Matthew A. Clarke

Computational biologist and mechanistic interpretability researcher. For more find me at:
&

[Matthew A. Clarke @MatthewACl31706]

0/7 Excited to publish my work from my @pibbssai Fellowship with @hrdkbhatnagar and @JBloomAus. We find that SAE latents are sometimes non-independent, instead forming clusters that map interpretable subspaces. Post: https://t.co/9lOtd47KDr and app: https://t.co/CoKwtWZhtB

[Charlie Barker @cgbarker_]

🚨 New preprint!🚨 Tackling non-small cell lung cancer (NSCLC) adenocarcinoma with in silico models:
🌟 Models tumor pathways (EGFR, AKT, JAK/STAT, WNT)
🌟 personalized drug & radiotherapy combos
🌟 Identifies a signature for patient radiotherapystratification

[Matthew A. Clarke @MatthewACl31706]

Special thanks to my co-first authors @cgbarker_
and @AJNics for their incredible work on this project, to all our collaborators, and especially to the Jasmin Fisher lab at @uclcancer!

[Matthew A. Clarke @MatthewACl31706]

Excited to share our new preprint exploring the potential to personalise treatment for non-small cell lung cancer (NSCLC) using in silico modelling: https://t.co/vodY0HHiuF

[Matthew A. Clarke @MatthewACl31706]

By predicting the effect of radiosensitisers, as well as over 10,000 combinations of drugs and driver mutations, we find promising strategies to improve treatment outcomes, and identify a 19-gene signature that could help predict response to radiotherapy.

[Matthew A. Clarke @MatthewACl31706]

7/7 Huge thanks to:
- @pibbssai for organising this project
- @NeelNanda5 and @GoogleDeepMind for releasing Gemma Scope, a set of SAEs critical to this work
- @neuronpedia / Decode Research @johnnylin @CurtTigges for an invaluable resource
- Everyone who gave feedback!

[Matthew A. Clarke @MatthewACl31706]

0/7 Excited to publish my work from my @pibbssai Fellowship with @hrdkbhatnagar and @JBloomAus. We find that SAE latents are sometimes non-independent, instead forming clusters that map interpretable subspaces. Post: https://t.co/9lOtd47KDr and app: https://t.co/CoKwtWZhtB

[Matthew A. Clarke @MatthewACl31706]

6/7 How confident are we? We focus on SAEs for two models (GPT2-Small and Gemma-2-2b) with different SAE architectures, and observe similar phenomena in both, but that Gemma clusters tend to be less interpretable. We also focus mostly on interpretability of small clusters.

[Nature Reviews Cancer @NatureRevCancer]

NEW Perspective! MA Clarke & J Fisher discuss how executable computational cancer models can be used to represent dynamic biological behaviours inherent in cancer & how they can help in precision medicine.

😎 https://t.co/y2DAga2GG2

@uclcancer @uclmedsci @uclnews @NatResCancer

[Rowan Howell @Howell_Rowan]

In our new paper, out today, we use executable modelling as a tool for drug repurposing in #COVID19. https://t.co/iTlXbaG43H

[Rowan Howell @Howell_Rowan]

Excited to see this work from my postdoc in the Fisher Lab @uclcancer out. In this project we combined a computational model of #melanoma and immune cells to understand the early stages of immune surveillance.

[Aron Vallinder @aronvallinder]

Very excited to announce a new paper—Cultural Evolution of Cooperation Among LLM agents—coauthored with @edwardfhughes

We study whether LLM agents can develop cooperative norms when interacting with each other, and find considerable differences across models.

[Helena Coggan @helena_coggan]

Thrilled to share the first research paper from my PhD, out today! Here we use agent-based simulations to shed light on how cells behave during the very first stages of lung cancer initiation. Thanks so much to @DrClareWeeden, @pearce_maths, (1/2)

https://t.co/r0H2aLuiud

[Charlie Barker @cgbarker_]

New preprint out! 🚨 Sumana Sharma, @e_petsalaki & I explored the surprising effects of ARID1A KO in melanoma using network-based multi-omics. Interesting findings on signaling & drug resistance! Check @e_petsalaki's tweetorial or read here: https://t.co/4nnU0CONOc

[Daniel Jacobson @DanH_Jacobson]

Really excited to share my PhD work with the Secrier lab which has just been published in @GenomeMedicine, exploring homologous recombination deficiency in multi-scale and its links with drug response and the TME!

https://t.co/cdOyoLTCIn

@mariasecrier @UGI_at_UCL @uclcancer

[Pedro Victori @pedrovictori_en]

I was very happy to be able to present the first results from my work within @WellcomeLeap Delta Tissue Program.