Applied topology PhD student @OxUniMaths
Oxford, UK
Joined November 2022
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1/5 Very happy to share our work on flexible, multiscale cell type assignment for subcellular spatial transcriptomics, now in @Nature
nature.com/articles/s41586-0…
Katherine Benjamin retweeted
This was a lot of work!
ProCyon is a model that integrates protein sequences, structures, and natural language to predict and generate protein phenotypes
Check the paper biorxiv.org/content/10.1101/…
@ImperialMed @KingsCollegeLon @imperial_mrcdtp @KingsIoPPN @imperialcollege
(1/4) Excited to introduce ProCyon: a multimodal foundation model to model, generate, and predict protein phenotypes, led by stellar @oq_35 @YepHuang Robert Calef @valegiunca
👉 biorxiv.org/content/10.1101/…
ProCyon is an 11B parameter multimodal model that integrates protein sequences, structures, and natural language
ProCyon models, predicts, and generates phenotypes with zero-shot task transfer, breaking past the limits of fixed vocabularies or ontologies
🔬 The Challenge: Predicting protein structure is advanced, but predicting protein phenotypes—observable traits linking molecular function to biology—is still an open problem. 40% of human proteins lack context-specific insights, while 20% remain almost entirely uncharacterized
Katherine Benjamin retweeted
When a team at @NDMOxford wanted to know more about cells they were studying as part of research in to kidney disease, they found perfect partners in @OxUniMaths & @mpicbg.
Read about @BetterKidneys @haharrington @kfbenjamin & colleagues' collaboration:
maths.ox.ac.uk/node/68470
2/5 This is joint work with the amazing Aneesha Bhandari, @haharrington, @BetterKidneys and many more.
We introduce TopACT, a method for automatic cell type annotation in next-generation spatial transcriptomics data which sidesteps the need for predefined cell boundaries.
4/5 In #StereoSeq data, TopACT precisely pinpoints rare immune cells in space.
We then use multiparameter persistent homology, a newly emerging method in topological data analysis, to generate and validate a hypothesis on immune cell organisation in lupus.
5/5 We're super excited about TopACT's ability to leverage the unparalleled resolution of next-generation spatial omics platforms.
Check out the article for more, including additional experiments on synthetic benchmark data and the mouse brain.
@OxUniMaths
Katherine Benjamin retweeted
Arguably one of the least utilised but most powerful features of persistent homology (PH) is functoriality. Large swathes of data come pre-divided into distinguished, disjoint subsets (a priori/via clustering). A functorial PH pipeline lets us analyse how these subsets interact!
Katherine Benjamin retweeted
Wonderful week of rainbows, maths and manuscripts! Chromatic work by Abhinav Natarajan @tomrchaplin @majirouses @adambrownphd Toric fibre products and MLE by Niharika Paul @JaneIvyCoons @tudresden_de @OxUniMaths arxiv.org/abs/2405.19303
arxiv.org/abs/2405.13897
Katherine Benjamin retweeted
So excited to see this 59 authors collaboration finally out! Kudos to @LucaTubiana for leading and coordinating this years long project @CostEutopia
As anticipated by @AlexanderRKlotz our review
"Topology in soft and biological matter" is finally out on Physics Reports! sciencedirect.com/science/ar…
This 59-authors manuscript is the final product of the Eutopia COST Action @CostEutopia (@COSTprogramme). A small thread 1/n
Katherine Benjamin retweeted
Really pleased to finally share my preprint: Diffusion Geometry
(1/4) Diffusion geometry defines Riemannian geometry for data and probability spaces!
arxiv.org/abs/2405.10858
Katherine Benjamin retweeted
This is going to be super interesting!
Hear about how mathematical topology can shed light on actual mecahnisms going on in our immune cells!
Sign up for this free online webinar as part of our @uclchimera programme .
Fri 26 April, 10-11am
We're back with another seminar, this time by @kfbenjamin on how multiscale topology classifies and quantifies cell types in subcellular spatial transcriptomic. The seminar will be hosted by @chrischirp . Sign up: events.teams.microsoft.com/e…
I had a great time presenting our research on spatial transcriptomics and topological data analysis today! Incredibly honoured to have been chosen as a medallist #STEM4Brit
Today the first sets of winners for the STEM for Britain 4th March 2024, @Mathematics, Gold/First Place, Daniel Gardham -University of Surrey, Silver/Second Place, Katherine Benjamin -University of Oxford, Bronze/Third Place, Francisco De Melo Virssimo – London School of Economic
Katherine Benjamin retweeted
Amazing to see this paper finally published!
@ProfHampshire @imperial_mrcdtp
New paper in Imaging Neuroscience by Valentina Giunchiglia, Adam Hampshire, et al:
Neural correlates of cognitive ability and visuo-motor speed: Validation of IDoCT on UK Biobank Data
doi.org/10.1162/imag_a_00087
Thanks @osumray for a very entertaining talk on quiver laplacians and applications 🎶
Katherine Benjamin retweeted
🌟Applications open - LOGML 2024🌟
👥 Mentor-led projects, expert talks, tutorials, socials, and a networking night
📝 Application form: logml.ai/
📅 Apply by 26 Jan 2024 📝
📩 Questions? [email protected]
#LOGML #Geometry #MachineLearning #SummerSchool
Katherine Benjamin retweeted
Our work on using algebraic topology for interpreting neural population activity has been featured as an NSF Math Institutes research highlight from ICERM @chadgiusti @prof_g @ICERM
mathinstitutes.org/highlight…
Katherine Benjamin retweeted
Want to mentor for a project at the interface of geometry and machine learning? Mentor applications close November 17th. Find out more at logml.ai/ and apply: forms.gle/HaHrY6JYpqn4UUyS7
Very excited for the return of LOGML next year – 2022 was amazing.
Strongly encourage all those interested in mentoring to apply, especially those in the applied topology and topological deep learning communities!
We're excited to announce that the LOGML Summer School will return in person next summer: July 8-12 2024.
We are currently seeking passionate mentors to lead group projects at the intersection of geometry and machine learning. Find out more and apply: logml.ai/
Katherine Benjamin retweeted
New preprint "The Topological Properties of the Protein Universe". Work carried on by PhD student @DegnbolMadsen, and with @syzmath, @theosysbio @DrDouglasPires and others biorxiv.org/content/10.1101/…
