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1. RiboA: a web application to identify ribosome A-site locations in ribosome profiling data

   https://doi.org/10.1186/s12859-021-04068-w  

   Shao, Danying; Ahmed, Nabeel; Soni, Nishant; O’Brien, Edward P. (December 2021, BMC Bioinformatics)

   null (Ed.)

   Abstract Background Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. Results We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. Conclusions The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/ . The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license. 

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2. PUG: a framework and practical implementation for why and why-not provenance

   https://doi.org/10.1007/s00778-018-0518-5  

   Lee, Seokki; Ludäscher, Bertram; Glavic, Boris (July 2018, The VLDB Journal)

   Explaining why an answer is (or is not) returned by a query is important for many applications including auditing, debugging data and queries, and answering hypothetical questions about data. In this work, we present the first practical approach for answering such questions for queries with negation (first-order queries). Specifically, we introduce a graph-based provenance model that, while syntactic in nature, supports reverse reasoning and is proven to encode a wide range of provenance models from the literature. The implementation of this model in our PUG (Provenance Unification through Graphs) system takes a provenance question and Datalog query as an input and generates a Datalog program that computes an explanation, i.e., the part of the provenance that is relevant to answer the question. Furthermore, we demonstrate how a desirable factorization of provenance can be achieved by rewriting an input query. We experimentally evaluate our approach demonstrating its efficiency. 

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3. Persist: Persistent and Reusable Interactions in Computational Notebooks

   https://doi.org/10.1111/cgf.15092  

   Gadhave, K; Cutler, Z; Lex, A (June 2024, Computer Graphics Forum)

   Computational notebooks, such as Jupyter, support rich data visualization. However, even when visualizations in notebooks are interactive, they are a dead end: Interactive data manipulations, such as selections, applying labels, filters, categorizations, or fixes to column or cell values, could be efficiently applied in interactive visual components, but interactive components typically cannot manipulate Python data structures. Furthermore, actions performed in interactive plots are lost as soon as the cell is re‐run, prohibiting reusability and reproducibility. To remedy this problem, we introduce Persist, a family of techniques to (a) capture interaction provenance, enabling the persistence of interactions, and (b) map interactions to data manipulations that can be applied to dataframes. We implement our approach as a JupyterLab extension that supports tracking interactions in Vega‐Altair plots and in a data table view. Persist can re‐execute interaction provenance when a notebook or a cell is re‐executed, enabling reproducibility and re‐use. We evaluate Persist in a user study targeting data manipulations with 11 participants skilled in Python and Pandas, comparing it to traditional code‐based approaches. Participants were consistently faster and were able to correctly complete more tasks with Persist. 

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4. ReDel: A Toolkit for LLM-Powered Recursive Multi-Agent Systems

   https://doi.org/10.18653/v1/2024.emnlp-demo.17  

   Zhu, Andrew; Dugan, Liam; Callison-Burch, Chris (January 2024, Association for Computational Linguistics)

   Recently, there has been increasing interest in using Large Language Models (LLMs) to construct complex multi-agent systems to perform tasks such as compiling literature reviews, drafting consumer reports, and planning vacations. Many tools and libraries exist for helping create such systems, however none support *recursive* multi-agent systems—where the models themselves flexibly decide when to delegate tasks and how to organize their delegation structure. In this work, we introduce ReDel: a toolkit for recursive multi-agent systems that supports custom tool-use, delegation schemes, event-based logging, and interactive replay in an easy-to-use web interface. We show that, using ReDel, we are able to achieve significant performance gains on agentic benchmarks and easily identify potential areas of improvements through the visualization and debugging tools. Our code, documentation, and PyPI package are open-source at https://github.com/zhudotexe/redel, and free to use under the MIT license. 

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5. Affective Learning Objectives for Communicative Visualizations

   https://doi.org/10.1109/TVCG.2022.3209500  

   Lee-Robbins, Elsie; Adar, Eytan (January 2023, IEEE Transactions on Visualization and Computer Graphics)

   When designing communicative visualizations, we often focus on goals that seek to convey patterns, relations, or comparisons (cognitive learning objectives). We pay less attention to affective intents–those that seek to influence or leverage the audience's opinions, attitudes, or values in some way. Affective objectives may range in outcomes from making the viewer care about the subject, strengthening a stance on an opinion, or leading them to take further action. Because such goals are often considered a violation of perceived ‘neutrality’ or are ‘political,’ designers may resist or be unable to describe these intents, let alone formalize them as learning objectives. While there are notable exceptions–such as advocacy visualizations or persuasive cartography–we find that visualization designers rarely acknowledge or formalize affective objectives. Through interviews with visualization designers, we expand on prior work on using learning objectives as a framework for describing and assessing communicative intent. Specifically, we extend and revise the framework to include a set of affective learning objectives. This structured taxonomy can help designers identify and declare their goals and compare and assess designs in a more principled way. Additionally, the taxonomy can enable external critique and analysis of visualizations. We illustrate the use of the taxonomy with a critical analysis of an affective visualization. 

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