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Nezar Abdennur

Publications and source records attributed to Nezar Abdennur.

3 recordsLinked to original sources

dtour: A Steerable Tour de Vis Through High-Dimensional Data

Understanding high-dimensional data requires projecting it into lower-dimensional spaces, but any single projection inevitably loses information or introduces distortions. Tours address this limitation through animation of 2D projection sequences, yet existing tools present tradeoffs in the freedom and steerability of projection traversal, providing little to no ability to move between expert-guided paths and unrestrained exploration. We present dtour, a tour interface that combines static projection previews, reversible scrubbing along continuous geodesic projection paths, manual projection manipulation, and a wandering grand tour, all within a single progressive exploration interface. dtour scales to millions of points via GPU-accelerated rendering, runs in any modern browser, and integrates with both Python and JavaScript ecosystems. We demonstrate dtour on text, image, and single-cell data for two usage scenarios: gradually revealing structure in high-dimensional data and validating non-linear dimensionality reduction outputs.

cs.HC

Gosling Designer: a Platform to Democratize Construction and Sharing of Genomics Data Visualization Tools

Analysis of genomics data is central to nearly all areas of modern biology. Despite significant progress in artificial intelligence (AI) and computational methods, these technologies require significant human oversight to generate novel and reliable biological insights. Consequently, the genomics community has developed a substantial number of diverse visualization approaches and a proliferation of tools that biologists rely on in their data analysis workflows. While there are a few commonly used visualization tools for genomics data, many tools target specific use cases for genomics data interpretation and offer only a limited, predefined set of visualization types. Moreover, static visualizations often fail to support exploratory analysis. Developing interactive visualizations and tools typically requires significant time and technical expertise, even when supported by modern LLM-powered coding assistants, and the resulting visualizations can be difficult to share among collaborators. We developed Gosling Designer, an all-in-one platform for editing, exploring, and sharing visualizations of genomics data. Gosling Designer addresses four key challenges observed in existing genomics visualization tools: (1) limited versatility, (2) difficulty of visualization authoring, (3) complexity of data management, and (4) barriers to sharing and collaboration.

q-bio.GN

Gene Expression Noise Facilitates Adaptation and Drug Resistance Independently of Mutation

We show that the effect of stress on the reproductive fitness of noisy cell populations can be modelled as first-passage time problem, and demonstrate that even relatively short-lived fluctuations in gene expression can ensure long-term survival of a drug-resistant population. We examine how this effect contributes to the development of drug-resistant cancer cells, and demonstrate that permanent immunity can arise independently of mutations.

physics.bio-ph