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A hallmark of human intelligence is the ability to construct self-contained chunks of knowledge and reuse them in novel combinations for solving different problems. Learning such compositional structures has been a challenge for artificial…

My research explores integrating deep learning and logic programming to set the basis for a new generation of AI systems. By combining neural networks with Inductive Logic Programming (ILP), the goal is to construct systems that make…

Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…

Large language models (LLMs) have shown impressive promise in code generation, yet their progress remains limited by the shortage of large-scale datasets that are both diverse and well-aligned with human reasoning. Most existing resources…

Agent systems based on large language models (LLMs) have shown great potential in complex reasoning tasks, but building efficient and generalizable workflows remains a major challenge. Most existing approaches rely on manually designed…

Evolutionary Algorithms are naturally inspired approximation optimisation algorithms that usually interfere with science problems when common mathematical methods are unable to provide a good solution or finding the exact solution requires…

The search for information on the web is faced with several problems, which arise on the one hand from the vast number of available sources, and on the other hand from their heterogeneity. A promising approach is the use of multi-agent…

Having a model and being able to implement open-ended evolutionary systems is important for advancing our understanding of open-endedness. Complex systems science and newest generation high-level programming languages provide intriguing…

Solving Inductive Logic Programming (ILP) problems with neural networks is a key challenge in Neural-Symbolic Ar- tificial Intelligence (AI). While most research has focused on designing novel network architectures for individual prob-…

We report on work towards flexible algorithms for solving decision problems represented as influence diagrams. An algorithm is given to construct a tree structure for each decision node in an influence diagram. Each tree represents a…

Natural evolution gives the impression of leading to an open-ended process of increasing diversity and complexity. If our goal is to produce such open-endedness artificially, this suggests an approach driven by evolutionary metaphor. On the…

For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…

The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…

Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…

Synthetic biology is an emerging field that involves the engineering and re-design of organisms for purposes such as food security, health, and environmental protection. As such, it poses numerous ethical, legal, and social implications…

Large Language Models (LLMs) have enabled automated heuristic design (AHD) for combinatorial optimization problems (COPs), but existing frameworks' reliance on fixed evolutionary rules and static prompt templates often leads to myopic…

The applications being developed within the U.S. Exascale Computing Project (ECP) to run on imminent Exascale computers will generate scientific results with unprecedented fidelity and record turn-around time. Many of these codes are based…

Probabilistic Logic Programming is an effective formalism for encoding problems characterized by uncertainty. Some of these problems may require the optimization of probability values subject to constraints among probability distributions…

The nature inspired algorithms are becoming popular due to their simplicity and wider applicability. In the recent past several such algorithms have been developed. They are mainly bio-inspired, swarm based, physics based and…

Automatic research with Large Language Models (LLMs) is rapidly gaining importance, driving the development of increasingly complex workflows involving multi-agent systems, planning, tool usage, code execution, and human-agent interaction…