iiinova — where your digital self keeps evolving

Reposted by Jan Aerts

Stephen Turner @stephenturner.us · 10/12/2025

The eXplainable Artificial Intelligence (XAI) Triad: Models, Importances, and Significance at Scale www.biorxiv.org/content/10.6... 🧬🖥️🧪 Bioconductor #Rstats pkg: www.bioconductor.org/packages/XAI... Source: github.com/GhislainFiev...

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Jan Aerts @janaerts.bsky.social · 10/12/2025

OK. Combining #logseq with #gemini_cli may finally be a way to really use it as an external memory. "I think I have scattered different ideas that I needed to remember across all my notes. Can you list them?"

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Jan Aerts @janaerts.bsky.social · 02/12/2025

Next year's halloween, I will either dress as MS Sharepoint, or a VCF file.

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Reposted by Jan Aerts

Information is Beautiful @infobeautiful.bsky.social · 06/11/2025

Now this is how you detect whether an election was stolen. Humans choose rounder numbers. by @TheEconomist

A scatter plot titled "Fair and square? Russian federal elections, 2000-21" which visualizes the results of Russian federal elections. The x-axis represents voter turnout in percentage, ranging from 0 to 100%. The y-axis represents the percentage of votes for Putin, Medvedev, or the United Russia party, also ranging from 0 to 100%. Each dot on the plot represents a polling station. A cluster of dots appears in the upper right corner, indicating high voter turnout and a high percentage of votes for the specified candidates. A dashed rectangle highlights a grid-like pattern of dots at numbers ending in zero and five, with an annotation suggesting this pattern indicates potential foul play. The source is cited as Kobak and Shpilkin (2021).

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Jan Aerts @janaerts.bsky.social · 01/07/2025

Dear interwebs. We're trying to find out how many scientific papers use a specific visual, e.g. upset or circos. Any ideas on how to identify these? A search for the term doesn't work because it is not always named. Also: a simple picture search seems too limited. Any ideas appreciated with a beer.

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Reposted by Jan Aerts

EMBL-EBI Training @training.ebi.embl.org · 25/06/2025

Thank you to all the organisers and participants for joining us at @ebi.embl.org for this week's data visualisation for biology course. Sign up for updates on 'Introduction to multi-omics data integration and visualisation' 2026 course: www.ebi.ac.uk/training/eve... @janaerts.bsky.social #dataviz

A group of people sit on stone steps outside an office building. They smile to the camera. Under them reads the text: Course at EMBL-EBI. Data visualisation for biology. 24 - 26 June 2025. EMBL's European Bioinformatics Institute. Hinxton, UK.

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Jan Aerts @janaerts.bsky.social · 10/06/2025

In preparation for a #dataviz course at the @training.ebi.embl.org later this month, I've created a cheatsheet for creating custom SVG images in #marimo #python. If anyone finds errors: let me know! aida-lab.be/assets/marim...

aida-lab.be

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Jan Aerts @janaerts.bsky.social · 16/05/2025

Being dependent on US services has become a clear liability. The head prosecutor of the International Criminal Court has lost access to his email (apnews.com/article/icc-...). Can #kuleuven move towards open source / EU software? cc @tinebaelmans.bsky.social #kuleuven #ict

apnews.com

Trump's sanctions on ICC prosecutor have halted tribunal's work

Nearly three months ago, U.S. President Donald Trump slapped sanctions on the International Criminal Court's chief prosecutor, Karim Khan.

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Reposted by Jan Aerts

barqueira @lbarqueira.bsky.social · 08/04/2025

Eigenvalues of a parameterized 4×4 matrix Each point corresponds to a non-real eigenvalue of a matrix of the form: [[0, 0, -1, -1], [1, -1, 0, 0], [0, 1, A, 0], [1, 0, -1, B]] where A and B are independently drawn from a continuous uniform distribution on (−3, 3). #mathart #Mathematics #p5js

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Reposted by Jan Aerts

Stephen Turner @stephenturner.us · 24/03/2025

SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/pyg-team/pyt...

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Jan Aerts @janaerts.bsky.social · 24/03/2025

For a #dataviz course I'm looking for scientific images in #SVG that could be improved by different colour schemes, removing unnecessary elements, better fonts, titles, etc. The students in the course can then use #inkscape to improve those images. If you know of good examples, let me know!

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Reposted by Jan Aerts

Inception Labs @inceptionlabs.bsky.social · 26/02/2025

We are excited to introduce Mercury, the first commercial-grade diffusion large language model (dLLM)! dLLMs push the frontier of intelligence and speed with parallel, coarse-to-fine text generation.

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Jan Aerts @janaerts.bsky.social · 06/03/2025

On how to use #mistral #llm to talk to your #zotero library: www.youtube.com/watch?v=x34I...

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Jan Aerts @janaerts.bsky.social · 24/02/2025

Google's AI co-scientist and similar tools may disrupt scientific research even more than AI is already doing. We'll still have to see how it pans out, but we'll need to be prepared. Also: not everyone will have the same access to these tools! storage.googleapis.com/coscientist_...

storage.googleapis.com

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Jan Aerts @janaerts.bsky.social · 18/02/2025

Just released a first version of my #graph #anywidget at pypi.org/project/grap... for displaying (and brushing) force-directed node-link diagrams in #marimo. With a little help from @manzt.sh

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Reposted by Jan Aerts

Helena Klara Jambor @helenajambor.bsky.social · 17/02/2025

📊 & 🧪 Join the #DataViz for #LifeScience course at EMBL-EBI! Organised by Jan Aerts/Ryo Sakai, this year with my Keynote! :) --> Application due March 9th www.ebi.ac.uk/training/eve...

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Reposted by Jan Aerts

EMBL-EBI Training @training.ebi.embl.org · 04/02/2025

If you would like to gain knowledge and practical experience in how to use data visualisation tools to gain insights into complex biological data, apply for this course by 9 March: www.ebi.ac.uk/training/eve... Some financial assistance is available - see course website for more info. #dataviz 🧪

Course at EMBL-EBI
Data visualisation for biology
24 - 26 June 2025
Hinxton, United Kingdom

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Jan Aerts @janaerts.bsky.social · 15/01/2025

Very interesting paper: "A Grammar of Hypotheses for Visualization, Data, and Analysis", by Remco Chang's group arxiv.org/abs/2204.14267 This will definitely go into my #dataviz course, and can anchor several of the discussions we have with collaborators.

The relationships between three hypothesis spaces, formalized using the author's proposed hypothesis grammar.

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Jan Aerts @janaerts.bsky.social · 13/01/2025

Are you a biologist interested in data visualisation to help you explore complex data or create effective visuals? If so, make sure to register for the course that we're organising at the EBI in June www.ebi.ac.uk/training/eve... #biovis #viz #dataviz

ebi.ac.uk

Data visualisation for biology -

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Jan Aerts @janaerts.bsky.social · 08/12/2024

Interesting paper by van den Brandt (TU/e): "Understanding Visualization Authoring Techniques for Genomics Data in the Context of Personas and Tasks" ieeexplore.ieee.org/stamp/stamp.... #omics #dataviz #biovis

ieeexplore.ieee.org

IEEE Xplore Full-Text PDF:

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Reposted by Jan Aerts

Christoph Molnar @christophmolnar.bsky.social · 22/11/2024

Just realized BlueSky allows sharing valuable stuff cause it doesn't punish links. 🤩 Let's start with "What are embeddings" by @vickiboykis.com The book is a great summary of embeddings, from history to modern approaches. The best part: it's free. Link: vickiboykis.com/what_are_emb...

Over the past decade, embeddings — numerical representations of
machine learning features used as input to deep learning models — have
become a foundational data structure in industrial machine learning
systems. TF-IDF, PCA, and one-hot encoding have always been key tools
in machine learning systems as ways to compress and make sense of
large amounts of textual data. However, traditional approaches were
limited in the amount of context they could reason about with increasing
amounts of data. As the volume, velocity, and variety of data captured
by modern applications has exploded, creating approaches specifically
tailored to scale has become increasingly important.
Google’s Word2Vec paper made an important step in moving from
simple statistical representations to semantic meaning of words. The
subsequent rise of the Transformer architecture and transfer learning, as
well as the latest surge in generative methods has enabled the growth
of embeddings as a foundational machine learning data structure. This
survey paper aims to provide a deep dive into what embeddings are,
their history, and usage patterns in industry.

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Jan Aerts @janaerts.bsky.social · 25/11/2024

@mithridates.bsky.social You may know this: what graph algorithms are available for #surrealdb? I'm talking about centrality measures (betweenness centrality, degree centrality, ...), shortest path, minimal spanning tree, etc?

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Reposted by Jan Aerts

Jérémy Cours 🌳 @jeremycours.bsky.social · 23/11/2024

First post on Bluesky, let’s share some websites offering many free illustrations for scientific figures 🖼️ 🧪 🌍 : scidraw.io bioart.niaid.nih.gov www.phylopic.org More well known but very nice though: www.freepik.com

scidraw.io

SciDraw | Scientific Drawings

SciDraw - an open repository of science drawings

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Jan Aerts @janaerts.bsky.social · 23/11/2024

This #surrealdb tutorial has some chunky bacon vibes: surrealdb.com/learn/book/w... (Check out _why's poignant guide to #ruby here: www.rubyinside.com/media/poigna...)

surrealdb.com

SurrealDB | Aeon's Surreal Renaissance | Prologue - your story

Prologue - your story

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Jan Aerts @janaerts.bsky.social · 22/11/2024

If you're handling complex data, have a look at #surrealdb It brings together relational, document, graph, key/value databases, but with querying similar to #SQL www.youtube.com/watch?v=W0Iz...

youtube.com

Why do you need a multi-model database? | SurrealDB

YouTube video by SurrealDB

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Reposted by Jan Aerts

Kai Kupferschmidt @kakape.bsky.social · 20/11/2024

“The majority has spoken, and researchers are moving en masse” to Bluesky, says @shaine.bsky.social. Couldn't help myself and had to write about science twitter, X, bluesky and "the migration"... www.science.org/content/arti... 🧪

science.org

Like ‘old Twitter’: The scientific community finds a new home on Bluesky

After recent changes to Elon Musk’s X, a gradual migration turns into a stampede

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Reposted by Jan Aerts

Stephen Turner @stephenturner.us · 19/11/2024

Amazing to see the influx of new users here 🤩🧬🖥️🧪 I've gotten 100s of requests to be added to my bioinfo starter pack. If your recent ~20 posts are -- (1) bioinfo-relevant, (2) original, not just reposts, (3) snark/politics-free, (4) free from breakfast/bird photos -- ask again, I'd love to add you!

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Reposted by Jan Aerts

Hendrik Strobelt @henstr.bsky.social · 19/11/2024

[Recent History] LSTMVis (2017) has been one of my first projects in the VIS+ML field. It tries to help identify meaningful state change patterns in RNN hidden states and map them to NLP concepts. #NLP #XAI #VIS lstmvis.vizhub.ai vimeo.com/172145096

vimeo.com

LSTMVis - Visual Analysis of Hidden State Dynamics in Recurrent Neural Networks

more on: lstm.seas.harvard.edu

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Reposted by Jan Aerts

Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 19/09/2024

If you hate statistics like I do, then you'll love my free lectures. Putting science before statistics, 20 lectures from basics of inference & causal modeling to multilevel models & dynamic state space models. It's all free, made with love and sympathy. 🧪 #stats www.youtube.com/playlist?lis...

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Jan Aerts @janaerts.bsky.social · 19/11/2024

I like this quote: "Visualizations act as a campfire around which we gather to tell stories." (Al Shalloway) True for research and for outreach/communication.

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Reposted by Jan Aerts

Mark SubbaRao @marksubbarao.bsky.social · 17/11/2024

This high resolution model (1.5km) 3D model of Carbon Dioxide shows its sources of emissions and its transport across the globe. Full details and credits here: svs.gsfc.nasa.gov/5196/

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Jan Aerts @janaerts.bsky.social · 16/11/2024

Great resource! But check that it's sandbox.bio instead of sandbox.io (cc @chrismiller.science )

sandbox.bio

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Jan Aerts @janaerts.bsky.social · 16/11/2024

Was looking up information on colourblind-safe colour schemes, and bumped (again) into this great write up by the ever-inspiring Martin Krzywinski on visualising biological data mk.bcgsc.ca/biovis2012/k... It's from 2012 but still equally relevant #biovis #dataviz #genomics #plots

mk.bcgsc.ca

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Matthias Stahl @higsch.com · 15/11/2024

Interactive canvases can be nicely built with Svelte renderless components. Here’s another example: stackblitz.com/edit/svelte-...

stackblitz.com

Svelte 5 + D3: Map on canvas - StackBlitz

Svelte 5 starter project that already includes D3 as a dependency

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Reposted by Jan Aerts

Devin Lange @devlange.bsky.social · 13/11/2024

I've noticed a lot of new followers recently — thanks to the Vis Researcher starter pack! If you're interested in visualization research, you might find vispubs.com useful. It's a site I created to make it easier to access visualization publications and related resources.

vispubs.com

Visualization Publications

Repository of visualization publications from VIS, EuroVis, and CHI.

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Helena Klara Jambor @helenajambor.bsky.social · 13/11/2024

Recipe for life: 500 genes, 21 amino acids, 4 nucleotides... now @jamessaenz.bsky.social shows: And only 2 lipids! 🧪

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Reposted by Jan Aerts

Jared Hutchins @pablohutch.bsky.social · 11/11/2024

I teach a class on data science here at Illinois and during the seminar I host a competition for the class called "The Hunt for the Worst Data Visualization." This was my most popular post on Xitter, so reproducing some of the best submissions from previous years here:

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Neil Kaye @neilrkaye.bsky.social · 08/11/2024

What is the difference between weather and climate. This #dataviz shows the "Central England" average temperature for periods ranging from 1 day (weather) to 30 years (climate). This shows the climate signal emerging. Note the varying y axis that covers the range of the data.

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Jan Aerts @janaerts.bsky.social · 11/11/2024

I have 3 MSc thesis students working on #biodiversity data in Belgium/Europe. This is some inspiration! @naturalis.bsky.social

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