Yang Xu

PhD @UTKnoxville and ML scientist @broadinstitute. Interested in deep learning for single-cell data integration

[Yang Xu @Yang_bio]

5. Many thanks to the team. It’s such a honor to work with a group of people who are talented but more importantly, great and caring.

[Yang Xu @Yang_bio]

So excited to share the very first project I did after joining @broadinstitute. We proposed an attention-incorporated VAE for modeling correspondence between cell state and perturbation response, CellCap (https://t.co/l5t9G6Lo2Y)

[Yang Xu @Yang_bio]

4. One example. we reanalyzed Norma et al CRISPR-activated data. We found only a subpopulation of perturbed K562 cells would respond to CEBP#-activation. CellCap identified that this subpopulation already shows a sign of granulocyte differentiation and is not in cell cycle

[Yang Xu @Yang_bio]

Over 6y stuck in the states, finally made the 1st step on my homeland. What an odd route of going home, DWF-ALK-NAD-HKG-WUH. Flying with @AmericanAir @FijiAirways @cathaypacific. So excited to see many old faces, my dear family and friends.

[Yang Xu @Yang_bio]

My flight touched down in Boston after a nice long vacation in Alaska. Right after, I received notification from USCIS, notifying my green card approval. After 6 years stuck in US, I am finally going home, with free will!

[Yang Xu @Yang_bio]

Check out our poster presented by @sikandhayat

[Yang Xu @Yang_bio]

@sikandhayat @Lufthansa_DE It sucks! They should reschedule your flights for free

[Yang Xu @Yang_bio]

A preprint for Phase 3 of this long ongoing study is out on biorxiv.

MASIv2 enables standardization and integration of multi-modal single-cell and spatial omics data with one general framework https://t.co/ViSURzp7zS

[Yang Xu @Yang_bio]

We have an ongoing research journey.
Phase 1 study https://t.co/QRXQW5l01d was published a year ago, and I am happy to see Phase 2 https://t.co/nH7NRMedEi is online @CommsBio now!
A preprint for Phase 3 will be ready soon in May!

[Sara Mostafavi @sara_mostafavi]

MLCB 2023, coming back in November 29-30 as a hybrid conference (Seattle !). Check out the fantastic list of invited speakers @elhamazizi @bidumit @alexrives : https://t.co/gyzccH2z2m
with great co-organizers @suinleelab @QuonBio @anshulkundaje @james_y_zou @david_a_knowles

[ICML-Compbio-Workshop @icml_compbio]

📢 Calling all #CompBio enthusiasts! Our ICML 2023 Computational Biology Workshop is now open for submissions! Don't miss this opportunity to showcase your cutting-edge research in this exciting field. check more details at https://t.co/6iu83yfXkm #ICML2023 #ComputationalBiology

[Yang Xu @Yang_bio]

@AmyDWillis @GenomeBiology My first 1st author publication was in review process with this journal. A terrible experience for me, and it’s in my blacklist.

[Yang Xu @Yang_bio]

@KelvinTuong My point is that there are other light ML models, for example Symphony, ScType, and CellTypist, that can achieve decent accuracy and serve my need. I don’t need a large DL that charges me more money and takes me more time to run a task that other methods already did great job.

[Yang Xu @Yang_bio]

I tweet this paper not bc I praise for their effort. On the contrary, this paper is selling a misunderstanding that a wasteful DL model guarantees accurate cell type annotation. Don’t waste ur time and money on trying it. https://t.co/uOjCEgDmeB

[Yang Xu @Yang_bio]

@AlexCope241 🎉 congratulations!

[Yang Xu @Yang_bio]

My second integration paper is finally out after I graduated. But the journey doesn’t end here. We have something followed-up! It would be the part 3 of my data integration journey. https://t.co/VNrSjM3sv9

[Yang Xu @Yang_bio]

@AlexCope241 It seems that they are the office managers😂