Abstract

Abstract
This work aims at improving the scalability of memory usage in Inductive Logic Programming systems. In this context, we propose two efficient data structures: the Trie, used to represent lists and clauses; and the RL-Tree, a novel data structure used to represent the clauses coverage. We evaluate their performance in the April system using well known datasets. Initial results show a substantial reduction in memory usage without incurring extra execution time overheads. Our proposal is applicable in any ILP system.

Abstract
ILP systems induce first-order clausal theories performing a search through very large hypotheses spaces containing redundant hypotheses. The generation of redundant hypotheses may prevent the systems from finding good models and increases the time to induce them. In this paper we propose a classification of hypotheses redundancy and show how expert knowledge can be provided to an ILP system to avoid it. Experimental results show that the number of hypotheses generated and execution time are reduced when expert knowledge is used to avoid redundancy.

Abstract
It is well known by Inductive Logic Programming (ILP) practioners that ILP systems usually take a long time to find valuable models (theories). The problem is specially critical for large datasets, preventing ILP systems to scale up to larger applications. One approach to reduce the execution time has been the parallelization of ILP systems. In this paper we overview the state-of-the-art on parallel ILP implementations and present work on the evaluation of some major parallelization strategies for ILP. Conclusions about the applicability of each strategy are presented.

Abstract
AbstractDiscovery of cancer drivers has traditionally focused on the identification of protein-coding genes. Here we present a comprehensive analysis of putative cancer driver mutations in both protein-coding and non-coding genomic regions across >2,500 whole cancer genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We developed a statistically rigorous strategy for combining significance levels from multiple driver discovery methods and demonstrate that the integrated results overcome limitations of individual methods. We combined this strategy with careful filtering and applied it to protein-coding genes, promoters, untranslated regions (UTRs), distal enhancers and non-coding RNAs. These analyses redefine the landscape of non-coding driver mutations in cancer genomes, confirming a few previously reported elements and raising doubts about others, while identifying novel candidate elements across 27 cancer types. Novel recurrent events were found in the promoters or 5’UTRs ofTP53, RFTN1, RNF34,andMTG2,in the 3’UTRs ofNFKBIZandTOB1,and in the non-coding RNARMRP.We provide evidence that the previously reported non-coding RNAsNEAT1andMALAT1may be subject to a localized mutational process. Perhaps the most striking finding is the relative paucity of point mutations driving cancer in non-coding genes and regulatory elements. Though we have limited power to discover infrequent non-coding drivers in individual cohorts, combined analysis of promoters of known cancer genes show little excess of mutations beyondTERT.

Abstract
AbstractWe present the most comprehensive catalogue of cancer-associated gene alterations through characterization of tumor transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes project. Using matched whole-genome sequencing data, we attributed RNA alterations to germline and somatic DNA alterations, revealing likely genetic mechanisms. We identified 444 associations of gene expression with somatic non-coding single-nucleotide variants. We found 1,872 splicing alterations associated with somatic mutation in intronic regions, including novel exonization events associated with Alu elements. Somatic copy number alterations were the major driver of total gene and allele-specific expression (ASE) variation. Additionally, 82% of gene fusions had structural variant support, including 75 of a novel class called “bridged” fusions, in which a third genomic location bridged two different genes. Globally, we observe transcriptomic alteration signatures that differ between cancer types and have associations with DNA mutational signatures. Given this unique dataset of RNA alterations, we also identified 1,012 genes significantly altered through both DNA and RNA mechanisms. Our study represents an extensive catalog of RNA alterations and reveals new insights into the heterogeneous molecular mechanisms of cancer gene alterations.