Commit
·
d9bfa88
1
Parent(s):
40eefe0
Initial commit
Browse files- README.md +17 -0
- config.json +52 -0
- invprojector_2023-05-25.pth +3 -0
- optimizer.pt +3 -0
- projector_2023-05-25.pth +3 -0
- pytorch_model.bin +3 -0
- rng_state.pth +3 -0
- scheduler.pt +3 -0
- special_tokens_map.json +7 -0
- tokenizer.json +293 -0
- tokenizer_config.json +11 -0
- trainer_state.json +3100 -0
- training_args.bin +3 -0
README.md
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---
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license: apache-2.0
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---
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---
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license: apache-2.0
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library_name: transformers
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pipeline_tag: feature-extraction
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tags:
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- chemistry
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- transformers
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---
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# selfies-ted2m
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selfies-ted is an transformer based encoder decoder model for molecular representations using SELFIES. This is a 2.2M parameter version of the model. For the full-sized version and more informatin on architecture, see [selfies-ted](https://huggingface.co/ibm-research/materials.selfies-ted).
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This version also includes a projection layer to convert the last hidden state of the BART model (256-dimensional vector per token) to a single 128-dimension vector for the whole SELFIES sequence.
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config.json
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{
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"_name_or_path": "/dccstor/ipd/small-bart/test_trainer/checkpoint-50050",
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"activation_dropout": 0.0,
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"activation_function": "gelu",
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"adapters": {
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"adapters": {},
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"config_map": {},
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"fusion_config_map": {},
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"fusions": {}
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},
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"architectures": [
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"BartForConditionalGeneration"
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],
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"attention_dropout": 0.0,
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"bos_token_id": 1,
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"classifier_dropout": 0.0,
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"d_model": 256,
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"decoder_attention_heads": 4,
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"decoder_ffn_dim": 256,
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"decoder_layerdrop": 0.0,
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"decoder_layers": 2,
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"decoder_start_token_id": 2,
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"dmodel": 256,
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"dropout": 0.1,
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"encoder_attention_heads": 4,
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"encoder_ffn_dim": 256,
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"encoder_layerdrop": 0.0,
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"encoder_layers": 2,
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"eos_token_id": 2,
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"forced_eos_token_id": 2,
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"id2label": {
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"0": "LABEL_0",
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"1": "LABEL_1",
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"2": "LABEL_2"
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},
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"init_std": 0.02,
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"is_encoder_decoder": true,
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"label2id": {
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"LABEL_0": 0,
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"LABEL_1": 1,
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"LABEL_2": 2
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},
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"max_position_embeddings": 128,
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"model_type": "bart",
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"num_hidden_layers": 6,
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"pad_token_id": 3,
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"scale_embedding": false,
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"torch_dtype": "float32",
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"transformers_version": "4.21.3",
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"use_cache": true,
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"vocab_size": 173
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}
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invprojector_2023-05-25.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:fc61f71e93f6990f753d3b58275cde1cb7e3f593f49657dfb3a9e05efecc0a04
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size 35988864
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optimizer.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:194a00dd868d2861c1ba80e94cdf387b07d5580369addce87e36e9f199c32b77
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size 17831061
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projector_2023-05-25.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:0939886f08074af8b8a723efc308e9e24d4252ae388b71cf729fbdfaacfd8882
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size 35923740
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pytorch_model.bin
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version https://git-lfs.github.com/spec/v1
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oid sha256:c56beb1afc07c44598564b3ff802d63bb2c3d364c068b0f27b126ff9f9df62bc
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size 8920081
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rng_state.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:7b9b9179f51efc8caa7a2c631cffc6bb347b285863b3d50ff6bfc6101bad2c0c
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size 17499
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scheduler.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:6e12f8d8befe78fabb83cfbf6b51ed6e72b79737572a3699bf9d838ed33a0d84
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size 623
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special_tokens_map.json
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{
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"cls_token": "[CLS]",
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"mask_token": "[MASK]",
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"pad_token": "[PAD]",
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"sep_token": "[SEP]",
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"unk_token": "[UNK]"
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}
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tokenizer.json
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{
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"version": "1.0",
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"truncation": null,
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"padding": null,
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"added_tokens": [
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{
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"id": 0,
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"content": "[UNK]",
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"single_word": false,
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"lstrip": false,
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"rstrip": false,
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"normalized": false,
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"special": true
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},
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{
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"id": 1,
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"content": "[CLS]",
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"single_word": false,
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"lstrip": false,
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"rstrip": false,
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"normalized": false,
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"special": true
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},
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{
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"id": 2,
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"content": "[SEP]",
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"single_word": false,
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"lstrip": false,
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"rstrip": false,
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"normalized": false,
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"special": true
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},
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{
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"id": 3,
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"content": "[PAD]",
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"single_word": false,
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| 37 |
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"lstrip": false,
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| 38 |
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"rstrip": false,
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"normalized": false,
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"special": true
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},
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{
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"id": 4,
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"content": "[MASK]",
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"single_word": false,
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"lstrip": false,
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| 47 |
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"rstrip": false,
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| 48 |
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"normalized": false,
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"special": true
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}
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],
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| 52 |
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"normalizer": null,
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| 53 |
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"pre_tokenizer": {
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| 54 |
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"type": "WhitespaceSplit"
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},
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| 56 |
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"post_processor": {
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| 57 |
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"type": "TemplateProcessing",
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| 58 |
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"single": [
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| 59 |
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{
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| 60 |
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"SpecialToken": {
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| 61 |
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"id": "[CLS]",
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| 62 |
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"type_id": 0
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| 63 |
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}
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| 64 |
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},
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{
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| 66 |
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"Sequence": {
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"id": "A",
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| 68 |
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"type_id": 0
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}
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},
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{
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"SpecialToken": {
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"id": "[SEP]",
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"type_id": 0
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}
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}
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],
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"pair": [
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{
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"Sequence": {
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"id": "A",
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"type_id": 0
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}
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},
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{
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"Sequence": {
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"id": "B",
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"type_id": 1
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}
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}
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],
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"special_tokens": {
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"[CLS]": {
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"id": "[CLS]",
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"ids": [
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1
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],
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"tokens": [
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"[CLS]"
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]
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},
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"[SEP]": {
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"id": "[SEP]",
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"ids": [
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2
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],
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"tokens": [
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| 108 |
+
"[SEP]"
|
| 109 |
+
]
|
| 110 |
+
}
|
| 111 |
+
}
|
| 112 |
+
},
|
| 113 |
+
"decoder": null,
|
| 114 |
+
"model": {
|
| 115 |
+
"type": "WordLevel",
|
| 116 |
+
"vocab": {
|
| 117 |
+
"[UNK]": 0,
|
| 118 |
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"[CLS]": 1,
|
| 119 |
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"[SEP]": 2,
|
| 120 |
+
"[PAD]": 3,
|
| 121 |
+
"[MASK]": 4,
|
| 122 |
+
"[17O]": 5,
|
| 123 |
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"[/S@@]": 6,
|
| 124 |
+
"[/N]": 7,
|
| 125 |
+
"[B@-1]": 8,
|
| 126 |
+
"[18OH1]": 9,
|
| 127 |
+
"[-/Ring2]": 10,
|
| 128 |
+
"[=17O]": 11,
|
| 129 |
+
"[/Br]": 12,
|
| 130 |
+
"[C@]": 13,
|
| 131 |
+
"[N@]": 14,
|
| 132 |
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"[Branch1]": 15,
|
| 133 |
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"[=Si]": 16,
|
| 134 |
+
"[=Branch2]": 17,
|
| 135 |
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"[Cl].[Cl-1]": 18,
|
| 136 |
+
"[/C]": 19,
|
| 137 |
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"[S].[Cl-1]": 20,
|
| 138 |
+
"[SH1]": 21,
|
| 139 |
+
"[Sn@]": 22,
|
| 140 |
+
"[#S]": 23,
|
| 141 |
+
"[NH1+1]": 24,
|
| 142 |
+
"[#Branch1]": 25,
|
| 143 |
+
"[#Branch1].[Cl-1]": 26,
|
| 144 |
+
"[BH2-1]": 27,
|
| 145 |
+
"[/NH1+1]": 28,
|
| 146 |
+
"[=P@]": 29,
|
| 147 |
+
"[I]": 30,
|
| 148 |
+
"[/S+1]": 31,
|
| 149 |
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"[S-1]": 32,
|
| 150 |
+
"[=S@+1]": 33,
|
| 151 |
+
"[NH0]": 34,
|
| 152 |
+
"[SnH1]": 35,
|
| 153 |
+
"[F]": 36,
|
| 154 |
+
"[BH1-1]": 37,
|
| 155 |
+
"[=Ring2]": 38,
|
| 156 |
+
"[CH1]": 39,
|
| 157 |
+
"[=Ring1]": 40,
|
| 158 |
+
"[/S@]": 41,
|
| 159 |
+
"[N@+1]": 42,
|
| 160 |
+
"[Sn+2]": 43,
|
| 161 |
+
"[Sn+3]": 44,
|
| 162 |
+
"[#N+1]": 45,
|
| 163 |
+
"[/F]": 46,
|
| 164 |
+
"[Si]": 47,
|
| 165 |
+
"[/O]": 48,
|
| 166 |
+
"[Sn]": 49,
|
| 167 |
+
"[P]": 50,
|
| 168 |
+
"[Ring2]": 51,
|
| 169 |
+
"[#Branch2].[Cl-1]": 52,
|
| 170 |
+
"[=P@@]": 53,
|
| 171 |
+
"[PH1+1]": 54,
|
| 172 |
+
"[/Cl]": 55,
|
| 173 |
+
"[C@@]": 56,
|
| 174 |
+
"[Sn@@]": 57,
|
| 175 |
+
"[=S@]": 58,
|
| 176 |
+
"[=S]": 59,
|
| 177 |
+
"[C@H1]": 60,
|
| 178 |
+
"[Ring2].[Cl-1]": 61,
|
| 179 |
+
"[O-1].[Cl-1]": 62,
|
| 180 |
+
"[N-1]": 63,
|
| 181 |
+
"[S@@H1]": 64,
|
| 182 |
+
"[/O-1]": 65,
|
| 183 |
+
"[/NH1]": 66,
|
| 184 |
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"[/C@@H1]": 67,
|
| 185 |
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"[B-1]": 68,
|
| 186 |
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"[OH0]": 69,
|
| 187 |
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"[Ring1]": 70,
|
| 188 |
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"[=O+1]": 71,
|
| 189 |
+
"[O+1]": 72,
|
| 190 |
+
"[=S@@+1]": 73,
|
| 191 |
+
"[=S+1]": 74,
|
| 192 |
+
"[/I]": 75,
|
| 193 |
+
"[Si@@]": 76,
|
| 194 |
+
"[=C]": 77,
|
| 195 |
+
"[P+1]": 78,
|
| 196 |
+
"[I].[Cl-1]": 79,
|
| 197 |
+
"[Branch1].[Cl-1]": 80,
|
| 198 |
+
"[P@@]": 81,
|
| 199 |
+
"[Branch1].[C]": 82,
|
| 200 |
+
"[Br+1]": 83,
|
| 201 |
+
"[=B]": 84,
|
| 202 |
+
"[CH1-1]": 85,
|
| 203 |
+
"[Sn+1]": 86,
|
| 204 |
+
"[Si-1]": 87,
|
| 205 |
+
"[/N+1]": 88,
|
| 206 |
+
"[N+1]": 89,
|
| 207 |
+
"[CH2]": 90,
|
| 208 |
+
"[SiH2]": 91,
|
| 209 |
+
"[/Sn]": 92,
|
| 210 |
+
"[=PH1]": 93,
|
| 211 |
+
"[=P+1]": 94,
|
| 212 |
+
"[S@@]": 95,
|
| 213 |
+
"[/C@H1]": 96,
|
| 214 |
+
"[N@@+1]": 97,
|
| 215 |
+
"[=S@@]": 98,
|
| 216 |
+
"[/NH2+1]": 99,
|
| 217 |
+
"[=N+1]": 100,
|
| 218 |
+
"[=C].[Cl-1]": 101,
|
| 219 |
+
"[=NH2+1]": 102,
|
| 220 |
+
"[=SH1]": 103,
|
| 221 |
+
"[/Si]": 104,
|
| 222 |
+
"[#N]": 105,
|
| 223 |
+
"[=N]": 106,
|
| 224 |
+
"[/OH0]": 107,
|
| 225 |
+
"[S]": 108,
|
| 226 |
+
"[Branch2].[Cl-1]": 109,
|
| 227 |
+
"[N@H1+1]": 110,
|
| 228 |
+
"[NH2+1]": 111,
|
| 229 |
+
"[Br]": 112,
|
| 230 |
+
"[O-1]": 113,
|
| 231 |
+
"[=Branch1]": 114,
|
| 232 |
+
"[CH0]": 115,
|
| 233 |
+
"[=Se]": 116,
|
| 234 |
+
"[#Branch2]": 117,
|
| 235 |
+
"[#C]": 118,
|
| 236 |
+
"[=Branch1].[Cl-1]": 119,
|
| 237 |
+
"[S@]": 120,
|
| 238 |
+
"[SiH1]": 121,
|
| 239 |
+
"[SiH3]": 122,
|
| 240 |
+
"[#C].[Cl-1]": 123,
|
| 241 |
+
"[#C-1]": 124,
|
| 242 |
+
"[S+1]": 125,
|
| 243 |
+
"[Cl]": 126,
|
| 244 |
+
"[#N].[Cl-1]": 127,
|
| 245 |
+
"[/C@@]": 128,
|
| 246 |
+
"[B@@-1]": 129,
|
| 247 |
+
"[F].[Cl-1]": 130,
|
| 248 |
+
"[Br].[Cl-1]": 131,
|
| 249 |
+
"[=Branch2].[Cl-1]": 132,
|
| 250 |
+
"[=P]": 133,
|
| 251 |
+
"[C].[Cl-1]": 134,
|
| 252 |
+
"[/B]": 135,
|
| 253 |
+
"[PH1]": 136,
|
| 254 |
+
"[C-1]": 137,
|
| 255 |
+
"[Si@@H1]": 138,
|
| 256 |
+
"[/P]": 139,
|
| 257 |
+
"[=O].[Cl-1]": 140,
|
| 258 |
+
"[O].[Cl-1]": 141,
|
| 259 |
+
"[N@@]": 142,
|
| 260 |
+
"[P].[Cl-1]": 143,
|
| 261 |
+
"[S@+1]": 144,
|
| 262 |
+
"[Branch2]": 145,
|
| 263 |
+
"[I+1]": 146,
|
| 264 |
+
"[-/Ring1]": 147,
|
| 265 |
+
"[/S]": 148,
|
| 266 |
+
"[P@]": 149,
|
| 267 |
+
"[P@@+1]": 150,
|
| 268 |
+
"[=Sn]": 151,
|
| 269 |
+
"[NH3+1]": 152,
|
| 270 |
+
"[=N-1]": 153,
|
| 271 |
+
"[=NH1+1]": 154,
|
| 272 |
+
"[NH1]": 155,
|
| 273 |
+
"[Si@]": 156,
|
| 274 |
+
"[N@@H1+1]": 157,
|
| 275 |
+
"[N]": 158,
|
| 276 |
+
"[Ring1].[Cl-1]": 159,
|
| 277 |
+
"[BH3-1]": 160,
|
| 278 |
+
"[B]": 161,
|
| 279 |
+
"[/C@]": 162,
|
| 280 |
+
"[C]": 163,
|
| 281 |
+
"[Si@H1]": 164,
|
| 282 |
+
"[O]": 165,
|
| 283 |
+
"[=NH0]": 166,
|
| 284 |
+
"[P@+1]": 167,
|
| 285 |
+
"[=N].[Cl-1]": 168,
|
| 286 |
+
"[/N-1]": 169,
|
| 287 |
+
"[S@@+1]": 170,
|
| 288 |
+
"[=O]": 171,
|
| 289 |
+
"[C@@H1]": 172
|
| 290 |
+
},
|
| 291 |
+
"unk_token": "[UNK]"
|
| 292 |
+
}
|
| 293 |
+
}
|
tokenizer_config.json
ADDED
|
@@ -0,0 +1,11 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"cls_token": "[CLS]",
|
| 3 |
+
"mask_token": "[MASK]",
|
| 4 |
+
"model_max_length": 512,
|
| 5 |
+
"name_or_path": "zinc22-16B-tokenizer",
|
| 6 |
+
"pad_token": "[PAD]",
|
| 7 |
+
"sep_token": "[SEP]",
|
| 8 |
+
"special_tokens_map_file": "/u/indra/.cache/huggingface/transformers/410b9713b9ff338491c4439bb9c3426a17c79e66c5a02f0a729b5455a334037a.7da70648c6cb9951e284c9685f9ba7ae083dd59ed1d6d84bdfc0584a4ea94b6d",
|
| 9 |
+
"tokenizer_class": "PreTrainedTokenizerFast",
|
| 10 |
+
"unk_token": "[UNK]"
|
| 11 |
+
}
|
trainer_state.json
ADDED
|
@@ -0,0 +1,3100 @@
|
|
|
|
|
|
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|
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|
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|
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|
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|
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|
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|
| 1 |
+
{
|
| 2 |
+
"best_metric": null,
|
| 3 |
+
"best_model_checkpoint": null,
|
| 4 |
+
"epoch": 1.0,
|
| 5 |
+
"global_step": 51465,
|
| 6 |
+
"is_hyper_param_search": false,
|
| 7 |
+
"is_local_process_zero": true,
|
| 8 |
+
"is_world_process_zero": true,
|
| 9 |
+
"log_history": [
|
| 10 |
+
{
|
| 11 |
+
"epoch": 0.0,
|
| 12 |
+
"learning_rate": 4.990284659477315e-05,
|
| 13 |
+
"loss": 0.0,
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| 14 |
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"step": 100
|
| 15 |
+
},
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| 16 |
+
{
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| 17 |
+
"epoch": 0.0,
|
| 18 |
+
"learning_rate": 4.98056931895463e-05,
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| 19 |
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"loss": 0.0,
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| 20 |
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"step": 200
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| 21 |
+
},
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| 22 |
+
{
|
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