Computational Intelligence Methods for Bioinformatics and Biostatistics : 10th International Meeting, CIBB 2013, Nice, France, June 20-22, 2013, Revised Selected Papers

International audienc

ElegansNet: a brief scientific report and initial experiments

This research report introduces ElegansNet, a neural network that mimics real-world neuronal network circuitry, with the goal of better understanding the interplay between connectome topology and deep learning systems. The proposed approach utilizes the powerful representational capabilities of living beings' neuronal circuitry to design and generate improved deep learning systems with a topology similar to natural networks. The Caenorhabditis elegans connectome is used as a reference due to its completeness, reasonable size, and functional neuron classes annotations. It is demonstrated that the connectome of simple organisms exhibits specific functional relationships between neurons, and once transformed into learnable tensor networks and integrated into modern architectures, it offers bio-plausible structures that efficiently solve complex tasks. The performance of the models is demonstrated against randomly wired networks and compared to artificial networks ranked on global benchmarks. In the first case, ElegansNet outperforms randomly wired networks. Interestingly, ElegansNet models show slightly similar performance with only those based on the Watts-Strogatz small-world property. When compared to state-of-the-art artificial neural networks, such as transformers or attention-based autoencoders, ElegansNet outperforms well-known deep learning and traditional models in both supervised image classification tasks and unsupervised hand-written digits reconstruction, achieving top-1 accuracy of 99.99% on Cifar10 and 99.84% on MNIST Unsup on the validation sets.Comment: 4 pages, short report before full paper submissio

Recycling of yttria-stabilized zirconia waste powders in glazes suitable for ceramic tiles

The aim of this work is to demonstrate the feasibility of valorizing and recycling Yttria-stabilized Zirconia thermal spray waste into high value products for industrial and residential use. Based on the powders chemistry and morphology, this work aims to realize products, like frits suitable for white glazes and ceramic tiles. The focus is on one class of powder: high-temperature and abrasion-resistant ceramics, like Yttria-stabilized zirconia. This study has revealed that the substitution of pure zirconia with waste Yttria-stabilized zirconia is possible in high percentages, up to 100% to prepare frits suitable for white glaze

Neural Networks and Photometric Redshifts

We present a neural network based approach to the determination of photometric redshift. The method was tested on the Sloan Digital Sky Survey Early Data Release (SDSS-EDR) reaching an accuracy comparable and, in some cases, better than SED template fitting techniques. Different neural networks architecture have been tested and the combination of a Multi Layer Perceptron with 1 hidden layer (22 neurons) operated in a Bayesian framework, with a Self Organizing Map used to estimate the accuracy of the results, turned out to be the most effective. In the best experiment, the implemented network reached an accuracy of 0.020 (interquartile error) in the range 0<zphot<0.3, and of 0.022 in the range 0<zphot<0.5.Comment: 9 pages, 5 figures, 3 table

A machine learning approach to investigate regulatory control circuits in bacterial metabolic pathways

In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than others in term of their multi-omics follows from the analysis of these circuits . This is a consequence of the alternation of the omic values of codon usage and protein abundance along with the circuits. In this work, the E.Coli's Glycolysis and its multi-omic circuit features are shown as an example.Comment: 5 pages, 3 figure

A study on multi-omic oscillations in Escherichia coli metabolic networks.

BACKGROUND: Two important challenges in the analysis of molecular biology information are data (multi-omic information) integration and the detection of patterns across large scale molecular networks and sequences. They are are actually coupled beause the integration of omic information may provide better means to detect multi-omic patterns that could reveal multi-scale or emerging properties at the phenotype levels. RESULTS: Here we address the problem of integrating various types of molecular information (a large collection of gene expression and sequence data, codon usage and protein abundances) to analyse the E.coli metabolic response to treatments at the whole network level. Our algorithm, MORA (Multi-omic relations adjacency) is able to detect patterns which may represent metabolic network motifs at pathway and supra pathway levels which could hint at some functional role. We provide a description and insights on the algorithm by testing it on a large database of responses to antibiotics. Along with the algorithm MORA, a novel model for the analysis of oscillating multi-omics has been proposed. Interestingly, the resulting analysis suggests that some motifs reveal recurring oscillating or position variation patterns on multi-omics metabolic networks. Our framework, implemented in R, provides effective and friendly means to design intervention scenarios on real data. By analysing how multi-omics data build up multi-scale phenotypes, the software allows to compare and test metabolic models, design new pathways or redesign existing metabolic pathways and validate in silico metabolic models using nearby species. CONCLUSIONS: The integration of multi-omic data reveals that E.coli multi-omic metabolic networks contain position dependent and recurring patterns which could provide clues of long range correlations in the bacterial genome

Determination of the zero-order fringe position in digital speckle pattern interferometry

A method for determining the position of the zero-order fringe in a metrological experiment with digital speckle pattern interferometry is proposed. It is based on an averaging procedure with shifted images obtained before and after a load is applied. This technique is a complement to the phase-shifting methods. Experimental examples are shown

Drug repositioning : a machine-learning approach through data integration

Existing computational methods for drug repositioning either rely only on the gene expression response of cell lines after treatment, or on drug-to-disease relationships, merging several information levels. However, the noisy nature of the gene expression and the scarcity of genomic data for many diseases are important limitations to such approaches. Here we focused on a drug-centered approach by predicting the therapeutic class of FDA-approved compounds, not considering data concerning the diseases. We propose a novel computational approach to predict drug repositioning based on state-of-the-art machine-learning algorithms. We have integrated multiple layers of information: i) on the distances of the drugs based on how similar are their chemical structures, ii) on how close are their targets within the protein-protein interaction network, and iii) on how correlated are the gene expression patterns after treatment. Our classifier reaches high accuracy levels (78%), allowing us to re-interpret the top misclassifications as re-classifications, after rigorous statistical evaluation. Efficient drug repurposing has the potential to significantly impact the whole field of drug development. The results presented here can significantly accelerate the translation into the clinics of known compounds for novel therapeutic uses