相关论文: Perfect Phylogeny Haplotyping is Complete for Logs…
${ NP}$-complete problem "Hamiltonian cycle"\ for graph $G=(V,E)$ is extended to the "Hamiltonian Complement of the Graph"\ problem of finding the minimal cardinality set $H$ containing additional edges so that graph $G=(V,E\cup H)$ is…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
If you are predicting the label $y$ of a new object with $\hat y$, how confident are you that $y = \hat y$? Conformal prediction methods provide an elegant framework for answering such question by building a $100 (1 - \alpha)\%$ confidence…
We introduce Probabilistic Gaussian Homotopy (PGH), a probability-space continuation framework for nonconvex optimization. Unlike classical Gaussian homotopy, which smooths the objective and uniformly averages gradients, PGH deforms the…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
The mapping between biological genotypes and phenotypes is central to the study of biological evolution. Here we introduce a rich, intuitive, and biologically realistic genotype-phenotype (GP) map, that serves as a model of self-assembling…
We show that there is a polynomial space algorithm that counts the number of perfect matchings in an $n$-vertex graph in $O^*(2^{n/2})\subset O(1.415^n)$ time. ($O^*(f(n))$ suppresses functions polylogarithmic in $f(n)$).The previously…
Many popular learning algorithms (E.g. Regression, Fourier-Transform based algorithms, Kernel SVM and Kernel ridge regression) operate by reducing the problem to a convex optimization problem over a vector space of functions. These methods…
Given two $k$-graphs $H$ and $F$, a perfect $F$-packing in $H$ is a collection of vertex-disjoint copies of $F$ in $H$ which together cover all the vertices in $H$. In the case when $F$ is a single edge, a perfect $F$-packing is simply a…
A graph $G$ covers a graph $H$ if there exists a locally bijective homomorphism from $G$ to $H$. We deal with regular covers where this homomorphism is prescribed by the action of a semiregular subgroup of $\textrm{Aut}(G)$. We study…
Packing problems are in general NP-hard, even for simple cases. Since now there are no highly efficient algorithms available for solving packing problems. The two-dimensional bin packing problem is about packing all given rectangular items,…
Using prototype methods to reduce the size of training datasets can drastically reduce the computational cost of classification with instance-based learning algorithms like the k-Nearest Neighbour classifier. The number and distribution of…
Symbolic regression encompasses a family of search algorithms that aim to discover the best fitting function for a set of data without requiring an a priori specification of the model structure. The most successful and commonly used…
Archetypal analysis is an unsupervised learning method for exploratory data analysis. One major challenge that limits the applicability of archetypal analysis in practice is the inherent computational complexity of the existing algorithms.…
We consider solutions to the equation f = h^r for polynomials f and h and integer r > 1. Given a polynomial f in the lacunary (also called sparse or super-sparse) representation, we first show how to determine if f can be written as h^r…
We introduce a concept of efficiency for which we can prove that it applies to all paddable languages, but still does not conflict with potential worst case intractability. Note that the family of paddable languages apparently includes all…
We study two computational problems, parameterised by a fixed tree H. #HomsTo(H) is the problem of counting homomorphisms from an input graph G to H. #WHomsTo(H) is the problem of counting weighted homomorphisms to H, given an input graph G…
The polytope containment problem is deciding whether a polytope is a contained within another polytope. This problem is rooted in computational convexity, and arises in applications such as verification and control of dynamical systems. The…