Related papers: Visualizing Multispecies Coalescent Trees: Drawing…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
The capability of making interpretable and self-explanatory decisions is essential for developing responsible machine learning systems. In this work, we study the learning to explain problem in the scope of inductive logic programming…
In this paper, we propose novel mixed-integer linear programming (MIP) formulations to model decision problems posed as influence diagrams. We also present a novel heuristic that can be employed to warm start the MIP solver, as well as…
We present a learning-based approach to computing solutions for certain NP-hard problems. Our approach combines deep learning techniques with useful algorithmic elements from classic heuristics. The central component is a graph…
This is a survey article on trees, with a modest number of proofs to give a flavor of the way these topologies can be efficiently handled. Trees are defined in set-theorist fashion as partially ordered sets in which the elements below each…
Consider the following problem: Given a planar graph $G$, what is the maximum number $p$ such that $G$ has a planar straight-line drawing with $p$ collinear vertices? This problem resides at the core of several graph drawing problems,…
We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…
In this paper we aim to construct piecewise-linear (PWL) approximations for functions of multiple variables and to build compact mixed-integer linear programming (MILP) formulations to represent the resulting PWL function. On the one hand,…
We present a study of several generic tree search techniques applied to the Sequential Ordering Problem. This study enables us to propose a simple and competitive tree search algorithm. It consists of an iterative Beam Search algorithm that…
Probabilistic inferences distill knowledge from graphs to aid human make important decisions. Due to the inherent uncertainty in the model and the complexity of the knowledge, it is desirable to help the end-users understand the inference…
Reconstruction of evolutionary relationships between species is an important topic in the field of computational biology. Pairwise compatibility graphs (PCGs) are used to model such relationships. A graph is a PCG if its edges can be…
Visual information plays an indispensable role in our daily interactions with environment. Such information is manipulated for a wide range of purposes spanning from basic object and material perception to complex gesture interpretations.…
We investigate the use of Genetic Programming (GP) as a convolutional predictor for missing pixels in images. The training phase is performed by sweeping a sliding window over an image, where the pixels on the border represent the inputs of…
We investigate the problem of constructing planar drawings with few bends for two related problems, the partially embedded graph problem---to extend a straight-line planar drawing of a subgraph to a planar drawing of the whole graph---and…
In this paper we suggest that, under suitable conditions, supervised learning can provide the basis to formulate at the microscopic level quantitative questions on the phenotype structure of multicellular organisms. The problem of…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
The visual complexity of a graph drawing is defined as the number of geometric objects needed to represent all its edges. In particular, one object may represent multiple edges, e.g., one needs only one line segment to draw two collinear…
Genetic Programming (GP) has been primarily used to tackle optimization, classification, and feature selection related tasks. The widespread use of GP is due to its flexible and comprehensible tree-type structure. Similarly, research is…
Decision trees are well-known due to their ease of interpretability. To improve accuracy, we need to grow deep trees or ensembles of trees. These are hard to interpret, offsetting their original benefits. Shapley values have recently become…