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Predicting the Effects of Mutations on Protein Function with ESM-2
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11Oshan Jayawardena
Oshan
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Predicting the Effects of Mutations on Protein Function with ESM-2
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#phdone - I defended my PhD yesterday! A key lesson: it is amazing how open science and open source can empower beginners with limited resources:
I first learned about instruction-based classifiers like BERT-NLI 3-4 years ago, through the @HuggingFace ZeroShotClassificationPipeline. Digging deeper into this, it was surprisingly easy to find new datasets, newer base models, and reusable fine-tuning scripts on the HF Hub to create my own zeroshot models - although I didn't know much about fine-tuning at the time.
Thanks to the community effect of the Hub, my models were downloaded hundreds of thousands of times after a few months. Seeing my research being useful for people motivated me to improve and upload newer models. Leaving my contact details in the model cards led to academic cooperation and consulting contracts (and eventually my job at HF).
That's the power of open science & open source: learning, sharing, improving, collaborating.
I mean every word in my thesis acknowledgments (screenshot). I'm very grateful to my supervisors @vanatteveldt @CasAndreu @KasperWelbers for their guidance; to @profAndreaRenda and @CEPS_thinktank for enabling me to work part-time during the first year; to @huggingface for creating awesome tools and an awesome platform; and to many others who are not active on social media.
Links to the full thesis and the collection of my most recent models are below.
PS: If someone happens to speak Latin, let me know if my diploma contains some hidden Illuminati code or something :D
I first learned about instruction-based classifiers like BERT-NLI 3-4 years ago, through the @HuggingFace ZeroShotClassificationPipeline. Digging deeper into this, it was surprisingly easy to find new datasets, newer base models, and reusable fine-tuning scripts on the HF Hub to create my own zeroshot models - although I didn't know much about fine-tuning at the time.
Thanks to the community effect of the Hub, my models were downloaded hundreds of thousands of times after a few months. Seeing my research being useful for people motivated me to improve and upload newer models. Leaving my contact details in the model cards led to academic cooperation and consulting contracts (and eventually my job at HF).
That's the power of open science & open source: learning, sharing, improving, collaborating.
I mean every word in my thesis acknowledgments (screenshot). I'm very grateful to my supervisors @vanatteveldt @CasAndreu @KasperWelbers for their guidance; to @profAndreaRenda and @CEPS_thinktank for enabling me to work part-time during the first year; to @huggingface for creating awesome tools and an awesome platform; and to many others who are not active on social media.
Links to the full thesis and the collection of my most recent models are below.
PS: If someone happens to speak Latin, let me know if my diploma contains some hidden Illuminati code or something :D
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