open-problems-single-cell-perturbations

[hoary siren]

I have given up on RNA and am gonna do this instead now :p

[nova kraken]

goodluckkk

[lone lance]

Has anyone had success opening the lincs data .gctx file? They are so huge and cmappy is struggling to open them.

[surreal light]

can anyone tell me what the target and the variables are? I'm getting a headache trying to read the dataset description @-@

[last olive]

Are zoom record available?

[surreal light]

yup It was just released

[last olive]

Webinar recording:
https://youtu.be/dRG3qTaALp0?si=vAxqIkzKljjuf2vW

[last olive]

Recording
https://youtu.be/6ySKxnjHX8Y?si=ICiv26d7j1LbYaKn

[tardy cloak]

Thanks for these very valuable sessions

This is my situation

[hidden magnet]

It it a hard competition. I tried a lot of methods and performance did not increase.

[rustic swift]

rip

was 12th a week ago got bombarded to 20s 😭

cant anymore man. need help

[acoustic turret]

Hey guys, does anyone know if de_train.parquet is corrupt? I tried installing it multiple times and opening it on multiple platforms, but all of them are throwing errors

[gloomy nexus]

Just jumped on this competition. Has anyone been successful with it so far?😃

[acoustic turret]

Also, I opened all other parquet files in the dataset just fine.

[last olive]

Video: https://youtu.be/lcc5vY-Pycs?si=NDz8KEarMFN8Llka

[acoustic turret]

Hey guys, the data description says: "We performed this experiment in human PBMCs because the cells are commercially available with pre-obtained consent for public release and PBMCs are a primary, disease-relevant tissue that contains multiple mature cell types (including T-cells, B-cells, myeloid cells, and NK cells) with established markers for annotation of cell types". Could anyone please tell me what established markers it is referring to?

[red crypt]

Hi, cant use Saturn Cloud. “You have chosen an option not available to you: max disk space 10Gib. ((40GiB required, 19GiB available) …” any suggestion?

[lone escarp]

This would refer to genes used as markers for each cell type. For example CD19 for B cells.

[last olive]

Now:

🚀 NIPS Workshop on Challenge "Open Problems – Single-Cell Perturbations"
"Predict how small molecules change gene expression in different cell types"
⌚️ 16 December 2023 at 13:30-16:30 CST (GMT-6). You can find the schedule and Zoom link on Google Sheets here: https://docs.google.com/spreadsheets/d/19VF9s9jDVE76Hg4wJDi9S8Dg3ZC1E1SAS4sdUazuTWI/edit?usp=sharing

Everyone is invited to attend. Link to information post: https://www.kaggle.com/competitions/open-problems-single-cell-perturbations/discussion/461113