Related papers: Checking Phylogenetic Decisiveness in Theory and i…
In this paper, an algorithm for determining 3-colorability, i.e. the decision problem (YES/NO), in planar graphs is presented. The algorithm, although not exact (it could produce false positives) has two very important features: (i) it has…
Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…
We investigate infinitary wellfounded systems for linear logic with fixed points, with transfinite branching rules indexed by some closure ordinal $\alpha$ for fixed points. Our main result is that provability in the system for some…
Rooted phylogenetic networks are often used to represent conflicting phylogenetic signals. Given a set of clusters, a network is said to represent these clusters in the "softwired" sense if, for each cluster in the input set, at least one…
We introduce regular graph constraints and explore their decidability properties. The motivation for regular graph constraints is 1) type checking of changing types of objects in the presence of linked data structures, 2) shape analysis…
The study of complex systems has attracted widespread attention from researchers in the fields of natural sciences, social sciences, and engineering. Prediction is one of the central issues in this field. Although most related studies have…
Population protocols [Angluin et al., PODC, 2004] are a model of distributed computation in which indistinguishable, finite-state agents interact in pairs to decide if their initial configuration, i.e., the initial number of agents in each…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
This paper describes a decision theoretic formulation of learning the graphical structure of a Bayesian Belief Network from data. This framework subsumes the standard Bayesian approach of choosing the model with the largest posterior…
Let $X$ be a finite set in $Z^d$. We consider the problem of optimizing linear function $f(x) = c^T x$ on $X$, where $c\in Z^d$ is an input vector. We call it a problem $X$. A problem $X$ is related with linear program $\max\limits_{x \in…
We develop a qualitative model of decision making with two aims: to describe how people make simple decisions and to enable computer programs to do the same. Current approaches based on Planning or Decisions Theory either ignore uncertainty…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
When animals are transported and pass through customs, some of them may have dangerous infectious diseases. Typically, due to the cost of testing, not all animals are tested: a reasonable selection must be made. How to test effectively…
A principled approach to understand network structures is to formulate generative models. Given a collection of models, however, an outstanding key task is to determine which one provides a more accurate description of the network at hand,…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short…
We apply decision tree induction to the problem of discourse clue word sense disambiguation with a genetic algorithm. The automatic partitioning of the training set which is intrinsic to decision tree induction gives rise to linguistically…
One of the main reasons to employ a description logic such as EL or EL++ is the fact that it has efficient, polynomial-time algorithmic properties such as deciding consistency and inferring subsumption. However, simply by adding negation of…
Formal XAI (explainable AI) is a growing area that focuses on computing explanations with mathematical guarantees for the decisions made by ML models. Inside formal XAI, one of the most studied cases is that of explaining the choices taken…
Lexicase selection is a widely used parent selection algorithm in genetic programming, known for its success in various task domains such as program synthesis, symbolic regression, and machine learning. Due to its non-parametric and…