Related papers: Reconstructing Trees from Traces
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
Integrated interpretability without sacrificing the prediction accuracy of decision making algorithms has the potential of greatly improving their value to the user. Instead of assigning a label to an image directly, we propose to learn…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
Empirical data on real complex systems are becoming increasingly available. Parallel to this is the need for new methods of reconstructing (inferring) the topology of networks from time-resolved observations of their node-dynamics. The…
Position heaps are index structures of text strings used for the string matching problem. They are rooted trees whose edges and nodes are labeled and numbered, respectively. This paper is concerned with variants of the inverse problem of…
We present graph-based translation models which translate source graphs into target strings. Source graphs are constructed from dependency trees with extra links so that non-syntactic phrases are connected. Inspired by phrase-based models,…
Synthesis from examples enables non-expert users to generate programs by specifying examples of their behavior. A domain-specific form of such synthesis has been recently deployed in a widely used spreadsheet software product. In this paper…
The overlap graphs of subtrees in a tree (SOGs) generalise many other graphs classes with set representation characterisations. The complexity of recognising SOGs in open. The complexities of recognising many subclasses of SOGs are known.…
It is a classical result that any finite tree with positively weighted edges, and without vertices of degree 2, is uniquely determined by the weighted path distance between each pair of leaves. Moreover, it is possible for a (small) strict…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
Multi-label classification is a challenging task, particularly in domains where the number of labels to be predicted is large. Deep neural networks are often effective at multi-label classification of images and textual data. When dealing…
Explaining why and how a tree $t$ structurally differs from another tree $t^\star$ is a question that is encountered throughout computer science, including in understanding tree-structured data such as XML or JSON data. In this article, we…
We propose an approach for learning optimal tree-based prescription policies directly from data, combining methods for counterfactual estimation from the causal inference literature with recent advances in training globally-optimal decision…
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Classification and Regression Trees (CARTs) are off-the-shelf techniques in modern Statistics and Machine Learning. CARTs are traditionally built by means of a greedy procedure, sequentially deciding the splitting predictor variable(s) and…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
We consider a network where an infection cascade has taken place and a subset of infected nodes has been partially observed. Our goal is to reconstruct the underlying cascade that is likely to have generated these observations. We reduce…
In this paper, we consider the problem of recovering a graph that represents the statistical data dependency among nodes for a set of data samples generated by nodes, which provides the basic structure to perform an inference task, such as…