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In recent years there have been a lot of interest to test for similarity between biological drug products, commonly known as biologics. Biologics are large and complex molecule drugs that are produced by living cells and hence these are…
Sampling-based decoding strategies have been widely adopted for Large Language Models (LLMs) in numerous applications, targeting a balance between diversity and quality via temperature tuning and tail truncation. Considering the strong…
Remote sensing research focusing on feature selection has long attracted the attention of the remote sensing community because feature selection is a prerequisite for image processing and various applications. Different feature selection…
Spectrum sharing allows different protocols of the same standard (e.g., 802.11 family) or different standards (e.g., LTE and DVB) to coexist in overlapping frequency bands. As this paradigm continues to spread, wireless systems must also…
A/B testing, a widely used form of Randomized Controlled Trial (RCT), is a fundamental tool in business data analysis and experimental design. However, despite its intent to maintain randomness, A/B testing often faces challenges that…
Recent advances in single cell sequencing and multi-omics techniques have significantly improved our understanding of biological phenomena and our capacity to model them. Despite combined capture of data modalities showing similar progress,…
Although bulk transcriptomic analyses have significantly contributed to an enhanced comprehension of multifaceted diseases, their exploration capacity is impeded by the heterogeneous compositions of biological samples. Indeed, by averaging…
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals…
Motivation: Algorithms for differential analysis of microarray data are vital to modern biomedical research. Their accuracy strongly depends on effective treatment of inter-gene correlation. Correlation is ordinarily accounted for in terms…
Emerging topics in biomedical research are continuously expanding, providing a wealth of information about genes and their function. This rapid proliferation of knowledge presents unprecedented opportunities for scientific discovery and…
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical…
Recent years have seen growing interest in the retrofitting of type systems onto dynamically-typed programming languages, in order to improve type safety, programmer productivity, or performance. In such cases, type system developers must…
Approximate matching (AM) is a concept in digital forensics to determine the similarity between digital artifacts. An important use case of AM is the reliable and efficient detection of case-relevant data structures on a blacklist, if only…
Four-dimensional Scanning Transmission Electron Microscopy (4D STEM) with data acquired using a defocused electron probe is a promising tool for characterising complex biological specimens and materials through a phase retrieval process…
Estimating and testing for differences in molecular phenotypes (e.g. gene expression, chromatin accessibility, transcription factor binding) across conditions is an important part of understanding the molecular basis of gene regulation.…
Spatial transcriptomics is a modern sequencing technology that allows the measurement of the activity of thousands of genes in a tissue sample and map where the activity is occurring. This technology has enabled the study of the so-called…
Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods…
This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a…
It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…
Design Research Methodology (DRM) supports systematic design research through representations such as Reference Models and Impact Models. However, the practical construction and maintenance of these models often remains manual, requiring…