Nelle Varoquaux

Eloïse Touron, Pedro L. C. Rodrigues, Julyan Arbel et al.

Inference from interaction maps, such as centromere identification from genome-wide chromosome conformation capture techniques -- notably Hi-C -- can be formulated as a generic inverse problem: infer a set of parameters given a map summarizing pairwise interactions between entities through blocks of variable numbers and sizes. In this work, we introduce a data-driven approach that leverages shared structure between these maps, such as global alignment between localized patterns, while handling the variability in number and size of entities arising in real-world data. Our approach relies on a transformer architecture capable of handling such variability and a custom simulator to generate abundant, yet computationally cheap synthetic data for training. Applied to the problem of centromere localization, the method accurately recovers their genomic positions across a wide range of species of various genome sizes.

R. Stuart Geiger, Nelle Varoquaux, Charlotte Mazel-Cabasse et al.

Computational research and data analytics increasingly relies on complex ecosystems of open source software (OSS) "libraries" -- curated collections of reusable code that programmers import to perform a specific task. Software documentation for these libraries is crucial in helping programmers/analysts know what libraries are available and how to use them. Yet documentation for open source software libraries is widely considered low-quality. This article is a collaboration between CSCW researchers and contributors to data analytics OSS libraries, based on ethnographic fieldwork and qualitative interviews. We examine several issues around the formats, practices, and challenges around documentation in these largely volunteer-based projects. There are many different kinds and formats of documentation that exist around such libraries, which play a variety of educational, promotional, and organizational roles. The work behind documentation is similarly multifaceted, including writing, reviewing, maintaining, and organizing documentation. Different aspects of documentation work require contributors to have different sets of skills and overcome various social and technical barriers. Finally, most of our interviewees do not report high levels of intrinsic enjoyment for doing documentation work (compared to writing code). Their motivation is affected by personal and project-specific factors, such as the perceived level of credit for doing documentation work versus more "technical" tasks like adding new features or fixing bugs. In studying documentation work for data analytics OSS libraries, we gain a new window into the changing practices of data-intensive research, as well as help practitioners better understand how to support this often invisible and infrastructural work in their projects.

Eloïse Touron, Pedro L. C. Rodrigues, Julyan Arbel et al.

The chromatin folding and the spatial arrangement of chromosomes in the cell play a crucial role in DNA replication and genes expression. An improper chromatin folding could lead to malfunctions and, over time, diseases. For eukaryotes, centromeres are essential for proper chromosome segregation and folding. Despite extensive research using de novo sequencing of genomes and annotation analysis, centromere locations in yeasts remain difficult to infer and are still unknown in most species. Recently, genome-wide chromosome conformation capture coupled with next-generation sequencing (Hi-C) has become one of the leading methods to investigate chromosome structures. Some recent studies have used Hi-C data to give a point estimate of each centromere, but those approaches highly rely on a good pre-localization. Here, we present a novel approach that infers in a stochastic manner the locations of all centromeres in budding yeast based on both the experimental Hi-C map and simulated contact maps.