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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/s4158…
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Katherine Benjamin
48 posts
Katherine Benjamin
@kfbenjamin
Applied topology PhD student @OxUniMaths
Oxford, UK Katılım Kasım 2022
62 Takip Edilen228 Takipçiler
Katherine Benjamin retweetledi
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/10.110…
@ImperialMed @KingsCollegeLon @imperial_mrcdtp @KingsIoPPN @imperialcollege
Marinka Zitnik@marinkazitnik
(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/10.110… 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
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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/s4158…
English
Katherine Benjamin retweetledi
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
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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
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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.
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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.
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Katherine Benjamin retweetledi
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!
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Katherine Benjamin retweetledi
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
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Katherine Benjamin retweetledi
So excited to see this 59 authors collaboration finally out! Kudos to @LucaTubiana for leading and coordinating this years long project @CostEutopia
Luca Tubiana @[email protected]@LucaTubiana
As anticipated by @AlexanderRKlotz our review "Topology in soft and biological matter" is finally out on Physics Reports! sciencedirect.com/science/articl… This 59-authors manuscript is the final product of the Eutopia COST Action @CostEutopia (@COSTprogramme). A small thread 1/n
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@iolo_jones congrats iolo!! amazing work, can’t wait to read
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Katherine Benjamin retweetledi
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
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Katherine Benjamin retweetledi
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
CHIMERA@uclchimera
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: @1faf88fe-a998-4c5b-93c9-210a11d9a5c2" target="_blank" rel="nofollow noopener">events.teams.microsoft.com/event/c51f43c9…
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@AgneseBarbensi @StolzBernadette thanks agnese, i owe you for introducing me to TDA :)
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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
STEM for Britain@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
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Katherine Benjamin retweetledi
Amazing to see this paper finally published!
@ProfHampshire @imperial_mrcdtp
Imaging Neuroscience@ImagingNeurosci
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…
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Katherine Benjamin retweetledi
🌟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? logml.committee@gmail.com
#LOGML #Geometry #MachineLearning #SummerSchool
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