@boyuan_data

Senior Data Scientist at Merck AI. Ex-Googler at DeepMind. PhD in biological data science at Harvard with Chris Sander and Aviv Regev.

 Cambridge, MA
Joined September 2020
  • Tweets55
  • Following186
  • Followers231
2Media
A long-awaited one-stop resource for machine learning on single-cell data in perturbation biology! Kudos to @SPeidli @the_tessallator and an amazing team! #PerturbationBiology #SingleCell #AI4Science
Tessa Green@the_tessallator26 Jan 2024
"scPerturb: harmonized single-cell perturbation data" is out now in Nature Methods!
scPerturb with a pastel logo reminiscent of a petri dish

ALT scPerturb with a pastel logo reminiscent of a petri dish

8
1,111
Thrilled to share our new paper describing a novel form of neural computation: single cells drastically change their tuning in <20ms, shifting from a code for face detection to one that enables fine face discrimination. Neural dynamics are much richer than previously conceived!
Doris Tsao
@doristsao7 Dec 2023
I am beyond excited to share a new paper “Rapid, concerted switching of the neural code in inferotemporal cortex,” led by @Yuelin_Shi and Dasheng Bi. We describe a new form of neural computation in which single neurons rapidly change their tuning to temporally multiplex different functions. In < 20 ms, cells switch from a code optimized for face detection to a code optimized for face discrimination. I think this discovery fundamentally changes our current concept of neural representation. (1/N) biorxiv.org/content/10.1101/…
10
50
6,722
(1/6) Very excited to share our work on @NatureMedicine using #AI to predict #cancer with disease history only (no CT scan!). Glad to co-lead the work with @davplacido @jessicaxhu Chunlei Zheng @sandercbio @TheBrunakLab and many more great colleagues nature.com/articles/s41591-0… .
3
28
2
75
17,176
more replies
(5/6) For cancer screening, what we care the most about is precision. Among many architectures, the attention-based transformer performs the best (50 times higher precision compared to non-sequential models). We also used IG interpretation to find the predictive features.
1
2
365
(6/6) For #patients People have been looking for ways to prevent cancer, and early diagnosis has been proved to be an useful approach. There are many ways AI can truly benefit society, and we hope our work demonstrates one of them. You won't wait too long - please stay tuned.
3
308
I am extremely excited to announce our next Q&A with the one and only @deboramarks. Come participate in our live Q&A on Slack on September 12 at 1:30pm PST/4:30pm EST (as always, you can find this on our calendar). This is a great opportunity to chat all things ML + bio
1
6
1
30
The Spotlight: A General Method for Discovering Systematic Errors in Deep Learning Models deepai.org/publication/the-s… by Greg d'Eon et al. #NeuralNetwork #Classifier

DeepAI

Artificially intelligent tools for naturally creative humans.

deepai.org
2
6
Check out our latest work at #simdl #ICLR2021 @iclr_conf today. The CellBox method works great for a melanoma cell line, but how general it can be? How about other network systems? What if we can take time series measurement - instead of a single snapshot - of the dynamic system?
arXiv Daily
@Arxiv_Daily15 Apr 2021
Inference of cell dynamics on perturbation data using adjoint sensitivity deepai.org/publication/infer… by Weiqi Ji et al. including @boyuan_data #MachineLearning #ComputerScience

DeepAI

Artificially intelligent tools for naturally creative humans.

deepai.org
1
1
1
9
Together with @hellocombustion and @JudyShen_yue, we demonstrated the effectiveness of CellBox for a diversity of “biological networks” proposed by @AdityaPratapa_ @t_m_murali et al. Also, adding synthetic ground truth enables us to directly evaluate the network learned from data
1
2
Besides, we adapted the original CellBox to Julia differential programming and augmented the method with adjoint sensitivity. So say hi to the newborn CellBox.jl!! github.com/jiweiqi/CellBox.j…

GitHub - jiweiqi/CellBox.jl: CellBox in Julia

CellBox in Julia. Contribute to jiweiqi/CellBox.jl development by creating an account on GitHub.

github.com
1
1
Interesting interview with Aviv Regev about her move to @genentech: How to deliver better medicine? 1. human biology, 2. high-res methods, 3. modalities, and 4. computation & maths, the latter for "predictive, generative and interpretable models". nature.com/articles/d41573-0…

Aviv Regev

Nature Reviews Drug Discovery - Aviv Regev, head of Genentech Research and Early Development (gRED), discusses how advances in human biology, massively parallel high-resolution methods, and...

nature.com
3
35
1
138
Honored that our work with @sandercbio @JudyShen_yue @canninl @anilkorkut in @CellSystemsCP got highlighted by the latest @NatComputSci. This is just a start. More to come - soon!!
Nature Computational Science@NatComputSci18 Mar 2021
We just recently published three Research Highlights! The first one highlights the work by @boyuan_data and colleagues that presents an interpretable deep-learning framework that can predict cell responses to unseen perturbations. nature.com/articles/s43588-0…
9
We are all Gang Chen
Zhigang Suo@zhigangsuo22 Jan 2021
A letter (draft) to the President @MIT from ~100 MIT faculty members. It compares facts and Government's allegations against Professor Gang Chen. Versions of it have been sent to many people, and it is in the public domain. A powerful ending: "We are all Gang Chen"
3
Excited to share our #preprint on inCITE-seq for measuring nuclear protein levels + transcriptome at single cell! Like CITE-seq for cell-surface proteins, we use DNA-conjugated antibodies to measure proteins, but now inside the nucleus + transcriptome. biorxiv.org/content/10.1101/…

Simultaneous single cell measurements of intranuclear proteins and gene expression

Identifying gene regulatory targets of nuclear proteins in tissues remains a challenge. Here we describe intranuclear Cellular Indexing of Transcriptomes and Epitopes (inCITE-seq), a scalable method...

biorxiv.org
8
113
18
423
There are so many tests in Boston that even the wastewater can turn positive now??
John Bachman@johnabachman18 Jan 2021
Interesting--researchers working on SARS-CoV-2 are testing positive (and hence required to quarantine) not because they are infected but because they are contaminated with SARS-CoV-2 nucleic acids from lab. Could affect Boston wastewater testing also. science.sciencemag.org/conte…
2
1
Allon Klein of @Harvard and #NASmember Aviv Regev of @genentech @broadinstitute @HHMInews, are the inaugural James Prize in Science and Technology Integration recipients! #NASaward #RNA Read more: ow.ly/GBu050DaVy0
1
19
12
144
Today our CellBox model is finally out in @CellSystemsCP. Predicting dynamic cellular responses to extracellular pertubations is hard. We wanted to use deep neural network but they are limited by its black-box explainability. In this paper we introduced a hybrid approach... (1/3)
2
68
1
283
Here we combined conventional dynamic sysbio modeling (ODE) with recurrent graph neural networks to make highly accurate but also *interpretable* predictions for drug combos in a cancer cell line. This is one of the first efforts to tackle biological problems with #SciML. (2/3)
2
1
8
The full paper is available here bit.ly/Cellbox and a tutorial is available too on github.com/dfci/CellBox. Go #SciML!(3/3)
2
7
Load more