Related papers: A read-filtering algorithm for high-throughput mar…
This paper proposes an online visual multi-object tracking algorithm using a top-down Bayesian formulation that seamlessly integrates state estimation, track management, clutter rejection, occlusion and mis-detection handling into a single…
Recent studies show that in supervised fine-tuning (SFT) of large language models (LLMs), data quality matters more than quantity. While most data cleaning methods concentrate on filtering entire samples, the quality of individual tokens…
Advances in high-throughput technologies have originated an ever-increasing availability of omics datasets. The integration of multiple heterogeneous data sources is currently an issue for biology and bioinformatics. Multiple kernel…
We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…
Optical coherence tomography (OCT) is one of the non-invasive and easy-to-acquire biomarkers (the thickness of the retinal layers, which is detectable within OCT scans) being investigated to diagnose Alzheimer's disease (AD). This work aims…
Despite their significant advantages over competing technologies, nanopore sequencers are plagued by high error rates, due to physical characteristics of the nanopore and inherent noise in the biological processes. It is thus paramount not…
With the recent move towards sequencing of accurate long reads, finding solutions that support efficient analysis of these reads becomes more necessary. The long execution time required for sequence alignment of long reads negatively…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…
Large language models generate high-quality responses with potential misinformation, underscoring the need for regulation by distinguishing AI-generated and human-written texts. Watermarking is pivotal in this context, which involves…
High throughput sequencing is a technology that allows for the generation of millions of reads of genomic data regarding a study of interest, and data from high throughput sequencing platforms are usually count compositions. Subsequent…
Sparse Filtering is a popular feature learning algorithm for image classification pipelines. In this paper, we connect the performance of Sparse Filtering with spectral properties of the corresponding feature matrices. This connection…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…
The neuroimage analysis community has neglected the automated segmentation of the olfactory bulb (OB) despite its crucial role in olfactory function. The lack of an automatic processing method for the OB can be explained by its challenging…
Optical coherence tomography (OCT) is a commonly-used method of extracting high resolution retinal information. Moreover there is an increasing demand for the automated retinal layer segmentation which facilitates the retinal disease…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…
Organic semiconductors are promising materials for cheap, scalable and sustainable electronics, light-emitting diodes and photovoltaics. For organic photovoltaic cells, it is a challenge to find compounds with suitable properties in the…
Many complex multi-target prediction problems that concern large target spaces are characterised by a need for efficient prediction strategies that avoid the computation of predictions for all targets explicitly. Examples of such problems…