BACKGROUND: The high growth of Next Generation Sequencing data currently demands new knowledge extraction methods. In particular, the RNA sequencing gene expression experimental technique stands out for case-control studies on cancer, which can be addressed with supervised machine learning techniques able to extract human interpretable models composed of genes, and their relation to the investigated disease. State of the art rule-based classifiers are designed to extract a single classification model, possibly composed of few relevant genes. Conversely, we aim to create a large knowledge base composed of many rule-based models, and thus determine which genes could be potentially involved in the analyzed tumor. This comprehensive and open access knowledge base is required to disseminate novel insights about cancer. RESULTS: We propose CamurWeb, a new method and web-based software that is able to extract multiple and equivalent classification models in form of logic formulas ("if then" rules) and to create a knowledge base of these rules that can be queried and analyzed. The method is based on an iterative classification procedure and an adaptive feature elimination technique that enables the computation of many rule-based models related to the cancer under study. Additionally, CamurWeb includes a user friendly interface for running the software, querying the results, and managing the performed experiments. The user can create her profile, upload her gene expression data, run the classification analyses, and interpret the results with predefined queries. In order to validate the software we apply it to all public available RNA sequencing datasets from The Cancer Genome Atlas database obtaining a large open access knowledge base about cancer. CamurWeb is available at http://bioinformatics.iasi.cnr.it/camurweb . CONCLUSIONS: The experiments prove the validity of CamurWeb, obtaining many classification models and thus several genes that are associated to 21 different cancer types. Finally, the comprehensive knowledge base about cancer and the software tool are released online; interested researchers have free access to them for further studies and to design biological experiments in cancer research.

MOTIVATION: Nowadays, knowledge extraction methods from Next Generation Sequencing data are highly requested. In this work, we focus on RNA-seq gene expression analysis and specifically on case-control studies with rule-based supervised classification algorithms that build a model able to discriminate cases from controls. State of the art algorithms compute a single classification model that contains few features (genes). On the contrary, our goal is to elicit a higher amount of knowledge by computing many classification models, and therefore to identify most of the genes related to the predicted class. RESULTS: We propose CAMUR, a new method that extracts multiple and equivalent classification models. CAMUR iteratively computes a rule-based classification model, calculates the power set of the genes present in the rules, iteratively eliminates those combinations from the data set, and performs again the classification procedure until a stopping criterion is verified. CAMUR includes an ad-hoc knowledge repository (database) and a querying tool.We analyze three different types of RNA-seq data sets (Breast, Head and Neck, and Stomach Cancer) from The Cancer Genome Atlas (TCGA) and we validate CAMUR and its models also on non-TCGA data. Our experimental results show the efficacy of CAMUR: we obtain several reliable equivalent classification models, from which the most frequent genes, their relationships, and the relation with a particular cancer are deduced. AVAILABILITY AND IMPLEMENTATION: dmb.iasi.cnr.it/camur.php CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Table of contents A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

Alzheimer's Disease (AD) and its preliminary stage - Mild Cognitive Impairment (MCI) - are the most widespread neurodegenerative disorders, and their investigation remains an open challenge. ElectroEncephalography (EEG) appears as a non-invasive and repeatable technique to diagnose brain abnormalities. Despite technical advances, the analysis of EEG spectra is usually carried out by experts that must manually perform laborious interpretations. Computational methods may lead to a quantitative analysis of these signals and hence to characterize EEG time series. The aim of this work is to achieve an automatic patients classification from the EEG biomedical signals involved in AD and MCI in order to support medical doctors in the right diagnosis formulation. The analysis of the biological EEG signals requires effective and efficient computer science methods to extract relevant information. Data mining, which guides the automated knowledge discovery process, is a natural way to approach EEG data analysis. Specifically, in our work we apply the following analysis steps: (i) pre-processing of EEG data; (ii) processing of the EEG-signals by the application of time-frequency transforms; and (iii) classification by means of machine learning methods. We obtain promising results from the classification of AD, MCI, and control samples that can assist the medical doctors in identifying the pathology.

We study an operation scheduling problem where a finite set of jobs with due dates must be completed by one machine: each job is completed as soon as a specific subset of unit operations is done. Distinct jobs may share operations, and when an operation is done, it is done for all the jobs that share it. The goal is to schedule operations so that the (weighted) number of tardy jobs is minimized. We reformulate the problem as maximum stable set problem on a special graph and study its structure. Valid inequalities and optimality cuts are derived, separated, and tested in a computational experience that identifies some features of hard instances and the potential contribution of the addition, at root, of various cut classes. © 2014 Wiley Periodicals, Inc. NETWORKS, Vol. 64(4), 306–320 2014

BACKGROUND: According to many field experts, specimens classification based on morphological keys needs to be supported with automated techniques based on the analysis of DNA fragments. The most successful results in this area are those obtained from a particular fragment of mitochondrial DNA, the gene cytochrome c oxidase I (COI) (the "barcode"). Since 2004 the Consortium for the Barcode of Life (CBOL) promotes the collection of barcode specimens and the development of methods to analyze the barcode for several tasks, among which the identification of rules to correctly classify an individual into its species by reading its barcode. RESULTS: We adopt a Logic Mining method based on two optimization models and present the results obtained on two datasets where a number of COI fragments are used to describe the individuals that belong to different species. The method proposed exhibits high correct recognition rates on a training-testing split of the available data using a small proportion of the information available (e.g., correct recognition approx. 97% when only 20 sites of the 648 available are used). The method is able to provide compact formulas on the values (A, C, G, T) at the selected sites that synthesize the characteristic of each species, a relevant information for taxonomists. CONCLUSION: We have presented a Logic Mining technique designed to analyze barcode data and to provide detailed output of interest to the taxonomists and the barcode community represented in the CBOL Consortium. The method has proven to be effective, efficient and precise.

This paper describes a method for learning logic relationships that correctly classify a given data set. The method derives from given logic data certain minimum cost satisfiability problems, solves these problems, and deduces from the solutions the desired logic relationships. Uses of the method include data mining, learning logic in expert systems, and identification of critical characteristics for recognition systems. Computational tests have proved that the method is fast and effective.

In data mining, two types of errors may occur when records are classified into two categories A and B: misclassifying an item in A as one of B and conversely misclassifying an item in B as one of A. Tight control over these two errors is needed in many practical situations since, for example, an error of one type may have far more serious consequences than one of the other type. Most previous work on two-class classifiers does not allow for such control. We describe a general approach that supports tight error control for two-class classification and that can utilize any two-class classification method as part of the decision mechanism. The main idea is to construct from the given training data a family of classifiers and then, using the training data once more, to estimate two distributions of certain vote totals. The error control is achieved via the two estimated distributions. The approach has been tested using several well-known classification problems. In each case, the two estimated distributions were very close to those obtained from verification data. Accordingly, good error control can be achieved.