Related papers: Automatic Network Reconstruction using ASP

There is significant interest in using existing repositories of biological entities, relationships, and models to automate biological model assembly and extension. Current methods aggregate human-curated biological information into…

While Artificial Neural Networks (ANNs) have yielded impressive results in the realm of simulated intelligent behavior, it is important to remember that they are but sparse approximations of Biological Neural Networks (BNNs). We go beyond…

Answer Set Programming (ASP) is a generic problem modeling and solving framework with a strong focus on knowledge representation and a rapid growth of industrial applications. So far, the study of complexity resulted in characterizing…

Answering realistic questions about biological systems and pathways similar to the ones used by text books to test understanding of students about biological systems is one of our long term research goals. Often these questions require…

Adaptive image restoration models can restore images with different degradation levels at inference time without the need to retrain the model. We present an approach that is highly accurate and allows a significant reduction in the number…

Provenance graphs are useful and powerful tools for representing system-level activities in cybersecurity; however, existing approaches often struggle with complex queries and flexible reasoning. This paper presents a novel approach using…

One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…

In biological evolution complex neural structures grow from a handful of cellular ingredients. As genomes in nature are bounded in size, this complexity is achieved by a growth process where cells communicate locally to decide whether to…

Answer-Set Programming (ASP) is an established declarative programming paradigm. However, classical ASP lacks subprogram calls as in procedural programming, and access to external computations (like remote procedure calls) in general. The…

Hybrid Answer Set Programming (Hybrid ASP) is an extension of Answer Set Programming (ASP) that allows ASP-like rules to interact with outside sources. The Splitting Set Theorem is an important and extensively used result for ASP. The paper…

Reliability on complex biological networks reconstructions remains a concern. Although observations are getting more and more precise, the data collection process is yet error prone and the proofs display uneven certitude. In the case of…

The design of embedded systems, that are ubiquitously used in mobile devices and cars, is becoming continuously more complex such that efficient system-level design methods are becoming crucial. My research aims at developing systems that…

Detecting small sets of relevant patterns from a given dataset is a central challenge in data mining. The relevance of a pattern is based on user-provided criteria; typically, all patterns that satisfy certain criteria are considered…

This paper offers a new perspective on Artificial Neural Networks (ANNs) architecture. Traditional ANNs commonly use tree-like or DAG structures for simplicity, which can be preset or determined by Neural Architecture Search (NAS). Yet,…

Previous research on relation classification has verified the effectiveness of using dependency shortest paths or subtrees. In this paper, we further explore how to make full use of the combination of these dependency information. We first…

Complex environments provide structured yet variable sensory inputs. To best exploit information from these environments, organisms must evolve the ability to anticipate consequences of unknown stimuli, and act on these predictions. We…

The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…

Biological systems are often modelled at different levels of abstraction depending on the particular aims/resources of a study. Such different models often provide qualitatively concordant predictions over specific parametrisations, but it…

We examine the practicality for a user of using Answer Set Programming (ASP) for representing logical formalisms. We choose as an example a formalism aiming at capturing causal explanations from causal information. We provide an…

Adapting techniques from database theory in order to optimize Answer Set Programming (ASP) systems, and in particular the grounding components of ASP systems, is an important topic in ASP. In recent years, the Magic Set method has received…