Related papers: CompostBin: A DNA composition-based algorithm for …

16S-ribosomal sequencing and other metagonomic techniques provide snapshots of microbial communities, revealing phylogeny and the abundances of microbial populations across diverse ecosystems. While changes in microbial community structure…

Designing novel proteins with desired characteristics remains a significant challenge due to the large sequence space and the complexity of sequence-function relationships. Efficient exploration of this space to identify sequences that meet…

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…

This paper proposes a general optimization strategy, which combines results from different optimization or parameter estimation methods to overcome shortcomings of a single method. Shotgun optimization is developed as a framework which…

Semantic segmentation consists in classifying each pixel of an image by assigning it to a specific label chosen from a set of all the available ones. During the last few years, a lot of attention shifted to this kind of task. Many computer…

The detailed analysis of molecular structures and properties holds great potential for drug development discovery through machine learning. Developing an emergent property in the model to understand molecules would broaden the horizons for…

Acceleration methods for diffusion models (e.g., token merging or downsampling) typically optimize synthesis quality under reduced compute, yet often ignore discriminative capacity. We revisit token compression with a joint objective and…

Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…

In robotics, methods and softwares usually require optimizations of hyperparameters in order to be efficient for specific tasks, for instance industrial bin-picking from homogeneous heaps of different objects. We present a developmental…

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…

Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…

Deep learning has revolutionized many industries by enabling models to automatically learn complex patterns from raw data, reducing dependence on manual feature engineering. However, deep learning algorithms are sensitive to input data, and…

Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…

System identification is normally involved in augmenting time series data by time shifting and nonlinearisation (e.g., polynomial basis), both of which introduce redundancy in features and samples. Many research works focus on reducing…

Improving charge carrier mobilities in organic semiconductors is a challenging task that has hitherto primarily been tackled by empirical structural tuning of promising core compounds. Knowledge-based methods can greatly accelerate such…

For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots…

There is a growing awareness of the important roles that microbial communities play in complex biological processes. Modern investigation of these often uses next generation sequencing of metagenomic samples to determine community…

This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a…

Molecular electronics studies have advanced from early, simple single-molecule experiments at cryogenic temperatures to complex and multifunctional molecules under ambient conditions. However, room-temperature environments increase the risk…

The increasing importance of carbon capture technologies for deployment in remediating CO2 emissions, and thus the necessity to improve capture materials to allow scalability and efficiency, faces the challenge of materials development,…