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instanovoplus-v1.1.0

Text Generation
PyTorch
Safetensors
proteomics
mass-spectrometry
peptide-sequencing
de-novo-sequencing
diffusion
multinomial-diffusion
biology
computational-biology
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BioGeek commited on
Commit
2d5dc5e
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1 Parent(s): b130812

Add instanovoplus-v1.1.0 config

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Files changed (1) hide show
  1. config.json +47 -25
config.json CHANGED
@@ -1,42 +1,64 @@
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  {
 
 
 
 
 
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  "attention_type": "wavlm",
 
 
 
 
 
 
 
 
 
 
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  "cond_cross_attn_layers": [
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  0,
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  3,
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  6,
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  9
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  ],
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- "cond_emb_dim": 768,
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- "conv_peak_encoder": false,
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  "conv_pos": 256,
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  "conv_pos_groups": 32,
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- "diffusion_s": 0.008,
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  "diffusion_type": "multinomial",
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- "dim": 768,
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- "dim_feedforward": 1024,
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- "drop_cond_prob": 0.1,
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- "dropout": 0.1,
 
 
 
 
 
 
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  "isotope_error_range": [
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  0,
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  1
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  ],
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- "layers": 12,
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- "max_charge": 10,
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  "max_length": 40,
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- "max_mz": 2500.0,
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- "min_intensity": 0.01,
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- "min_mz": 50.0,
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- "n_peaks": 200,
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- "nheads": 8,
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- "pos_encoding": "relative",
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- "precursor_mass_tol": 50,
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- "remove_precursor_tol": 2.0,
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- "t_emb_dim": 768,
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- "t_emb_max_period": 10000,
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- "time_steps": 20,
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- "use_flash_attention": false,
38
- "vocab_size": 33,
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- "wav_encoder": "wavlm",
40
- "wavlm_max_dist": 280,
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- "wavlm_num_bucket": 140
 
 
 
 
 
 
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  }
 
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  {
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+ "vocab_size": 33,
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+ "layers": 12,
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+ "dim": 768,
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+ "nheads": 8,
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+ "dropout": 0.1,
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  "attention_type": "wavlm",
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+ "time_steps": 20,
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+ "wav_encoder": "wavlm",
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+ "wavlm_num_bucket": 140,
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+ "wavlm_max_dist": 280,
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+ "dim_feedforward": 1024,
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+ "max_charge": 10,
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+ "t_emb_dim": 768,
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+ "t_emb_max_period": 10000,
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+ "cond_emb_dim": 768,
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+ "drop_cond_prob": 0.1,
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  "cond_cross_attn_layers": [
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  0,
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  3,
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  6,
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  9
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  ],
 
 
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  "conv_pos": 256,
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  "conv_pos_groups": 32,
 
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  "diffusion_type": "multinomial",
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+ "diffusion_s": 0.008,
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+ "pos_encoding": "relative",
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+ "use_flash_attention": false,
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+ "conv_peak_encoder": false,
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+ "n_peaks": 200,
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+ "min_mz": 50.0,
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+ "max_mz": 2500.0,
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+ "min_intensity": 0.01,
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+ "remove_precursor_tol": 2.0,
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+ "precursor_mass_tol": 50,
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  "isotope_error_range": [
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  0,
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  1
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  ],
 
 
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  "max_length": 40,
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+ "diffusion_schedule": [
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+ 0.9959956407546997,
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+ 0.9899116158485413,
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+ 0.9837409257888794,
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+ 0.9774042963981628,
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+ 0.9708139896392822,
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+ 0.9638685584068298,
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+ 0.9564463496208191,
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+ 0.9483951926231384,
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+ 0.9395192861557007,
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+ 0.9295578598976135,
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+ 0.9181517958641052,
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+ 0.9047877192497253,
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+ 0.8887006044387817,
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+ 0.8686933517456055,
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+ 0.8427781462669373,
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+ 0.8073800206184387,
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+ 0.7553581595420837,
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+ 0.6700572371482849,
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+ 0.5015214085578918,
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+ 0.03162277489900589
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+ ]
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  }