INESC-ID

About: INESC-ID is a nonprofit organization based out in Lisbon, Portugal. It is known for research contribution in the topics: Computer science & Context (language use). The organization has 932 authors who have published 2618 publications receiving 37658 citations.

On computing minimal correction subsets

Abstract: A set of constraints that cannot be simultaneously satisfied is over-constrained. Minimal relaxations and minimal explanations for over-constrained problems find many practical uses. For Boolean formulas, minimal relaxations of over-constrained problems are referred to as Minimal Correction Subsets (MCSes). MCSes find many applications, including the enumeration of MUSes. Existing approaches for computing MCSes either use a Maximum Satisfiability (MaxSAT) solver or iterative calls to a Boolean Satisfiability (SAT) solver. This paper shows that existing algorithms for MCS computation can be inefficient, and so inadequate, in certain practical settings. To address this problem, this paper develops a number of novel techniques for improving the performance of existing MCS computation algorithms. More importantly, the paper proposes a novel algorithm for computing MCSes. Both the techniques and the algorithm are evaluated empirically on representative problem instances, and are shown to yield the most efficient and robust solutions for MCS computation.

D2STM: Dependable Distributed Software Transactional Memory

Abstract: At current date the problem of how to build distributed and replicated Software Transactional Memory (STM) to enhance both dependability and performance is still largely unexplored. This paper fills this gap by presenting D2STM, a replicated STM whose consistency is ensured in a transparent manner, even in the presence of failures. Strong consistency is enforced at transaction commit time by a non-blocking distributed certification scheme, which we name BFC (Bloom Filter Certification). BFC exploits a novel Bloom Filter-based encoding mechanism that permits to significantly reduce the overheads of replica coordination at the cost of a user tunable increase in the probability of transaction abort. Through an extensive experimental study based on standard STM benchmarks we show that the BFC scheme permits to achieve remarkable performance gains even for negligible (e.g. 1%) increases of the transaction abort rate.

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae.

Abstract: The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT-www.yeastract.com) information system has been, for 11 years, a key tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in Saccharomyces cerevisiae. Since its last update in June 2017, YEASTRACT includes approximately 163000 regulatory associations between transcription factors (TF) and target genes in S. cerevisiae, based on more than 1600 bibliographic references; it also includes 247 specific DNA binding consensus recognized by 113 TFs. This release of the YEASTRACT database provides new visualization tools to visualize each regulatory network in an interactive fashion, enabling the user to select and observe subsets of the network such as: (i) considering only DNA binding evidence or both DNA binding and expression evidence; (ii) considering only either positive or negative regulatory associations; or (iii) considering only one set of related environmental conditions. A further tool to observe TF regulons is also offered, enabling a clear-cut understanding of the exact meaning of the available data. We believe that with this new version, YEASTRACT will improve its role as an open web resource instrumental for Yeast Biologists and Systems Biology researchers.

On Computing Minimum Unsatisfiable Cores

Abstract: Certifying a SAT solver for unsatisfiable instances is a computationally hard problem Nevertheless, in the utilization of SAT in industrial settings, one often needs to be able to generate unsatisfiability proofs, either to guarantee the correctness of the SAT solver or as part of the utilization of SAT in some applications (eg in model checking) As part of the process of generating unsatisfiable proofs, one is also interested in unsatisfiable subformulas of the original formula, also known as unsatisfiable cores Furthermore, it may by useful identifying theminimum unsatisfiable core of a given problem instance, ie the smallest number of clauses that make the instance unsatisfiable This approach is be very useful in AI problems where identifying the minimum core is crucial for correcting the minimum amount of inconsistent information (eg in knowledge bases)