Sign in

David Fischer

@davidsebfischer.bsky.social
1.2K followers 1.1K following 24 posts

I develop mechanistic machine learning tools for single-cell and spatial omics data to understand the regulatory patterns underlying human disease dynamics. ai4biomedicine.org

PostsRepliesMedia
David Fischer @davidsebfischer.bsky.social · 26/11/2025
Find out more:
 Preprint: www.biorxiv.org/content/10.1... Code: github.com/davidfischerlab/kai
 Blog: ai4biomedicine.org/agenticai
biorxiv.org
Notebook-based alignment of human and agentic reasoning in single-cell biology
Agentic AI is increasingly deployed on complex problems, often using chain-of-thought prompting to ground predictions in stepwise reasoning. In biomedical research, assistive agents could make this re...
060
David Fischer @davidsebfischer.bsky.social · 26/11/2025
kai is an assistant for single-cell biology optimized for human-agent collaboration. Like AI assistants in other domains, kai enhances human efficiency while maintaining accountability – a key advantage over fully autonomous systems in science.
150
David Fischer @davidsebfischer.bsky.social · 26/11/2025
We compared kai with one-shot analysis generation by LLMs by scoring the generated Jupyter notebooks based on various criteria. kai consistently outperforms one-shot analysis generation.
kai benchmarking heatmap
110
David Fischer @davidsebfischer.bsky.social · 26/11/2025
We tested kai on complex scenarios in single-cell biology. kai consistently completed analyses and reasoned (LLM reasoning + analysis execution) for longer than 20 minutes.
110
David Fischer @davidsebfischer.bsky.social · 26/11/2025
The output of kai’s reasoning process is this Jupyter notebook: a transparent documentation of all analyses performed and decisions made. Human scientists can inspect, modify, and give feedback on each step of the analysis.
100
David Fischer @davidsebfischer.bsky.social · 26/11/2025
kai interacts with human scientists through a chat interface in VS Code and directly edits and executes Jupyter notebooks. This design enables kai to autonomously perform analyses while maintaining full accountability.
A an example chat interaction between kai and the user.
100
David Fischer @davidsebfischer.bsky.social · 26/11/2025
This motivated us to build kai: an agentic AI that uses Jupyter notebooks – the same interface that humans use to collaborate.
kai architecture
100
David Fischer @davidsebfischer.bsky.social · 26/11/2025
We started by asking: how do humans build trust with each other? In collaborations, they document their reasoning in computational notebooks, e.g. Jupyter notebooks.
100
David Fischer @davidsebfischer.bsky.social · 26/11/2025
For example, how can I verify the product of 20 minutes of autonomous work by an agent without blindly hoping that it didn’t hallucinate at a key decision point at minute 5?
100
David Fischer @davidsebfischer.bsky.social · 26/11/2025
In cell biology, agentic AI systems need to reason over text, code, and analysis results. How do we ensure accountability in this complex multimodal setting to inspire trust in the predictions made by agents?
100
David Fischer @davidsebfischer.bsky.social · 26/11/2025
Agentic AI systems are becoming available for use in science – but can we trust them?
121
Reposted by David Fischer
Nature Reviews Genetics @natrevgenet.nature.com · 18/07/2025
Our featured article: Adapting systems biology to address the complexity of human disease in the single-cell era go.nature.com/3XBo6Vh #Review by @davidsebfischer.bsky.social, Martin A. Villanueva, Peter S. Winter & ‪@shaleklab.bsky.social‬ @broadinstitute.org @mit.edu @ragoninstitute.bsky.social
go.nature.com
Adapting systems biology to address the complexity of human disease in the single-cell era - Nature Reviews Genetics
Differences between humans and experimental models create a translational gap that makes it difficult to extrapolate research findings. The authors review systems-focused approaches to identify and co...
021
Reposted by David Fischer
Sten Linnarsson @sten.linnarsson.org · 25/06/2025
A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)
2116109
David Fischer @davidsebfischer.bsky.social · 06/05/2025
Check out this drone footage of our institute!
010
David Fischer @davidsebfischer.bsky.social · 02/05/2025
Cool positions for AI x biology in Belgium!
042
David Fischer @davidsebfischer.bsky.social · 13/03/2025
This review is a product of a great team effort together with Martin Villanueva, Peter Winter and Alex Shalek! www.nature.com/articles/s41... & rdcu.be/ecTna
nature.com
Adapting systems biology to address the complexity of human disease in the single-cell era - Nature Reviews Genetics
Differences between humans and experimental models create a translational gap that makes it difficult to extrapolate research findings. The authors review systems-focused approaches to identify and co...
010
David Fischer @davidsebfischer.bsky.social · 13/03/2025
In summary, we outline how systems biology is being adapted to the multiscale dynamics of human health and disease in omics-driven as what is effectively a two-loop cycle over discovery and validation.
100
David Fischer @davidsebfischer.bsky.social · 13/03/2025
We review strategies that can manage this distance and dissect how it relates to understanding cellular systems at specific spatiotemporal scales - be it the cellular scale often considered in the context of single-cell-resolved experiments, or the tissue niche scale captured with spatial omics.
100
David Fischer @davidsebfischer.bsky.social · 13/03/2025
Both are needed to build quantitative models are faithful to human biology and validated through perturbation experiments. However, the usage of two distinct systems incurs a "translational distance" that complicates systems biology approaches that utilize information from the two.
100
David Fischer @davidsebfischer.bsky.social · 13/03/2025
In this review, we discuss how one can rationalize what information about a multiscale cellular system is actually captured by on omics study. We leverage that insight to describe how one can translate between discovery efforts in human tissues and validation efforts in experimental model systems.
100
David Fischer @davidsebfischer.bsky.social · 13/03/2025
However, the dynamics of human tissues in disease settings is multiscale - not only does that impact quantitative models, it also reflects in experimental design and the resources of publicly available data that we have access to. This obstructs attempts at building such quantitative models.
100
David Fischer @davidsebfischer.bsky.social · 13/03/2025
Currently, there's a lot of interest in quantitative models that would help us understand and predict features of the complex cellular systems that underlie human health and disease - think about virtual cells, for example. On can trace some of these ideas back to the early days of systems biology.
1136
Reposted by David Fischer
Ty Miller Lab @tymillerlab.bsky.social · 27/02/2025
Proud to share our @nature.com paper, co-led by Chadi El Farran & Charles Couturier under mentorship of Brad Bernstein where we develop a new framework to understand immunomodulatory myeloid cells in #glioma & lay a foundation to develop more effective immunotherapies. www.nature.com/articles/s41...
nature.com
Programs, origins and immunomodulatory functions of myeloid cells in glioma - Nature
A study of myeloid cells in gliomas, a type of brain tumour, used a factor-based computational framework to reveal four immunomodulatory gene-expression programs that are expressed across myeloid cell...
4289
David Fischer @davidsebfischer.bsky.social · 07/01/2025
Read about self-supervision in models of scRNA-seq data in this deep dive!
060
Reposted by David Fischer
Kristina Ulicna @kristinaulicna.bsky.social · 19/12/2024
Exciting news! 🚀 The Learning Meaningful Representations of Life ( #LMRL 🌟) workshop is returning at #ICLR2025! 🎉 On 27th / 28th April 2025 in Singapore 🇸🇬, this popular event returns with a fresh organizing team 👇 & bold new ideas 🧠 to explore bridging AI & life sciences 🧬
13813
Reposted by David Fischer
Anshul Kundaje @anshulkundaje.bsky.social · 25/12/2024
Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
biorxiv.org
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...
723189
David Fischer @davidsebfischer.bsky.social · 19/12/2024
What cellular & multicellular changes underpin aging of ovaries? We used spatial transcriptomics to study this process in mice, capturing dynamic changes in cells, follicles, and tissue across the estrous cycle. Read about the age-related changes in these dynamics we discovered!
091
Reposted by David Fischer
Rita Strack @ritastrack.bsky.social · 06/12/2024
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
nature.com
Method of the Year 2024: spatial proteomics - Nature Methods
Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.
3614170
David Fischer @davidsebfischer.bsky.social · 27/11/2024
You are already in this one @jasmineplummer.bsky.social!
000
Reposted by David Fischer
Leander @le-and-er.bsky.social · 21/11/2024
Super excited to share our Human Neural Organoid Atlas, now out in Nature! Led by @zhisonghe.bsky.social @josch1.bsky.social, and myself, this resource was created from 36 scRNA-seq datasets—totalling over 1.7 million cells! 🔬✨
 www.nature.com/articles/s41...
 Find out how it can serve you ⏬
 🧵1/8
nature.com
An integrated transcriptomic cell atlas of human neural organoids - Nature
A human neural organoid cell atlas integrating 36 single-cell transcriptomic datasets shows cell types and states and estimates transcriptomic similarity between primary and organoid counterparts, sho...
37723
Reposted by David Fischer
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 20/11/2024
I think Pack 2 is up to 135/150 now, so between the two you can follow 285 bioml researchers in about 4 clicks!
1122
David Fischer @davidsebfischer.bsky.social · 20/11/2024
To expedite the development of a network focussed on single-cell and spatial genomics on this platform, I started to collect accounts of scientists & groups that are broadly active in these fields. This is work in progress, DM if you want to be added or have suggestions! go.bsky.app/HZTJxbZ
84514
Reposted by David Fischer
Jacob Schreiber @jmschreiber91.bsky.social · 18/11/2024
My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body. If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
612243
Reposted by David Fischer
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 18/11/2024
Two BioML starter packs now: Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc DM if you want to be included (or nominate people who should be!)
1011956
Reposted by David Fischer
Andre Rendeiro @andre-rendeiro.com · 16/11/2024
What if we could look at a human tissue image🔬and quantify its biological age?🧬 And how could we get the same insights without collecting the tissue sample? In our new @biorxivpreprint, we create "tissue clocks" ⏳to do just that! www.biorxiv.org/content/10.1... 📝 #aging #tissue thread below⬇️
23713