Francois Nicolas

Finding maximum colorful subtrees in practice.

In metabolomics and other fields dealing with small compounds, mass spectrometry is applied as a sensitive high-throughput technique. Recently, fragmentation trees have been proposed to automatically analyze the fragmentation mass spectra recorded by such instruments. Computationally, this leads to the problem of finding a maximum weight subtree in an edge-weighted and vertex-colored graph, such that every color appears, at most once in the solution. We introduce new heuristics and an exact algorithm for this Maximum Colorful Subtree problem and evaluate them against existing algorithms on real-world and artificial datasets. Our tree completion heuristic consistently scores better than other heuristics, while the integer programming-based algorithm produces optimal trees with modest running times. Our fast and accurate heuristic can help determine molecular formulas based on fragmentation trees. On the other hand, optimal trees from the integer linear program are useful if structure is relevant, for example for tree alignments.

On the decidability of semigroup freeness

This paper deals with the decidability of semigroup freeness. More precisely, the freeness problem over a semigroup S is defined as: given a finite subset X ⊆ S, decide whether each element of S has at most one factorization over X. To date, the decidabilities of two freeness problems have been closely examined. In 1953, Sardinas and Patterson proposed a now famous algorithm for the freeness problem over the free monoid. In 1991, Klarner, Birget and Satterfield proved the undecidability of the freeness problem over three-by-three integer matrices. Both results led to the publication of many subsequent papers. The aim of the present paper is three-fold: (i) to present general results concerning freeness problems, (ii) to study the decidability of freeness problems over various particular semigroups (special attention is devoted to multiplicative matrix semigroups), and (iii) to propose precise, challenging open questions in order to promote the study of the topic.

Finding maximum colorful subtrees in practice

In metabolomics and other fields dealing with small compounds, mass spectrometry is applied as sensitive high-throughput technique. Recently, fragmentation trees have been proposed to automatically analyze the fragmentation mass spectra recorded by such instruments. Computationally, this leads to the problem of finding a maximum weight subtree in an edge weighted and vertex colored graph, such that every color appears at most once in the solution. We introduce new heuristics and an exact algorithm for this Maximum Colorful Subtree problem, and evaluate them against existing algorithms on real-world datasets. Our tree completion heuristic consistently scores better than other heuristics, while the integer programming-based algorithm produces optimal trees with modest running times. Our fast and accurate heuristic can help to determine molecular formulas based on fragmentation trees. On the other hand, optimal trees from the integer linear program are useful if structure is relevant, e.g., for tree alignments.