A Probabilistic Linear Genetic Programming with Stochastic Context-Free Grammar for solving Symbolic Regression problems

Traditional Linear Genetic Programming (LGP) algorithms are based only on the selection mechanism to guide the search. Genetic operators combine or mutate random portions of the individuals, without knowing if the result will lead to a fitter individual. Probabilistic Model Building Genetic Programming (PMB-GP) methods were proposed to overcome this issue through a probability model that captures the structure of the fit individuals and use it to sample new individuals. This work proposes the use of LGP with a Stochastic Context-Free Grammar (SCFG), that has a probability distribution that is updated according to selected individuals. We proposed a method for adapting the grammar into the linear representation of LGP. Tests performed with the proposed probabilistic method, and with two hybrid approaches, on several symbolic regression benchmark problems show that the results are statistically better than the obtained by the traditional LGP.Comment: Genetic and Evolutionary Computation Conference (GECCO) 2017, Berlin, German

Synthesizing Program Input Grammars

We present an algorithm for synthesizing a context-free grammar encoding the language of valid program inputs from a set of input examples and blackbox access to the program. Our algorithm addresses shortcomings of existing grammar inference algorithms, which both severely overgeneralize and are prohibitively slow. Our implementation, GLADE, leverages the grammar synthesized by our algorithm to fuzz test programs with structured inputs. We show that GLADE substantially increases the incremental coverage on valid inputs compared to two baseline fuzzers

Flexible RNA design under structure and sequence constraints using formal languages

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. In this study, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on concepts of language theory, namely context-free grammars and finite automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size. From there, we use generic generic algorithms to perform a (weighted) random generation, or an exhaustive enumeration, of candidate sequences. The resulting method, whose complexity scales linearly with the length of the RNA, was implemented as a standalone program. The resulting software was embedded into a publicly available dedicated web server. The applicability demonstrated of the method on a concrete case study dedicated to Exon Splicing Enhancers, in which our approach was successfully used in the design of \emph{in vitro} experiments.Comment: ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013

Three New Probabilistic Models for Dependency Parsing: An Exploration

After presenting a novel O(n^3) parsing algorithm for dependency grammar, we develop three contrasting ways to stochasticize it. We propose (a) a lexical affinity model where words struggle to modify each other, (b) a sense tagging model where words fluctuate randomly in their selectional preferences, and (c) a generative model where the speaker fleshes out each word's syntactic and conceptual structure without regard to the implications for the hearer. We also give preliminary empirical results from evaluating the three models' parsing performance on annotated Wall Street Journal training text (derived from the Penn Treebank). In these results, the generative (i.e., top-down) model performs significantly better than the others, and does about equally well at assigning part-of-speech tags.Comment: 6 pages, LaTeX 2.09 packaged with 4 .eps files, also uses colap.sty and acl.bs