Related papers: Approximate Search for Known Gene Clusters in New …
We develop the Blooming Tree Algorithm, a new technique that uses spectroscopic redshift data alone to identify the substructures and the surrounding groups of galaxy clusters, along with their member galaxies. Based on the estimated…
Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the…
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…
Convolutional neural networks (CNNs) are effective at solving difficult problems like visual recognition, speech recognition and natural language processing. However, performance gain comes at the cost of laborious trial-and-error in…
We present a new approach for efficient approximate nearest neighbor (ANN) search in high dimensional spaces, extending the idea of Product Quantization. We propose a two-level product and vector quantization tree that reduces the number of…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
We propose an algorithm for clustering high dimensional data. If $P$ features for $N$ objects are represented in an $N\times P$ matrix ${\bf X}$, where $N\ll P$, the method is based on exploiting the cluster-dependent structure of the…
The Quantitative Group Testing (QGT) is about learning a (hidden) subset $K$ of some large domain $N$ using a sequence of queries, where a result of a query provides information about the size of the intersection of the query with the…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
Given a reference set $R$ of $n$ points and a query set $Q$ of $m$ points in a metric space, this paper studies an important problem of finding $k$-nearest neighbors of every point $q \in Q$ in the set $R$ in a near-linear time. In the…
Locality-sensitive hashing (LSH) is a well-known solution for approximate nearest neighbor (ANN) search with theoretical guarantees. Traditional LSH-based methods mainly focus on improving the efficiency and accuracy of query phase by…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
Similarity search, the task of identifying objects most similar to a given query object under a specific metric, has gathered significant attention due to its practical applications. However, the absence of coordinate information to…
Finding spanning trees under various constraints is a classic problem with applications in many fields. Recently, a novel notion of "dense" ("sparse") tree, and in particular spanning tree (DST and SST respectively), is introduced as the…
Finding optimal evolutionary trees from sequence data is typically an intractable problem, and there is usually no way of knowing how close to optimal the best tree from some search truly is. The problem would seem to be particularly acute…
Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer, i.e., cancer phylogenies, offer valuable insights about cancer development and guide treatment strategies. Many…
The goal of trace reconstruction is to reconstruct an unknown $n$-bit string $x$ given only independent random traces of $x$, where a random trace of $x$ is obtained by passing $x$ through a deletion channel. A Statistical Query (SQ)…
Identification of cancer driver genes is fundamental for the development of targeted therapeutic interventions. The integration of mutational profiles with protein-protein interaction (PPI) networks offers a promising avenue for their…
We consider a modification of the Quantifier Elimination (QE) problem called Partial QE (PQE). In PQE, only a small part of the formula is taken out of the scope of quantifiers. The appeal of PQE is that many verification problems, e.g.…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…