Yuyang Zhou

Ph.D. candidate in Westlake University. Currently working on AI+bios

[fajie yuan @duguyuan]

🧬✨Excited to share our online demo " Natural language → De Novo Protein design"

Live demo: http://113.45.254.183:8888/
The demo version Pinal is 1.2B.🔬

You try very detailed textual prompt up to 500 words.
https://t.co/f8b7vxzOQS

[Jin Su @LTEnjoy]

Used SaprotHub to predict mutations for eTDG, a uracil-N-glycosylase variant. 🧬
Lab results: 17 out of top 20 mutations had higher T-to-G editing efficiency than wild type (marked as red), with 3 showing nearly 2x improvement! 🚀

[Jin Su @LTEnjoy]

The found Cas13an (UniProt ID: A0A7C5SD50) was annotated as an uncharacterized protein in the database. We used ProTrek to annotate it and the results were related to CRISPR, showing ProTrek is capable of indentifying unknown proteins.

[fajie yuan @duguyuan]

Recruited 12 bio students, no coding exp, to use ColabSaprot for re-training, zero-shot mutation, & protein design. They matched AI experts w/o hyper-parameter tuning!
With SaprotHub, any biologist can train protein models! @sokrypton @LTEnjoy

https://t.co/sLKVkcMxdB

[fajie yuan @duguyuan]

Introducing ProTrek, a 3-modal PLM for protein seq, struc, and func:

✨ Trained on 40M protein-text pairs, 100x larger than ProteinCLIP, ProtST, ProteinCLAP
🚀 30x/60x better accuracy than ProtST, ProteinCLAP
⚡ 100x faster than Foldseek, MMseq2 for similar function searches

[Sergey Ovchinnikov @sokrypton]

Now everyone customize/share protein language models for their custom task/dataset via
@GoogleColab 🤓

Paper: https://t.co/In0PNg9avy

Colab: https://t.co/qqdlYRw1cS

Credit: @LTEnjoy, Zhikai Li, @ChenchenHa42849, @BonnieSwt, Junjie Shan, @XibinBayesZhou, Dacheng Ma, @duguyuan

[Google DeepMind @GoogleDeepMind]

Announcing AlphaFold 3: our state-of-the-art AI model for predicting the structure and interactions of all life’s molecules. 🧬

Here’s how we built it with @IsomorphicLabs and what it means for biology. 🧵 https://t.co/gjw6Ip4F2M

[Fred Peng @pengzhangzhi1]

Excited to see how PTM-Mamba opens the door for PTM-aware structure prediction and protein design.

[Anthropic @AnthropicAI]

Today, we're announcing Claude 3, our next generation of AI models.

The three state-of-the-art models—Claude 3 Opus, Claude 3 Sonnet, and Claude 3 Haiku—set new industry benchmarks across reasoning, math, coding, multilingual understanding, and vision.

[HongyeJin@COLM @serendip410]

Despite the mixed feelings about Google's latest Gemma model, we're big fans! @GoogleAI Why? Coz we found it pairs incredibly well with our SelfExtend 🤣🤣🤣 - like, perfectly! With Self-Extend, no fine-tuning needed, we effortlessly expanded Gemma's window from 8k to 90k+! On the 'Needle in the haystack' task, Gemma-2b-it even struggled at 8k, but with SelfExtend, Gemma-2b-it easily tackles it within 90k range! #AI #Gemma #SelfExtend #LLMs 🚀

Paper: https://t.co/9lwtnrDpOL
Github: https://t.co/FmGkJpdpQn

[Eric Nguyen @exnx]

Is DNA all you need?

Introducing Evo, a long context 7B foundation model for biology

Evo has SOTA *zero-shot* prediction across DNA, RNA, and protein modalities

Evo can generate DNA, RNA+proteins & make CRISPR-Cas systems for first time

blog https://t.co/5xzGhJPfnK

[fajie yuan @duguyuan]

Our paper on engineering uracil-N-glycosylase using protein language model ESM is now published in Molecular Cell. @XibinBayesZhou

Would love to know if replacing ESM with our Saprot (https://t.co/tdzY59ejZn) would result in better performance.

https://t.co/VDOrPsYUhf

[Yuyang Zhou @BonnieSwt]

@AndrewTang518 pat pat