefficient between the observed and predicted binary classifications. The experiments have been performed for three datasets of amyloidogenic hexapeptides, and our results are compared with those obtained using the graph approaches, the current state-of-the-art methods in heuristic automata induction, and the support vector machine. The results showed the superior performance of the new grammatical inference algorithm on fixed-length amyloid datasets

Unsupervised Statistical Learning of Context-free Grammar

In this paper, we address the problem of inducing (weighted) context-free grammar (WCFG) on data given. The induction is performed by using a new model of grammatical inference, i.e., weighted Grammar-based Classifier System (wGCS). wGCS derives from learning classifier systems and searches grammar structure using a genetic algorithm and covering. Weights of rules are estimated by using a novelty Inside-Outside Contrastive Estimation algorithm. The proposed method employs direct negative evidence and learns WCFG both form positive and negative samples. Results of experiments on three synthetic context-free languages show that wGCS is competitive with other statistical-based method for unsupervised CFG learning

D0L-System Inference from a Single Sequence with a Genetic Algorithm

In this paper, we proposed a new method for image-based grammatical inference of deterministic, context-free L-systems (D0L systems) from a single sequence. This approach is characterized by first parsing an input image into a sequence of symbols and then, using a genetic algorithm, attempting to infer a grammar that can generate this sequence. This technique has been tested using our test suite and compared to similar algorithms, showing promising results, including solving the problem for systems with more rules than in existing approaches. The tests show that it performs better than similar heuristic methods and can handle the same cases as arithmetic algorithms

Anticipatory Classifier System with Average Reward Criterion in Discretized Multi-Step Environments

Initially, Anticipatory Classifier Systems (ACS) were designed to address both single and multistep decision problems. In the latter case, the objective was to maximize the total discounted rewards, usually based on Q-learning algorithms. Studies on other Learning Classifier Systems (LCS) revealed many real-world sequential decision problems where the preferred objective is the maximization of the average of successive rewards. This paper proposes a relevant modification toward the learning component, allowing us to address such problems. The modified system is called AACS2 (Averaged ACS2) and is tested on three multistep benchmark problems

Improved (Non)fixed TSS methods for promoter prediction

Abstract—Recognizing bacterial promoters is an important step towards understanding gene regulation. In this paper, we address the problem of predicting the location of promoters and their transcription start sites (TSSs) in Escherichia coli. Our approaches to TSS prediction are based upon fixed and none fixed TSS algorithms. Introduced improvements significantly bumped up the efficiency of the algorithms. I