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Deep convolutional neural networks (CNNs) have achieved remarkable success in various fields. However, training an excellent CNN is practically a trial-and-error process that consumes a tremendous amount of time and computer resources. To…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of…
Novel Class Discovery (NCD) is the problem of trying to discover novel classes in an unlabeled set, given a labeled set of different but related classes. The majority of NCD methods proposed so far only deal with image data, despite tabular…
Scatterplots are one of the simplest and most commonly-used visualizations for understanding quantitative, multidimensional data. However, since scatterplots only depict two attributes at a time, analysts often need to manually generate and…
Non-linear dimensionality reduction can be performed by \textit{manifold learning} approaches, such as Stochastic Neighbour Embedding (SNE), Locally Linear Embedding (LLE) and Isometric Feature Mapping (ISOMAP). These methods aim to produce…
GeneVis is a web-based tool to visualize complementary data sets of different disciplines within the field of genetics. It overlays gene-cluster information, gene-interaction data and gene-disease association data by means of web-based…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
We propose an interactive visual analytics tool, Vis-SPLIT, for partitioning a population of individuals into groups with similar gene signatures. Vis-SPLIT allows users to interactively explore a dataset and exploit visual separations to…
Despite the fact that computational fluid dynamics (CFD) software is now (relatively) fast and freely available, it is still amazingly difficult to use. Inaccessible software imposes a significant entry barrier on students and junior…
Renard (Relationships Extraction from NARrative Documents) is a Python library that allows users to define custom natural language processing (NLP) pipelines to extract character networks from narrative texts. Contrary to the few existing…
Graph theory is a cornerstone of Computer Science education, yet entry-level students often struggle to map abstract node-edge relationships to practical applications. This paper presents the design and architecture of a Minecraft-based…
Scikit-network is a Python package inspired by scikit-learn for the analysis of large graphs. Graphs are represented by their adjacency matrix in the sparse CSR format of SciPy. The package provides state-of-the-art algorithms for ranking,…
Data workers use various scripting languages for data transformation, such as SAS, R, and Python. However, understanding intricate code pieces requires advanced programming skills, which hinders data workers from grasping the idea of data…
We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as an image, (ii) computes distances between these images, and (iii) uses these distances to output a map wherein each sequence is a…
We report the development of a user-friendly nano-visualization software program which can acquaint high-school students with nanotechnology. The visual introduction to atoms and molecules, which are the building blocks of this technology,…
Scientists often explore and analyze large-scale scientific simulation data by leveraging two- and three-dimensional visualizations. The data and tasks can be complex and therefore best supported using myriad display technologies, from…
Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the machine-readable newick format. There are thus thousands of published trees in the scientific literature…
While accurate protein structure predictions are now available for nearly every observed protein sequence, predicted structures lack much of the functional context offered by experimental structure determination. We address this gap with…
We introduce 3DB: an extendable, unified framework for testing and debugging vision models using photorealistic simulation. We demonstrate, through a wide range of use cases, that 3DB allows users to discover vulnerabilities in computer…