evolutionaryscale/esm

Issues

• How do you handle stereoisomerism?

  #115 opened a month ago by dannyoo
  1

• Problems when loading esm3 model

  #114 opened 3 months ago by HelloWorldLTY
  2

• where is attention_contacts in esm2?

  #79 opened 5 months ago by linshuxi
  3

• from_pretrained() Error. Cannot use a path to import local model?

  #132 opened 2 months ago by 1830416002
  4

• ESM3 for Distributed Training

  #137 opened 2 months ago by DianGoodluck2024
  0

• multichain protein structure predicrion

  #134 opened 2 months ago by InvincibleZZH
  1

• Availability of UniRef validation set

  #107 opened 2 months ago by roman-bushuiev
  2

• Missing esm.utils.structure.metrics in v3.0.7

  #126 opened 2 months ago by gohdavid
  0

• ModuleNotFoundError: No module named 'biotite.structure.io.npz'

  #96 opened 2 months ago by navvye
  3

• Idea RE: cancer, evolution, and mutation

  #122 opened 2 months ago by Tylersuard
  1

• No module named 'esm.utils.structure.metrics'

  #127 opened 2 months ago by Paulther
  3

• About Getting Protein Sequence Embeddings

  #128 opened 2 months ago by WzWang-2000
  0

• Missing side-chain info for predicted structure

  #124 opened 2 months ago by ahof1704
  0

• Ambiguous amino acid notation, including positive charged/negative charged

  #123 opened 2 months ago by QuasiLegendre
  1

• How can we get attention weights from example sequence and structure?

  #119 opened 3 months ago by what-is-what
  1

• How to get a per protein embedding?

  #116 opened 2 months ago by lpkoh
  1

• Is it possible to map esm3 embedding back to sequence?

  #94 opened 2 months ago by johnnytam100
  3

• How to deal with the beginning and end residues for "compute_vectors" function?

  #106 opened 2 months ago by KatarinaYuan
  1

• Question regarding VQ-VAE optimization

  #92 opened 4 months ago by FranklinHu1
  3

• The mask token of function track

  #108 opened 2 months ago by wwzll123
  1

• ESM3 embeddings

  #105 opened 2 months ago by xf-omics
  1

• Zero-shot Viral Fitness Prediction

  #87 opened 2 months ago by jiaolifengmi
  1

• Cannot reproduce results on CAMEO (194 targets) and CASP14 (71 targets)

  #63 opened 5 months ago by zhujianwei31415
  13

• How to get embeddings from multiple sequences in a single step

  #120 opened 3 months ago by francescopatane96
  1

• Getting the sequence embeddings

  #66 opened 5 months ago by elhambuxton
  2

• Regarding license restrictions

  #111 opened 3 months ago by mjslee0921
  0

• Decoder validation benchmark values

  #109 opened 3 months ago by OliviaViessmann
  0

• Re-train or fine tuning ESM-3 model

  #97 opened 4 months ago by anonimoustt
  2

• global flag for bfloat16?

  #70 opened 5 months ago by mlsbio
  4

• No support for Apple Silicon Devices

  #74 opened 5 months ago by Ruchir3003
  2

• How the 3D structure was captures in ESM-3 model

  #91 opened 4 months ago by anonimoustt
  5

• esm3 not working on google colab

  #89 opened 4 months ago by sokrypton
  10

• Limit AA alphabet

  #64 opened 4 months ago by neuwirtter
  1

• Codebook Structure tokens

  #85 opened 4 months ago by nbrosse
  2

• Can we input only structural tokens, without structure coordinates?

  #71 opened 4 months ago by KatarinaYuan
  1

• Question about track dropout

  #88 opened 4 months ago by violet-sto
  1

• The dimension of sequence logist

  #86 opened 4 months ago by wwzll123
  1

• Batch Support for Obtaining Residue Embeddings

  #81 opened 4 months ago by Junseok0207
  2

• Finetuning and training clarifications

  #78 opened 4 months ago by mjslee0921
  1

• How to add structure information in generating embeddings of a sequence?

  #84 opened 4 months ago by anonimoustt
  1

• Shape mismatch across ESMProteinTensor and forward pass for ESM3

  #56 opened 4 months ago by devpatelio
  5

• Reopening #67 Issue

  #75 opened 5 months ago by sdow1ll
  3

• Release of Structural Tokenizers Trained Before Stage 2

  #72 opened 5 months ago by KatarinaYuan
  1

• Wonder the data!!!

  #62 opened 5 months ago by Yaoyaolingbro
  2

• Get Corresponding Token from Output Logits

  #67 opened 5 months ago by sdow1ll
  2

• Unexpected results of unconditional sequence generations

  #69 opened 5 months ago by pengzhangzhi
  2

• How To Compute Perplexity of Generated Sequences + Interpretation of ESM-3's sequence logits values

  #68 opened 5 months ago by issah-samori
  1

• Missing Inverse Folding files and weights

  #65 opened 5 months ago by yingtaoluo
  1

• Folding Multimers

  #61 opened 5 months ago by ejmeitz
  1

• Mismatch between the shapes of logits from ESM3 outputs and paper description

  #55 opened 5 months ago by KatarinaYuan
  2