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We compared the calibration of various machine learning uncertainty estimation methods for protein engineering. No method excels across all scenarios, and uncertainty-based strategies for optimization often did not outperform methods without uncertainty.
We benchmarked ProteinMPNN, ESM-IF, LM-Design, and AntiFold for the CDR design of Fab and VHH antibodies. None are a one-model-fits-all solution! Improvements to training sets and eval metrics will help deliver more effective designs. #AI #Antibody #ProteinDesign #AntibodyDesign
We benchmarked ProteinMPNN, ESM-IF, LM-Design, and AntiFold for the CDR design of Fab and VHH antibodies. None are a one-model-fits-all solution! Improvements to training sets and eval metrics will help deliver more effective designs. #AI #Antibody #ProteinDesign #AntibodyDesign
With the #NeurIPS2024 bio-related workshops right around the corner, we wanted to open-source some of our team's notes from the last AI x Bio conference we attended: MoML. Expect more from us as NeurIPS 2024 draws to a close. Full Article > tinyurl.com/tx7du7xm
The February issue of @NatureBiotech is a focus on protein engineering. There are so many great news & views, primers, and reviews. 1/
"Protein language models learn evolutionary statistics of interacting sequence motifs" has been the most interesting paper I've read in 2024 so far Their method to tease out the contact maps was super cool, but this part blew my mind:
Absolutely captivating article from @fraser_lab and Mark Murcko! Very down to earth discussion on what protein "structures" really are cell.com/cell/fulltext/…
Way to learn about sticky molecules lol
Way to learn about sticky molecules lol
Midjourney tip: here is how I use knolling in my prompts Knolling is a special way of arranging objects nicely. But most people don't know that you can do knolling for jobs too! Prompt: knolling of a [JOB/PROFESSION] Perfect for magazines & educational books. Here's the key:…
Someone figured out you could use Stable Diffusion (+ControlNet) to adapt QRs into images while still having them work reliably: reddit.com/r/StableDiffus…
Great write up of LoRA
YOLO NAS is a phenomenon. A real-time object detector with <5 millisecond latency. This will eventually be integrated into mobile cameras, and have “click to buy this item” functionality. Would not be surprised to see Apple integrate this soon.
猜测不少人跟我一样，曾信誓旦旦，计划五一跟吴恩达老师学Prompt Engineering课，实际假期都在吃喝玩乐。 直到今天才开始学，课程地址：learn.deeplearning.ai/chatgpt-prompt… 学习笔记如下： 一、善用分隔符 以前我的Prompt写法，帮我做 xxxx ，加上“：”号，后面跟待处理的文本。例：帮我翻译成中文：hello…
A Visual Tour of the Meta-Tidyverse For years, I’ve been trying out different non-tidyverse implementations of tidyverse. It’s fun seeing folks mold languages to run analysis code inspired by it. If you like screenshots of code, come along for a visual tour. Let’s start w/ R.
watch a 2 layer neural network learn to separate two classes to the left and right
#biology 🔬🔬🔬🔬🔬🔬🔬🔬🔬 DNA --> RNA real-time speed. Gene Transcription at real-time speed. Transcription is the first step in gene expression. It involves copying a gene's DNA sequence to make an RNA molecule. Transcription is performed by
Obsidian 收集网页的体验真流畅，在知乎上复制完，ob 里直接 Ctrl+V 粘贴，自动将复制的 html 转成 markdown ，格式什么都在，唯一问题，图片是远程的，再点右上角的下载按钮，两秒后，文档里的远程图片全部被下载好，放到设定好的目录，同时笔记里的图片连接全部自动改为本地连接；从上到下一气呵成
Bioicons.com Here is an alternative to BioRender that is TRULY FREE and actively maintained. Over 1500 vectorized images sorted by license type (all creative commons or MIT). Fully editable icons and soon they will launch an Inkscape library.
If you missed it, the talks and slides are now ONLINE!! ebi.ac.uk/training/event…
If you missed it, the talks and slides are now ONLINE!! ebi.ac.uk/training/event… https://t.co/RhpMRIFqTk
For my latest attempt at introducing proteins to students, I made a Google Colab Notebook that predicts proteins from a single sequence. I asked the students to tweak the sequence to get a helix or two helices or... (1/5) colab.research.google.com/github/sokrypt…
Lucia Urcelay @luciaurcelayg
89 Followers 448 Following ml research scientist @ferruz_noelia lab @crgenomica | protein design | prev @novartis @bsc_cns
Malika @gfFt2r2WCZ043
32 Followers 1K Following Coffee addict ☕ | Bookworm 📚 | Traveler ✈️ | Dreamer 💭
Brian Naughton @btnaughton
3K Followers 2K Following genetics/data/programming. ex-Hexagon ex-Stanford ex-23andMe ex-TCD https://t.co/77VRsi7znN 🇮🇪
Roland Dunbrack 🏳�... @RolandDunbrack
4K Followers 2K Following Comp struct bio. Gay&proud 🏳️🌈. Views my own & not my employer's.
Yi Zhou @dugu9sword
155 Followers 257 Following Research scientist @ ByteDance. I build foundation models. CryoSTAR & CryoFM: https://t.co/KMKKgzKzIY Opinions are my own
Mehnaz Qureshi @qureshimeh
943 Followers 4K Following | Mum | PhDing | Vet | Virologist🦠 | Influenza 🔬 | B cells | Nanobodies | Antibody🧬 | Curious 🧐 | Views are my own |
Little orange. @GordonSymons11
380 Followers 2K Following The longest thing is time, because it is always endless, and the shortest thing is time, because all our plans are too late to be completed.
Sergey Ovchinnikov @sokrypton
16K Followers 4K Following Scientist, Assistant Professor @MITBiology, #FirstGen, ProteinBERTologist, 🇺🇦 No Human is illegal. Moving to: https://t.co/sow6IRD3jj
bottega boy @bottega_boy
29 Followers 2K Following
Philipp Leippe @PLeippe
182 Followers 689 Following Biosensor engineer & transporter aficionado. Cyclist, mountaineer and chef in my free time. https://t.co/fWyY43jLh6
amelie_schreiber @amelie_iska
2K Followers 561 Following @amelie-iska.bsky.social I ❤️ proteins! intersex=awesome😎✡️🏳️🌈🏳️⚧️💻🧬🧫🧪🦠(🇮🇱❤️🩹🇵🇸) let’s be חברות
Biswanath Shaw @Bis_acrylamide
306 Followers 2K Following Exploring Biophysics @Cornell | Curious about Finance & Businesses | Love 🚴, podcasts & Audiobooks | IISc UG | HSMS | iGEMer
Calvin McCarter @CalvinMccarter
565 Followers 1K Following AI + bio | Views not always my own, but never more than my own | Occasional notes: https://t.co/L1Fgejca1H | Feedback: https://t.co/uooUlZyRdE
Protein ML papers @jashleym6975
16 Followers 96 Following Deep Learning for protein design #Proteins #ML #CompBio #BetterThanTianlai
Eric @apextw
86 Followers 3K Following
Shunhua Han @hanshunhua
177 Followers 689 Following Bioinformatics Scientist @illumina working on finding challenging variants.
Rohit Goswami @rg0swami
355 Followers 3K Following Doctoral Researcher @ UI. Software Engineer, @quansightai Labs. FOSS. ex-Senior Project Associate @ IITK. Code, coffee, academia, @[email protected]
Caitty @tryerxyz
65 Followers 1K Following
Jd Dantes @jddantes
573 Followers 5K Following Mapping out a Theory of Success: From Organizations to Individuals, Across Industries and Periods Background in AI and computer engineering.
Noah Legall, Ph. D. @noah_legall
459 Followers 870 Following Microbial Interaction Researcher - Hybrid Lab Approaches - Nextflow Developer - Algal/Bacterial Interaction Engineering
Js @IM_realJohnson
8 Followers 129 Following
sasha @pearlymuklg
127 Followers 93 Following
Donna Izzo @Dizz1628
476 Followers 5K Following Everything about Wall Street, Life Science, and Rare Disease
Daniel @DanielHUST
160 Followers 2K Following
Ricardo Rodriguez @ricarrodrig
455 Followers 5K Following software developer 🖥️ me gustan las motos 🏍️
Gaurav Vij @Gaurav_vij137
806 Followers 2K Following Founder @withneo - Fully autonomous AI4AI Agent with SOTA scores on OpenAI MLE-Bench. Previously - R&D in HPC Computing & LLM Ops. Checkout 👇
SUPER GET GEMS CLASH @kristinaaliev12
167 Followers 4K Following ONLINE! REAL TAKE MORE GOLD AND GEMS FOR YOUR ACCOUNT! CHECK OUR SITE BELOW!
Hou Chao @houchao1
343 Followers 648 Following Protein dynamics, Protein language model, Mutation effect, Genetics | Postdoc @ColumbiaSysBio | PhD 2023 & Bachelor 2020 @PKU1898
Jue Wang @jueseph
2K Followers 759 Following Research scientist @googledeepmind. Formerly @UWproteindesign @ginkgo @HMS_SysBio.
Zhuoran Qiao / 乔卓... @ZhuoranQ
1K Followers 748 Following A chemical physicist working on AI. #AI4Science @chaidiscovery . Previous: @iambic_ai Research lead; @Caltech PhD *22; @PKU1898 BSc *19. Ptr: @YuanjinZhang1
Rowan @RowanSci
2K Followers 4 Following molecular design and simulation tools for scientists. (also see our literature-posting account @RowanReads.) (cover image from @owl_posting)
Alex Chu @alexechu_
2K Followers 747 Following Deep learning & protein design. @googledeepmind PhD @Stanford
chris bahl @bahl_lab
3K Followers 249 Following President, CEO, Founder @AI_Proteins. Scientific Advisor @bioloomics, @photophysicslab. Founder, Co-organizer @proteinboston. @TEDFellow @ProteinSociety
Genentech @genentech
125K Followers 226 Following Official Twitter for Genentech. See our community guidelines here: https://t.co/yas51FPhKU
GenBio AI @genbioai
9K Followers 0 Following Building the World’s First AI-Driven Digital Organism (AIDO). We're hiring: https://t.co/JwdGBJvhkL
Joseph Watson @_JosephWatson
3K Followers 97 Following Co-Founder @ Xaira Therapeutics Former Baker Lab PostDoc at @UWproteindesign. Interested in generative modelling for molecular design. Views my own.
plasmidsaurus @plasmidsaurus
11K Followers 10K Following Pioneers in the sequencing of whole plasmids, amplicons, whole bacterial genomes & more. 900+ dropboxes and 10 labs globally.
Nathan C. Frey @nc_frey
4K Followers 1K Following CTO & Co-Founder, Coefficient Bio | Ex-@PrescientDesign • @Genentech | Advisor @atomscale & @guidelabsai | @MIT, @Penn PhD, @BerkeleyLab
Yi Zhou @dugu9sword
155 Followers 257 Following Research scientist @ ByteDance. I build foundation models. CryoSTAR & CryoFM: https://t.co/KMKKgzKzIY Opinions are my own
Valence Labs @valence_ai
6K Followers 30 Following Decoding biology to radically improve lives. Powered by @recursionpharma
Simon Barnett @SimonDBarnett
3K Followers 2K Following Partner + Head of Research @_DimensionCap | Focused on the Intersection of Compute + Bio | Prev: Public Biotech Investor | Chemical Engineering @JohnsHopkins
Eric Xing @ericxing
8K Followers 22 Following Researcher, educator, entrepreneur, and administrator in computer science, artificial intelligence, and healthcare.
Jeremy Wohlwend @jeremyWohlwend
789 Followers 60 Following PhD Grad @ MIT CSAIL, former Research Engineer at ASAPP Inc.
Gabriele Corso @GabriCorso
8K Followers 710 Following PhD student @MIT • Research on Generative Models and Geometric Deep Learning for Biophysics • BA @CambridgeUni • Former @TwitterResearch, @DEShawGroup and @IBM
Lilian Weng @lilianweng
167K Followers 166 Following Co-founder of Thinking Machines Lab @thinkymachines; Ex-VP, AI Safety & robotics, applied research @OpenAI; Author of Lil'Log
Martin Pacesa @MartinPacesa
5K Followers 992 Following Structural biologist working on 🖥️ protein design, machine learning🤖, crystallography💎, and cryoEM🔬. Avid weirdness connoisseur 🎩
Biology+AI Daily @BiologyAIDaily
14K Followers 266 Following Protein/Antibody Designer, AI for drug design, Deep learning and large language model. Share daily papers on biology + AI
David S. Goodsell �... @dsgoodsell
25K Followers 109 Following ~molecular art | molecular science~ free digital files of my paintings at RCSB PDB: https://t.co/gJwOxh1GXU…
george church @geochurch
58K Followers 21 Following Professor @Harvard @MIT @PGorg @WyssInstitute tech dev: #CRISPR #NGS #BRAINi
Feng Zhang @zhangf
54K Followers 55 Following Engineer and molecular biologist. Curious about the world and optimistic to make it better.
Roland Dunbrack 🏳�... @RolandDunbrack
4K Followers 2K Following Comp struct bio. Gay&proud 🏳️🌈. Views my own & not my employer's.
Roshan Rao @proteinrosh
3K Followers 570 Following he/him. Research scientist @EvoscaleAI. Foundation models for biology. Prev: RS @MetaAI, PhD @berkeley_ai.
Ellen Zhong @ZhongingAlong
8K Followers 883 Following Assistant Professor @PrincetonCS. #ai4science #proteins247 #cryoem #cryodrgn ❄️🐉 Prev: @MIT @DeepMind @DEShawResearch. Currently moonlighting @generate_biomed.
Frank Noe @FrankNoeBerlin
12K Followers 548 Following Scientist, #MachineLearning and #AI for the Sciences (esp. Physics/Chemistry). Scuba Diver and Traveler.
Samuel Hume @DrSamuelBHume
29K Followers 1K Following I’m a resident doctor, I write about progress in medicine
naturalantibody @naturalantibody
130 Followers 7 Following Enabling acceleration of antibody therapeutic pipelines with advanced computational solutions.
Gabriel Rocklin @grocklin
3K Followers 594 Following High-throughput protein design and biophysics | Asst Prof, Northwestern Pharmacology @NuFeinbergMed @NUSynBio.
Ali Madani @thisismadani
7K Followers 1K Following Founder & CEO of Profluent (https://t.co/GpoVdKW1zQ, we're hiring!). AI+Biology to cure disease. Berkeley PhD. formerly Research @ Salesforce AI.
Kathy Y. Wei, Ph.D. @KathyYWei1
4K Followers 76 Following CSO https://t.co/hgiMCBxCXJ. AI/ML protein design expert. According to ChatGPT: writing the future of biology — one protein at a time :)
Zeyuan Allen-Zhu, Sc.... @ZeyuanAllenZhu
21K Followers 465 Following physics of language models @ Meta (FAIR, not GenAI, not TBD) 🎓：Tsinghua Physics — MIT CSAIL — Princeton/IAS 🏅：IOI x 2 — ACM-ICPC — USACO — Codejam — math MCM
Boston Protein Design... @ProteinBoston
5K Followers 77 Following a community of computational protein engineers and modelers from both academia and industry an @openmsf project organized by @bahl_lab @nickpolizzi_ @sokrypton
amelie_schreiber @amelie_iska
2K Followers 561 Following @amelie-iska.bsky.social I ❤️ proteins! intersex=awesome😎✡️🏳️🌈🏳️⚧️💻🧬🧫🧪🦠(🇮🇱❤️🩹🇵🇸) let’s be חברות
Oxford Protein Inform... @OPIGlets
2K Followers 240 Following Research group led by Charlotte Deane, based in the Department of Statistics at the University of Oxford.
Sergey Ovchinnikov @sokrypton
16K Followers 4K Following Scientist, Assistant Professor @MITBiology, #FirstGen, ProteinBERTologist, 🇺🇦 No Human is illegal. Moving to: https://t.co/sow6IRD3jj
Leo Zang @LeoTZ03
3K Followers 485 Following Protein Designer | Share Reading Notes (AI+Protein/RNA/DNA) | PhD student @harvardmed @DeboraMarksLab | Hosting @ml4proteins
Alex Rives @alexrives
10K Followers 906 Following AI for scientific discovery. Broad and MIT. Chief scientist at @EvoscaleAI and founder and scientific director of the ESM project previously @Meta.
Machine learning for ... @ml4proteins
8K Followers 122 Following Seminar series on machine learning for protein engineering. Details for seminars and slack are on our website. DM us if you're interested in presenting!
Quanquan Gu @QuanquanGu
16K Followers 2K Following Professor @UCLA, Pretraining and Scaling at ByteDance Seed | Recent work: Build AGI | Opinions are my own
Michele Invernizzi @inve_michele
838 Followers 484 Following Computational physicist @PeptoneLtd. (PhD @GroupParrinello, PostDoc @FrankNoeBerlin). AI for Science, Molecular Dynamics, Enhanced Sampling
Mohammed AlQuraishi @MoAlQuraishi
11K Followers 350 Following MLing biomolecules en route to structural systems biology. Asst Prof of Systems Biology and CS @Columbia. Prev. @Harvard SysBio; @Stanford Genetics, Stats.Trends for United States
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