Related papers: Sashimi plots: Quantitative visualization of RNA s…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
Large Vision-Language Models (LVLMs) have demonstrated remarkable performance across a wide range of multimodal tasks. However, fine-tuning these models for domain-specific applications remains a computationally intensive challenge. This…
In this work, we present a methodology and a corresponding code-base for constructing mock integral field spectrograph (IFS) observations of simulated galaxies in a consistent and reproducible way. Such methods are necessary to improve the…
This note is concerned with accurate and computationally efficient approximations of moments of Gaussian random variables passed through sigmoid or softmax mappings. These approximations are semi-analytical (i.e. they involve the numerical…
The scalability of a particular visualization approach is limited by the ability for people to discern differences between plots made with different datasets. Ideally, when the data changes, the visualization changes in perceptible ways.…
We propose a series of methods to represent the evolution of a field of science at different levels: namely micro, meso and macro levels. We use a previously introduced asymmetric measure of paradigmatic proximity between terms that enables…
Plot-based Graphic API recommendation (Plot2API) is an unstudied but meaningful issue, which has several important applications in the context of software engineering and data visualization, such as the plotting guidance of the beginner,…
Large language models (LLMs) have demonstrated remarkable advancements, primarily due to their capabilities in modeling the hidden relationships within text sequences. This innovation presents a unique opportunity in the field of life…
A method for automated quantification of the alignment of one-dimensional nanostructures from microscopy imaging is presented. Nanostructure alignment metrics are formulated and shown to able to rigorously quantify the orientational order…
RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…
Medical imaging and multi-modal clinical settings often face the challange of missing modality in their diagnostic pipelines. Existing imputation methods either lack representational capacity or are computationally expensive. We propose…
In computational biology, biological entities such as genes or proteins are usually annotated with terms extracted from Gene Ontology (GO). The functional similarity among terms of an ontology is evaluated by using Semantic Similarity…
We introduce \emph{Nutri-bullets}, a multi-document summarization task for health and nutrition. First, we present two datasets of food and health summaries from multiple scientific studies. Furthermore, we propose a novel…
Self-supervised Learning (SSL) has become a powerful paradigm for representation learning without manual annotations. However, most existing frameworks focus on global alignment and struggle to capture the hierarchical, multi-scale lesion…
Efforts to utilize growing volumes of clinical imaging data to generate tumor evaluations continue to require significant manual data wrangling owing to the data heterogeneity. Here, we propose an artificial intelligence-based solution for…
{\it SimRank} is a classic measure of the similarities of nodes in a graph. Given a node $u$ in graph $G =(V, E)$, a {\em single-source SimRank query} returns the SimRank similarities $s(u, v)$ between node $u$ and each node $v \in V$. This…
The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate…
Visualization onboarding supports users in reading, interpreting, and extracting information from visual data representations. General-purpose onboarding tools and libraries are applicable for explaining a wide range of graphical user…
RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking…
Computational intensity and sequential nature of estimation techniques for Bayesian methods in statistics and machine learning, combined with their increasing applications for big data analytics, necessitate both the identification of…