Derivation of Context-free Stochastic L-Grammar Rules for Promoter Sequence Modeling Using Support Vector Machine

Formal grammars can used for describing complex repeatable structures such as DNA sequences. In this paper, we describe the structural composition of DNA sequences using a context-free stochastic L-grammar. L-grammars are a special class of parallel grammars that can model the growth of living organisms, e.g. plant development, and model the morphology of a variety of organisms. We believe that parallel grammars also can be used for modeling genetic mechanisms and sequences such as promoters. Promoters are short regulatory DNA sequences located upstream of a gene. Detection of promoters in DNA sequences is important for successful gene prediction. Promoters can be recognized by certain patterns that are conserved within a species, but there are many exceptions which makes the promoter recognition a complex problem. We replace the problem of promoter recognition by induction of context-free stochastic L-grammar rules, which are later used for the structural analysis of promoter sequences. L-grammar rules are derived automatically from the drosophila and vertebrate promoter datasets using a genetic programming technique and their fitness is evaluated using a Support Vector Machine (SVM) classifier. The artificial promoter sequences generated using the derived L- grammar rules are analyzed and compared with natural promoter sequences

Interpretable Categorization of Heterogeneous Time Series Data

Understanding heterogeneous multivariate time series data is important in many applications ranging from smart homes to aviation. Learning models of heterogeneous multivariate time series that are also human-interpretable is challenging and not adequately addressed by the existing literature. We propose grammar-based decision trees (GBDTs) and an algorithm for learning them. GBDTs extend decision trees with a grammar framework. Logical expressions derived from a context-free grammar are used for branching in place of simple thresholds on attributes. The added expressivity enables support for a wide range of data types while retaining the interpretability of decision trees. In particular, when a grammar based on temporal logic is used, we show that GBDTs can be used for the interpretable classi cation of high-dimensional and heterogeneous time series data. Furthermore, we show how GBDTs can also be used for categorization, which is a combination of clustering and generating interpretable explanations for each cluster. We apply GBDTs to analyze the classic Australian Sign Language dataset as well as data on near mid-air collisions (NMACs). The NMAC data comes from aircraft simulations used in the development of the next-generation Airborne Collision Avoidance System (ACAS X).Comment: 9 pages, 5 figures, 2 tables, SIAM International Conference on Data Mining (SDM) 201

Decision Making in the Medical Domain: Comparing the Effectiveness of GP-Generated Fuzzy Intelligent Structures

ABSTRACT: In this work, we examine the effectiveness of two intelligent models in medical domains. Namely, we apply grammar-guided genetic programming to produce fuzzy intelligent structures, such as fuzzy rule-based systems and fuzzy Petri nets, in medical data mining tasks. First, we use two context-free grammars to describe fuzzy rule-based systems and fuzzy Petri nets with genetic programming. Then, we apply cellular encoding in order to express the fuzzy Petri nets with arbitrary size and topology. The models are examined thoroughly in four real-world medical data sets. Results are presented in detail and the competitive advantages and drawbacks of the selected methodologies are discussed, in respect to the nature of each application domain. Conclusions are drawn on the effectiveness and efficiency of the presented approach

Automated DNA Motif Discovery

Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal. The evolved motif suggests the presence of Thymine followed by one or more Adenines etc. early in transcripts indicate a non-protein coding gene. Keywords: pseudogene, short and microRNAs, non-coding transcripts, systems biology, machine learning, Bioinformatics, motif, regular expression, strongly typed genetic programming, context-free grammar.Comment: 12 pages, 2 figure

Learning to solve planning problems efficiently by means of genetic programming

Declarative problem solving, such as planning, poses interesting challenges for Genetic Programming (GP). There have been recent attempts to apply GP to planning that fit two approaches: (a) using GP to search in plan space or (b) to evolve a planner. In this article, we propose to evolve only the heuristics to make a particular planner more efficient. This approach is more feasible than (b) because it does not have to build a planner from scratch but can take advantage of already existing planning systems. It is also more efficient than (a) because once the heuristics have been evolved, they can be used to solve a whole class of different planning problems in a planning domain, instead of running GP for every new planning problem. Empirical results show that our approach (EVOCK) is able to evolve heuristics in two planning domains (the blocks world and the logistics domain) that improve PRODIGY4.0 performance. Additionally, we experiment with a new genetic operator - Instance-Based Crossover - that is able to use traces of the base planner as raw genetic material to be injected into the evolving population.Publicad

Genetic Algorithm for Grammar Induction and Rules Verification through a PDA Simulator

The focus of this paper is towards developing a grammatical inference system uses a genetic algorithm (GA), has a powerful global exploration capability that can exploit the optimum offspring. The implemented system runs in two phases: first, generation of grammar rules and verification and then applies the GA’s operation to optimize the rules. A pushdown automata simulator has been developed, which parse the training data over the grammar’s rules. An inverted mutation with random mask and then ‘XOR’ operator has been applied introduces diversity in the population, helps the GA not to get trapped at local optimum. Taguchi method has been incorporated to tune the parameters makes the proposed approach more robust, statistically sound and quickly convergent. The performance of the proposed system has been compared with: classical GA, random offspring GA and crowding algorithms. Overall, a grammatical inference system has been developed that employs a PDA simulator for verification

Maintaining regularity and generalization in data using the minimum description length principle and genetic algorithm: case of grammatical inference

In this paper, a genetic algorithm with minimum description length (GAWMDL) is proposed for grammatical inference. The primary challenge of identifying a language of infinite cardinality from a finite set of examples should know when to generalize and specialize the training data. The minimum description length principle that has been incorporated addresses this issue is discussed in this paper. Previously, the e-GRIDS learning model was proposed, which enjoyed the merits of the minimum description length principle, but it is limited to positive examples only. The proposed GAWMDL, which incorporates a traditional genetic algorithm and has a powerful global exploration capability that can exploit an optimum offspring. This is an effective approach to handle a problem which has a large search space such the grammatical inference problem. The computational capability, the genetic algorithm poses is not questionable, but it still suffers from premature convergence mainly arising due to lack of population diversity. The proposed GAWMDL incorporates a bit mask oriented data structure that performs the reproduction operations, creating the mask, then Boolean based procedure is applied to create an offspring in a generative manner. The Boolean based procedure is capable of introducing diversity into the population, hence alleviating premature convergence. The proposed GAWMDL is applied in the context free as well as regular languages of varying complexities. The computational experiments show that the GAWMDL finds an optimal or close-to-optimal grammar. Two fold performance analysis have been performed. First, the GAWMDL has been evaluated against the elite mating pool genetic algorithm which was proposed to introduce diversity and to address premature convergence. GAWMDL is also tested against the improved tabular representation algorithm. In addition, the authors evaluate the performance of the GAWMDL against a genetic algorithm not using the minimum description length principle. Statistical tests demonstrate the superiority of the proposed algorithm. Overall, the proposed GAWMDL algorithm greatly improves the performance in three main aspects: maintains regularity of the data, alleviates premature convergence and is capable in grammatical inference from both positive and negative corpora