Non-Direct Encoding Method Based on Cellular Automata to Design Neural Network Architectures

Architecture design is a fundamental step in the successful application of Feed forward Neural Networks. In most cases a large number of neural networks architectures suitable to solve a problem exist and the architecture design is, unfortunately, still a human expert’s job. It depends heavily on the expert and on a tedious trial-and-error process. In the last years, many works have been focused on automatic resolution of the design of neural network architectures. Most of the methods are based on evolutionary computation paradigms. Some of the designed methods are based on direct representations of the parameters of the network. These representations do not allow scalability; thus, for representing large architectures very large structures are required. More interesting alternatives are represented by indirect schemes. They codify a compact representation of the neural network. In this work, an indirect constructive encoding scheme is proposed. This scheme is based on cellular automata representations and is inspired by the idea that only a few seeds for the initial configuration of a cellular automaton can produce a wide variety of feed forward neural networks architectures. The cellular approach is experimentally validated in different domains and compared with a direct codification scheme.Publicad

Reverse Engineering Gene Networks with ANN: Variability in Network Inference Algorithms

Motivation :Reconstructing the topology of a gene regulatory network is one of the key tasks in systems biology. Despite of the wide variety of proposed methods, very little work has been dedicated to the assessment of their stability properties. Here we present a methodical comparison of the performance of a novel method (RegnANN) for gene network inference based on multilayer perceptrons with three reference algorithms (ARACNE, CLR, KELLER), focussing our analysis on the prediction variability induced by both the network intrinsic structure and the available data. Results: The extensive evaluation on both synthetic data and a selection of gene modules of "Escherichia coli" indicates that all the algorithms suffer of instability and variability issues with regards to the reconstruction of the topology of the network. This instability makes objectively very hard the task of establishing which method performs best. Nevertheless, RegnANN shows MCC scores that compare very favorably with all the other inference methods tested. Availability: The software for the RegnANN inference algorithm is distributed under GPL3 and it is available at the corresponding author home page (http://mpba.fbk.eu/grimaldi/regnann-supmat

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues