Related papers: Minimum error correction-based haplotype assembly:…
Homomorphic encryption (HE) is a promising technique used for privacy-preserving computation. Since HE schemes only support primitive polynomial operations, homomorphic evaluation of polynomial approximations for non-polynomial functions…
The random equivalent sampling (RES) is a well-known sampling technique that can be used to capture a high-speed repetitive waveform with low sampling rate. In this paper, the feasibility of spectrum-blind multiband signal reconstruction…
Maximum likelihood is a popular technique for isoform reconstruction. Here, we show that isoform reconstruction using short RNA-Seq reads by maximum likelihood is NP-hard.
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…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Metric learning methods for dimensionality reduction in combination with k-Nearest Neighbors (kNN) have been extensively deployed in many classification, data embedding, and information retrieval applications. However, most of these…
We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…
The maximum entropy method (MEM) is a well known deconvolution technique in radio-interferometry. This method solves a non-linear optimization problem with an entropy regularization term. Other heuristics such as CLEAN are faster but highly…
Class imbalance refers to the significant difference in the number of samples from different classes within a dataset, making it challenging to identify minority class samples correctly. This issue is prevalent in real-world classification…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
Multi-Electrode Arrays (MEAs) have been widely used to record neuronal activities, which could be used in the diagnosis of gene defects and drug effects. In this paper, we address the problem of classifying in vitro MEA recordings of mouse…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Feature detection is an important procedure for image matching, where unsupervised feature detection methods are the detection approaches that have been mostly studied recently, including the ones that are based on repeatability requirement…
In this paper, association results from genome-wide association studies (GWAS) are combined with a deep learning framework to test the predictive capacity of statistically significant single nucleotide polymorphism (SNPs) associated with…
Genome-wide association studies (GWASs) aim to detect genetic risk factors for complex human diseases by identifying disease-associated single-nucleotide polymorphisms (SNPs). The traditional SNP-wise approach along with multiple testing…
Photon-counting computed tomography has demonstrated significant advancements in recent years; however, micro photon-counting CT (Micro-PCCT) systems are still limited by pixel-wise detector response nonuniformity, which degrades…
Subtyping neuropsychiatric disorders like schizophrenia is essential for improving the diagnosis and treatment of complex diseases. Subtyping schizophrenia is challenging because it is polygenic and genetically heterogeneous, rendering the…
To solve the Grammatical Error Correction (GEC) problem , a mapping between a source sequence and a target one is needed, where the two differ only on few spans. For this reason, the attention has been shifted to the non-autoregressive or…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
We investigate the dependence of the maximum entropy method (MEM) reconstruction performance on the default model. The maximum entropy method is a reconstruction technique that utilizes prior information, referred to as the default model,…