Related papers: Tree decomposition and parameterized algorithms fo…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
We consider Convolutional Neural Networks (CNNs) with 2D structured features that are symmetric in the spatial dimensions. Such networks arise in modeling pairwise relationships for a sequential recommendation problem, as well as secondary…
We introduce an algorithm that conjectures the structure of a permutation class in the form of a disjoint cover of "rules"; similar to generalized grid classes. The cover is usually easily verified by a human and translated into an…
Graph decompositions are the natural generalisation of tree decompositions where the decomposition tree is replaced by a genuine graph. Recently they found theoretical applications in the theory of sparsity, topological graph theory,…
In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…
In this paper we derive the generating function of RNA structures with pseudoknots. We enumerate all $k$-noncrossing RNA pseudoknot structures categorized by their maximal sets of mutually intersecting arcs. In addition we enumerate…
Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D…
Network reconstruction consists in determining the unobserved pairwise couplings between $N$ nodes given only observational data on the resulting behavior that is conditioned on those couplings -- typically a time-series or independent…
The theory of complex trees is introduced as a new approach to study a broad class of self-similar sets. Systems of equations encoded by complex trees tip-to-tip equivalence relations are used to obtain one-parameter families of connected…
The structure of a protein is crucial in determining its functionality, and is much more conserved than sequence during evolution. A key task in structural biology is to compare protein structures in order to determine evolutionary…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…
Thresholding--the pruning of nodes or edges based on their properties or weights--is an essential preprocessing tool for extracting interpretable structure from complex network data, yet existing methods face several key limitations.…
Deep neural networks (DNNs) are nowadays witnessing a major success in solving many pattern recognition tasks including skeleton-based classification. The deployment of DNNs on edge-devices, endowed with limited time and memory resources,…
We construct tree-decompositions of graphs that distinguish all their k-blocks and tangles of order k, for any fixed integer k. We describe a family of algorithms to construct such decompositions, seeking to maximize their diversity subject…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
Asking which sets are fixed-parameter tractable for a given parameterization constitutes much of the current research in parameterized complexity theory. This approach faces some of the core difficulties in complexity theory. By focussing…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
We propose a generalized convolutional neural network (CNN) architecture that first decomposes the input signal into subbands by an adaptive filter bank structure, and then uses convolutional layers to extract features from each subband…