snap-stanford/UCE

Issues

• Running UCE on new species

  #52 opened 2 months ago by PeterZZQ
  3

• UCE using multi-gpu

  #49 opened 2 months ago by BioAmelie
  1

• Gene SYMBOL of other species in “protein_embeddings”

  #51 opened 3 months ago by kelimeike
  1

• IMA sample dataset missing X_uce embeddings

  #50 opened 3 months ago by xqiu625
  1

• visualise UCE embeddings of a new dataset in the existing large graph

  #46 opened 4 months ago by andykwok
  1

• /model_files/all_tokens.torch is missing?

  #47 opened 4 months ago by Evenlyeven
  0

• Which ESM model to use for UCE input?

  #13 opened a year ago by vinettey
  2

• No source information about remainder of the IMA (composed of 2.3 million cells from 28 datasets) in Extended Data Table 2

  #44 opened 5 months ago by litxiaoyao
  3

• Issue with Multi-GPU Distributed Computing Using UCE Model

  #37 opened 5 months ago by kelimeike
  1

• Preprocessing of chicken retina dataset

  #35 opened 5 months ago by JiriBruthans
  1

• RNG and embedding stability in UCE

  #45 opened 5 months ago by VictorCurean
  1

• Genes without protein LLM embeddings

  #39 opened 7 months ago by bschilder
  3

• IMA logistic classifiers

  #38 opened 7 months ago by bschilder
  2

• Ontology ID mappings

  #43 opened 7 months ago by bschilder
  3

• `Unexpected key(s) in state_dict: "transformer_encoder.layers...`

  #41 opened 7 months ago by bschilder
  5

• Can I adjust the dimensions of the output from 1280 to 512?

  #40 opened 7 months ago by ZexiChen502
  1

• How to get gene embeddings

  #36 opened 7 months ago by kelimeike
  3

• Producing UCE embeddings for cell lines

  #34 opened 8 months ago by Ontos46
  1

• probabilities contain NaN in numpy.random.mtrand.RandomState.choice

  #33 opened 8 months ago by mcrewcow
  8

• How to Use Multi-GPU to Inference the Embeddings

  #31 opened 9 months ago by KatarinaYuan
  1

• AnnData eval issue: cannot unpack non-iterable NoneType object

  #5 opened 9 months ago by viriditax
  15

• What does the dimension 145469 mean?

  #32 opened 9 months ago by KatarinaYuan
  1

• How to get the pretrained weight file

  #30 opened 9 months ago by coffee19850519
  1

• Input data of processed data

  #29 opened 10 months ago by fengzhanying
  1

• Gene names in IMA dataset

  #11 opened a year ago by zhuizhui-jj
  1

• What's the difference between the 4-layer model and the 33-layer model

  #28 opened 10 months ago by ZexiChen502
  1

• Understanding data integration

  #19 opened a year ago by maestriev
  7

• Original log-norm expression space

  #27 opened 10 months ago by chrarnold
  3

• Other "Output dimension"

  #26 opened 10 months ago by fengzhanying
  1

• Training UCE

  #25 opened 10 months ago by v-mahughes
  1

• IMA sample issue

  #24 opened 10 months ago by v-mahughes
  7

• Human lymph node AMI figure 2d

  #21 opened 10 months ago by v-mahughes
  7

• Need help: Data Preparation and Model Setup for Data Integration Using UCE

  #23 opened 10 months ago by Yafei611
  6

• Data information is missing

  #22 opened a year ago by kimmo1019
  0

• About New Species

  #20 opened a year ago by zhonghuaxiaodangjiayo
  4

• is there training code available?

  #3 opened a year ago by szalata
  4

• RuntimeError: [enforce fail at inline_container.cc:129] . file in archive is not in a subdirectory: species_offsets.pkl

  #6 opened a year ago by Abhishaike
  6

• Mismatch error when running UCE on ESM embedding of a new species.

  #16 opened a year ago by vinettey
  12

• Reproduce Logistic Classifier results

  #17 opened a year ago by v-mahughes
  9

• NaN error during embeddings

  #18 opened a year ago by DanLesman
  6

• Location of human protein embeddings

  #15 opened a year ago by vinettey
  1

• File potentially missing

  #14 opened a year ago by y-doctor
  3

• file not found

  #4 opened a year ago by killerz99
  27

• Questions about average running time

  #9 opened a year ago by HelloWorldLTY
  4

• Task we can address based on the embeddings

  #7 opened a year ago by HelloWorldLTY
  5