Related papers: Finding easy regions for short-read variant callin…
Conformal prediction is a generic methodology for finite-sample valid distribution-free prediction. This technique has garnered a lot of attention in the literature partly because it can be applied with any machine learning algorithm that…
Numerous challenges persist that delay clinical interpretation of human genetic variants, to name a few: (1) un- structured PubMed articles are the most abundant source of evidence, yet their variant annotations are difficult to query…
In forensic genetics, short tandem repeats (STRs) are used for human identification (HID). Degraded biological trace samples with low amounts of short DNA fragments (low-quality DNA samples) pose a challenge for STR typing. Predefined…
PURPOSE: The popularity of germline genetic panel testing has led to a vast accumulation of variant-level data. Variant names are not always consistent across laboratories and not easily mappable to public variant databases such as ClinVar.…
Sparse representation classification achieves good results by addressing recognition problem with sufficient training samples per subject. However, SRC performs not very well for small sample data. In this paper, an inverse-projection group…
A DNA palindrome is a segment of double-stranded DNA sequence with inver- sion symmetry which may form secondary structures conferring significant biolog- ical functions ranging from RNA transcription to DNA replication. To test if the…
The recent development of metagenomic sequencing makes it possible to sequence microbial genomes including viruses in an environmental sample. Identifying viral sequences from metagenomic data is critical for downstream virus analyses. The…
Semi-supervised semantic segmentation aims to learn from a small amount of labeled data and plenty of unlabeled ones for the segmentation task. The most common approach is to generate pseudo-labels for unlabeled images to augment the…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…
We consider the problem of uncertainty quantification in change point regressions, where the signal can be piecewise polynomial of arbitrary but fixed degree. That is we seek disjoint intervals which, uniformly at a given confidence level,…
Current machine learning has made great progress on computer vision and many other fields attributed to the large amount of high-quality training samples, while it does not work very well on genomic data analysis, since they are notoriously…
We design an efficient algorithm that outputs tests for identifying predominantly homogeneous subcohorts of patients from large in-homogeneous datasets. Our theoretical contribution is a rounding technique, similar to that of Goemans and…
While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read…
Public security vulnerability reports (e.g., CVE reports) play an important role in the maintenance of computer and network systems. Security companies and administrators rely on information from these reports to prioritize tasks on…
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. Most methods for viral diversity estimation…
We study the {\em robust proper learning} of univariate log-concave distributions (over continuous and discrete domains). Given a set of samples drawn from an unknown target distribution, we want to compute a log-concave hypothesis…
Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
Objective: Assessing the appropriateness of diagnostic referrals is critical for improving healthcare efficiency and reducing unnecessary procedures. However, this task becomes challenging when referral reasons are recorded only as free…