Related papers: A comparative analysis of progressive multiple seq…

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…

Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…

This paper introduces a novel approach to the task of data association within the context of pedestrian tracking, by introducing a two-stage learning scheme to match pairs of detections. First, a Siamese convolutional neural network (CNN)…

Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…

Over the past two decades, descent methods have received substantial attention within the multiobjective optimization field. Nonetheless, both theoretical analyses and empirical evidence reveal that existing first-order methods for…

This paper presents enhancements to the projection pursuit tree classifier and visual diagnostic methods for assessing their impact in high dimensions. The original algorithm uses linear combinations of variables in a tree structure where…

Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…

We present joint multi-dimension pruning (abbreviated as JointPruning), an effective method of pruning a network on three crucial aspects: spatial, depth and channel simultaneously. To tackle these three naturally different dimensions, we…

In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…

In 2007, Eickmeyer et al. showed that the tree topologies outputted by the Neighbor-Joining (NJ) algorithm and the balanced minimum evolution (BME) method for phylogenetic reconstruction are each determined by a polyhedral subdivision of…

The continuation method is a popular approach in non-convex optimization and computer vision. The main idea is to start from a simple function that can be minimized efficiently, and gradually transform it to the more complicated original…

Knowledge Tracing is the process of tracking mastery level of different skills of students for a given learning domain. It is one of the key components for building adaptive learning systems and has been investigated for decades. In…

UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a widely used clustering method. Here we show that UPGMA is a greedy heuristic for the normalized equidistant minimum evolution (NEME) problem, that is, finding a rooted tree that…

The alignment of optical systems is a critical step in their manufacture. Alignment normally requires considerable knowledge and expertise of skilled operators. The automation of such processes has several potential advantages, but requires…

Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…

Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive…

We investigate a family of approximate multi-step proximal point methods, framed as implicit linear discretizations of gradient flow. The resulting methods are multi-step proximal point methods, with similar computational cost in each…

Fast and precise beam alignment is crucial to support high-quality data transmission in millimeter wave (mmWave) communication systems. In this work, we propose a novel deep learning based hierarchical beam alignment method that learns two…

We introduce a semiparametric approach to neighbor-based classification. We build off the recently proposed Boundary Trees algorithm by Mathy et al.(2015) which enables fast neighbor-based classification, regression and retrieval in large…