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We introduce a code generator that converts unoptimized C++ code operating on sparse data into vectorized and parallel CPU or GPU kernels. Our approach unrolls the computation into a massive expression graph, performs redundant expression…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees.…
Tree projections provide a unifying framework to deal with most structural decomposition methods of constraint satisfaction problems (CSPs). Within this framework, a CSP instance is decomposed into a number of sub-problems, called views,…
We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
We study the complexity of finding communication trees with the lowest possible completion time for rooted, irregular gather and scatter collective communication operations in fully connected, $k$-ported communication networks under a…
For an arbitrary tree we investigate the problems of constructing a maximum matching which minimizes or maximizes the cardinality of a maximum matching of the graph obtained from original one by its removal and present corresponding…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
Bringing high-level machine learning models to efficient and well-suited machine implementations often invokes a bunch of tools, e.g.~code generators, compilers, and optimizers. Along such tool chains, abstractions have to be applied. This…
Tree-based models have proven to be an effective solution for web ranking as well as other problems in diverse domains. This paper focuses on optimizing the runtime performance of applying such models to make predictions, given an…
In deep neural networks, better results can often be obtained by increasing the complexity of previously developed basic models. However, it is unclear whether there is a way to boost performance by decreasing the complexity of such models.…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
Ensemble learning methods are designed to benefit from multiple learning algorithms for better predictive performance. The tradeoff of this improved performance is slower speed and larger size of ensemble learning systems compared to single…
Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
The problem of selecting small groups of itemsets that represent the data well has recently gained a lot of attention. We approach the problem by searching for the itemsets that compress the data efficiently. As a compression technique we…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…