Steven Ge

When plotting, LLMs see what they expect to see - Posit Data science agents need to accurately read plots even when the content contradicts their expectations. Our testing shows today's LLMs still struggle here.

To be effective, data science agents need to be able to read plots reliably. @sara-altman.bsky.social and I wrote about some concerning findings on LLMs' ability to interpret plots when the content contradicts their expectations on the @posit.co blog.

posit.co/blog/introdu...

GitHub - gexijin/vibe: Vibe coding via Claude Code & Codex Vibe coding via Claude Code & Codex. Contribute to gexijin/vibe development by creating an account on GitHub.

This is my R development setup — built on VS Code and running both Claude Code and OpenAI’s Codex inside a Docker container. It also supports Shiny apps and has been working great for me.

I am on Windows. These coding agents were initially designed for Linux, I think.

github.com/gexijin/vibe

The data is searchable on this site that the Renthal lab put together (thanks to Shams in Will's lab for leading this): painseq.shinyapps.io/u19humandrga...

New iDEP feature: instantly annotate k-means clusters with enriched pathways. Fewer clicks, better insights. Explore your data! Give it a spin on your RNA-seq data: bioinformatics.sdstate.edu/idep/

GitHub Copilot Chat in Positron Assistant 🤖

Positron Assistant now supports GitHub Copilot for both completions and chat!

Add GitHub Copilot as a model provider for access to its models, chat participants, and tools.

Learn more: positron.posit.co/assistant

Minimalist Async Evaluation Framework for R Designed for simplicity, a mirai evaluates an R expression asynchronously, locally or distributed over the network. Built on nanonext and NNG for modern networking and concurrency, scales efficiently ...

I put out a patch release of mirai today. Version 2.5.2 really improves the OpenTelemetry integration so you can more easily see into your async workflows. Other key ecosystem packages will roll out with this enabled - next up: Shiny!

mirai.r-lib.org

#Rstats

iDEP website: bioinformatics.sdstate.edu/idep/

YouTube video by Steven Ge Analyze RNA-Seq data with IDEP, an interactive website

In this video, I show how to use iDEP to interpret bulk RNA-seq data. Start with QC plots and exploratory analyses before identifying differentially exp. genes and pathways. We picked up on high mitochondrial rRNA counts, one male mixed in with 7 female mice.
www.youtube.com/watch?v=ta1o...

The Forecaster | Rami Krispin | Substack A newsletter about time series analysis and forecasting. Click to read The Forecaster, by Rami Krispin, a Substack publication with hundreds of subscribers.

I kicked off a new newsletter focused on time series analysis and forecasting.

My goal is to use it as both a framework and motivation to write my upcoming books on time series and forecasting.

If you are interested, please sign up here:
theforecaster.substack.com

#timeseries #rstats #python

letter from the statistics department chair at UNL

The Department of Statistics at the University of Nebraska–Lincoln is under threat of closure, with tenured faculty facing dismissal. This is a small but globally impactful department.
Please consider writing a letter of support. Your voice could make a real difference.

5 tools to visualize genomic datasets 🧵
1. Karyoploter bernatgel.github.io/karyoploter...

I had a 26GB TSV file. R choked. So I turned to UNIX. And it worked.
1/
You only need 500 columns.
But the file is 26GB.
R freezes. Memory bleeds.
You need the data—but you don’t need the pain.
Here’s what I did.

The Cagent Project, The Bayesian Data Analysis Book, Getting Started with Claude Code A weekly curated update on data science and engineering topics and resources.

My weekly newsletter is out!

ramikrispin.substack.com/p/the-cagent...

The Snakemake Project, the AI Advantage Book, Claude Code Tutorials and More A weekly curated update on data science and engineering topics and resources.

My weekly newsletter is out!

ramikrispin.substack.com/p/the-snakem...

#llm #ai #python

Getting Started with Docker Model Runner Docker recently introduced a new feature for Docker Desktop — Docker Model Runner, which allows running and interacting with LLMs locally…

My Docker Model Runner tutorial is also available on Medium (for paid subscribers). Alternatively, for non-subscribers, it is open in my newsletter.

medium.com/data-science...

AIOps newsletter: theaiops.substack.com

#ai #docker #datascience

Understand NGS sequencing files
bioinf.comav.upv.es/courses/seq...

The PandasAI Project, Learning SQL Book, Fine-Tuning Local LLMs A weekly curated update on data science and engineering topics and resources.

My weekly newsletter is out!

This week:
🔹 Open Source of the Week - The PandasAI project
🔹 New learning resources
🔹 Book of the week - Learning SQL by Alan Beaulieu

📌 Join 30k subscribers and subscribe for weekly updates.

ramikrispin.substack.com/p/the-pandas...

#ai #python #datascience #sql

Hello #dataBS (& especially #TidyTuesday) fam! I'm trying to organize a thing to help me keep TidyTuesday running smoothly, but first I need to get a bit of a runway. Every week I curate a TT dataset, and it's wearing me down. Please see github.com/rfordatascie... for some ways you can help! #RStats

Life-saving idea! Pass it on!

My weekly newsletter is out!

This week's agenda:
🛠️ The social-media-kit project
📝 New learning resources
📚Book of the week - Models Demystified by Michael Clark and Seth Berry

📌 Join 30k subscribers and subscribe for weekly updates.

ramikrispin.substack.com/p/new-book-m...

#datascience #ai

From left to right, Dr. Albert Mulenga, William Tae Heung Kim, Dr. Thu Thuy Nguyen, Dr. Alex Kiarie Gaithuma, Dr Hassan Hakimi and Emily Bencosme Cuevas. Kim is a Texas A&M researcher who was detained in San Francisco last Monday despite being a permanent resident of the United States and a green card holder. COURTESY OF TEXAS A&M UNIVERSITY

I NEED to tell you the story of Tae Heung “William” Kim.

He's a graduate student at Texas A&M where he's working on a vaccine for Lyme disease.

He's a *legal permanent resident* of the United States.

And he's been in ICE detention for 12 days & counting, transferred Tuesday to South Texas.

A black and white portrait of a scientist looking back at the camera with a serious expression. She has short black hair, simple but elegant dangling earrings, and a white lab coat. The background is blurry.

Flossie Wong-Staal (1946 – 2020) was a Chinese-American virologist and molecular biologist.
She was the first scientist to clone HIV and determine the function of its genes, which was a major step in proving that HIV is the cause of AIDS.
🔬🧪 #WomenInSTEM

Virtual Speaker Series: Data Science Tools in Action Join us at the Kohl Centre at Virginia Tech for a dynamic speaker series showcasing cutting-edge data science tools and their real-world applications. This series aims to make modern analytics more ac...

I will present on AI-powered data science platforms on Monday, July 21, at 11 am EST at the Univ of Virginia. Zoom link:

kohl.aaec.vt.edu/events/data-...

Posit Orbital is a new library that converts Scikit-learn pipelines into SQL queries, enabling machine learning model inference directly within SQL databases.

Orbital - new OSS from Posit, looks super practical application for ML pipelines 👇🏼

posit.co/blog/introdu...

#python #rstats #datascience

New blog post: @posit.co Positron Assistant provides inline completions with GitHub Copilot and chat/agent using Claude 4 Sonnet. Demo: using agent mode to create an #Rstats package with Roxygen2 docs and testthat unit tests. doi.org/10.59350/gkj...

🚨 BREAKING 🚨 The National Science Foundation has sent an email out to its members to collect signatures for a dissent declaration similar to the NIH’s Bethesda Declaration and the EPA’s Declaration of Dissent.

This comes on the heels of Lee Zeldin putting 139 EPA declaration signers on admin leave

Mayor Brandon Scott has reduced crime in Baltimore by 62%, and now has the lowest homicide rate in Baltimore history.

How did he do it?

NOT be spending more on police. He did it by MAJOR investment in afterschool and literacy programs.

Socialism works

What's in the Big Beautiful Bill?
I made a simple chatbot!
You can ask questions, and AI will answer based on the 500-page document. Ask for summaries or explanations. See the impact on different groups.

Kids are off to sleepovers. I'm home alone, bored to tears. ☺️
www.orditus.com/bbb/

Hadley Wickham in a white t-shirt and jeans sits on a light-colored couch across from Michael Chow, wearing a dark green shirt and pants, who is seated on an orange pouf. Between them is a white coffee table with books. In the background, there's a dark bar with shelves displaying numerous bottles, a wood-paneled wall, and a black, modern fireplace. Text overlay reads "Hadley Wickham CHIEF SCIENTIST, POSIT".

Ever wonder how the #tidyverse came to be? 🤔

#TheTestSet's first episode features @hadley.nz on his accidental empire of #RStats packages, bear encounters, and more!

Stream it at thetestset.co, Spotify, or Apple Podcasts.

#DataAnalytics #PodcastLaunch

I gave a talk on good enough practices for reproducible Bioinformatics at the DataDrivenPharma event organized by Ilya. Thanks, Eric Ma, for hosting us. Please find the slide deck at this link divingintogeneticsandgenomics.com/talk/2025-m...