README.md

metadata

tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - dense
  - generated_from_trainer
  - dataset_size:2184
  - loss:BatchAllTripletLoss
base_model: kiarashmo/chembberta-77m-mlm-safetensors
widget:
  - source_sentence: CC(C)CNCc1ccc(-c2ccccc2S(=O)(=O)N2CCCC2)cc1
    sentences:
      - >-
        C=C1CC2CCC34CC5OC6C(OC7CCC(CC(=O)CC8C(CC9OC(CCC1O2)CC(C)C9=C)OC(CC(O)CN)C8OC)OC7C6O3)C5O4
      - C[NH+](C)CCC=C1c2ccccc2CCc2ccccc21
      - CC(C)Cn1cnc2c(N)nc3ccccc3c21
  - source_sentence: >-
      COC(=O)NC(C(=O)NC(Cc1ccccc1)C(O)CN(Cc1ccc(-c2ccccn2)cc1)NC(=O)C(NC(=O)OC)C(C)(C)C)C(C)(C)C
    sentences:
      - >-
        C=C1CC2CCC34CC5OC6C(OC7CCC(CC(=O)CC8C(CC9OC(CCC1O2)CC(C)C9=C)OC(CC(O)CN)C8OC)OC7C6O3)C5O4
      - C[NH+]1CCCC(CC2c3ccccc3Sc3ccccc32)C1
      - C[NH2+]C1(c2ccccc2Cl)CCCCC1=O
  - source_sentence: >-
      C[NH+]1CC(C(=O)NC2(C)OC3(O)C4CCCN4C(=O)C(Cc4ccccc4)N3C2=O)CC2c3cccc4[nH]cc(c34)CC21
    sentences:
      - C[NH+](C)CCC=C1c2ccccc2COc2ccc(CC(=O)[O-])cc21
      - C[NH+]1CCC(=C2c3ccccc3CCn3c(C=O)c[nH+]c32)CC1
      - >-
        COC(=O)NC(C(=O)NC(Cc1ccccc1)C(O)CN(Cc1ccc(-c2ccccn2)cc1)NC(=O)C(NC(=O)OC)C(C)(C)C)C(C)(C)C
  - source_sentence: C[NH2+]CCCC12CCC(c3ccccc31)c1ccccc12
    sentences:
      - C[N+]1(C)CCC(=C(c2ccccc2)c2ccccc2)CC1
      - CC(CN1CC(=O)NC(=O)C1)[NH+]1CC(=O)NC(=O)C1
      - C[NH+](C)CCc1c[nH]c2ccc(CC3COC(=O)N3)cc12
  - source_sentence: CC(C)CNCc1ccc(-c2ccccc2S(=O)(=O)N2CCCC2)cc1
    sentences:
      - >-
        COC(=O)NC(C(=O)NC(Cc1ccccc1)C(O)CN(Cc1ccc(-c2ccccn2)cc1)NC(=O)C(NC(=O)OC)C(C)(C)C)C(C)(C)C
      - COc1ccc(C(=O)CC(=O)c2ccc(C(C)(C)C)cc2)cc1
      - >-
        COC1CC(OC2C(C)C(=O)OC(C)C(C)C(OC(C)=O)C(C)C(=O)C3(CO3)CC(C)C(OC3OC(C)CC([NH+](C)C)C3OC(C)=O)C2C)OC(C)C1OC(C)=O
pipeline_tag: sentence-similarity
library_name: sentence-transformers
metrics:
  - cosine_accuracy
  - cosine_accuracy_threshold
  - cosine_f1
  - cosine_f1_threshold
  - cosine_precision
  - cosine_recall
  - cosine_ap
  - cosine_mcc
model-index:
  - name: SentenceTransformer based on kiarashmo/chembberta-77m-mlm-safetensors
    results:
      - task:
          type: binary-classification
          name: Binary Classification
        dataset:
          name: val sim
          type: val-sim
        metrics:
          - type: cosine_accuracy
            value: 0.671
            name: Cosine Accuracy
          - type: cosine_accuracy_threshold
            value: 0.8630315065383911
            name: Cosine Accuracy Threshold
          - type: cosine_f1
            value: 0.7042889390519187
            name: Cosine F1
          - type: cosine_f1_threshold
            value: -0.3091595470905304
            name: Cosine F1 Threshold
          - type: cosine_precision
            value: 0.5763546798029556
            name: Cosine Precision
          - type: cosine_recall
            value: 0.9052224371373307
            name: Cosine Recall
          - type: cosine_ap
            value: 0.7370675686338501
            name: Cosine Ap
          - type: cosine_mcc
            value: 0.24685118679448836
            name: Cosine Mcc

SentenceTransformer based on kiarashmo/chembberta-77m-mlm-safetensors

This is a sentence-transformers model finetuned from kiarashmo/chembberta-77m-mlm-safetensors. It maps sentences & paragraphs to a 384-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, text classification, clustering, and more.

Model Details

Model Description

• Model Type: Sentence Transformer
• Base model: kiarashmo/chembberta-77m-mlm-safetensors
• Maximum Sequence Length: 512 tokens
• Output Dimensionality: 384 dimensions
• Similarity Function: Cosine Similarity

Model Sources

• Documentation: Sentence Transformers Documentation
• Repository: Sentence Transformers on GitHub
• Hugging Face: Sentence Transformers on Hugging Face

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 512, 'do_lower_case': False, 'architecture': 'RobertaModel'})
  (1): Pooling({'word_embedding_dimension': 384, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
)

Usage

Direct Usage (Sentence Transformers)

First install the Sentence Transformers library:

pip install -U sentence-transformers

Then you can load this model and run inference.

from sentence_transformers import SentenceTransformer

# Download from the 🤗 Hub
model = SentenceTransformer("sentence_transformers_model_id")
# Run inference
sentences = [
    'CC(C)CNCc1ccc(-c2ccccc2S(=O)(=O)N2CCCC2)cc1',
    'COC(=O)NC(C(=O)NC(Cc1ccccc1)C(O)CN(Cc1ccc(-c2ccccn2)cc1)NC(=O)C(NC(=O)OC)C(C)(C)C)C(C)(C)C',
    'COc1ccc(C(=O)CC(=O)c2ccc(C(C)(C)C)cc2)cc1',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 384]

# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities)
# tensor([[ 1.0000,  0.8293, -0.3326],
#         [ 0.8293,  1.0000, -0.0993],
#         [-0.3326, -0.0993,  1.0000]])

Evaluation

Metrics

Binary Classification

• Dataset: val-sim
• Evaluated with BinaryClassificationEvaluator

Metric	Value
cosine_accuracy	0.671
cosine_accuracy_threshold	0.863
cosine_f1	0.7043
cosine_f1_threshold	-0.3092
cosine_precision	0.5764
cosine_recall	0.9052
cosine_ap	0.7371
cosine_mcc	0.2469

Training Details

Training Dataset

Unnamed Dataset

• Size: 2,184 training samples
• Columns: text and label
• Approximate statistics based on the first 1000 samples:

  	text	label
  type	string	int
  details	min: 3 tokens mean: 43.69 tokens max: 221 tokens	0: ~92.10% 1: ~7.90%

• Samples:

  text	label
  CC(C)CC(NC(=O)CNC(=O)c1cc(Cl)ccc1Cl)B(O)O	1
  O=C(NCC(O)CO)c1c(I)c(C(=O)NCC(O)CO)c(I)c(N(CCO)C(=O)CO)c1I	0
  Clc1cc(Cl)c(OCC#CI)cc1Cl	0

• Loss: BatchAllTripletLoss

Evaluation Dataset

Unnamed Dataset

• Size: 282 evaluation samples
• Columns: text and label
• Approximate statistics based on the first 282 samples:

  	text	label
  type	string	int
  details	min: 18 tokens mean: 65.88 tokens max: 244 tokens	0: ~50.00% 1: ~50.00%

• Samples:

  text	label
  CC(C)CNCc1ccc(-c2ccccc2S(=O)(=O)N2CCCC2)cc1	1
  CC(C)Cn1cnc2c(N)nc3ccccc3c21	0
  CC(C)CN(CC(O)C(Cc1ccccc1)NC(=O)OC1COC2OCCC12)S(=O)(=O)c1ccc(N)cc1	0

• Loss: BatchAllTripletLoss

Training Hyperparameters

Non-Default Hyperparameters

• eval_strategy: steps
• per_device_train_batch_size: 32
• per_device_eval_batch_size: 32
• num_train_epochs: 100
• warmup_steps: 100
• load_best_model_at_end: True

All Hyperparameters

Click to expand

• overwrite_output_dir: False
• do_predict: False
• eval_strategy: steps
• prediction_loss_only: True
• per_device_train_batch_size: 32
• per_device_eval_batch_size: 32
• per_gpu_train_batch_size: None
• per_gpu_eval_batch_size: None
• gradient_accumulation_steps: 1
• eval_accumulation_steps: None
• torch_empty_cache_steps: None
• learning_rate: 5e-05
• weight_decay: 0.0
• adam_beta1: 0.9
• adam_beta2: 0.999
• adam_epsilon: 1e-08
• max_grad_norm: 1.0
• num_train_epochs: 100
• max_steps: -1
• lr_scheduler_type: linear
• lr_scheduler_kwargs: {}
• warmup_ratio: 0.0
• warmup_steps: 100
• log_level: passive
• log_level_replica: warning
• log_on_each_node: True
• logging_nan_inf_filter: True
• save_safetensors: True
• save_on_each_node: False
• save_only_model: False
• restore_callback_states_from_checkpoint: False
• no_cuda: False
• use_cpu: False
• use_mps_device: False
• seed: 42
• data_seed: None
• jit_mode_eval: False
• use_ipex: False
• bf16: False
• fp16: False
• fp16_opt_level: O1
• half_precision_backend: auto
• bf16_full_eval: False
• fp16_full_eval: False
• tf32: None
• local_rank: 0
• ddp_backend: None
• tpu_num_cores: None
• tpu_metrics_debug: False
• debug: []
• dataloader_drop_last: False
• dataloader_num_workers: 0
• dataloader_prefetch_factor: None
• past_index: -1
• disable_tqdm: False
• remove_unused_columns: True
• label_names: None
• load_best_model_at_end: True
• ignore_data_skip: False
• fsdp: []
• fsdp_min_num_params: 0
• fsdp_config: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}
• fsdp_transformer_layer_cls_to_wrap: None
• accelerator_config: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}
• deepspeed: None
• label_smoothing_factor: 0.0
• optim: adamw_torch
• optim_args: None
• adafactor: False
• group_by_length: False
• length_column_name: length
• ddp_find_unused_parameters: None
• ddp_bucket_cap_mb: None
• ddp_broadcast_buffers: False
• dataloader_pin_memory: True
• dataloader_persistent_workers: False
• skip_memory_metrics: True
• use_legacy_prediction_loop: False
• push_to_hub: False
• resume_from_checkpoint: None
• hub_model_id: None
• hub_strategy: every_save
• hub_private_repo: None
• hub_always_push: False
• hub_revision: None
• gradient_checkpointing: False
• gradient_checkpointing_kwargs: None
• include_inputs_for_metrics: False
• include_for_metrics: []
• eval_do_concat_batches: True
• fp16_backend: auto
• push_to_hub_model_id: None
• push_to_hub_organization: None
• mp_parameters:
• auto_find_batch_size: False
• full_determinism: False
• torchdynamo: None
• ray_scope: last
• ddp_timeout: 1800
• torch_compile: False
• torch_compile_backend: None
• torch_compile_mode: None
• include_tokens_per_second: False
• include_num_input_tokens_seen: False
• neftune_noise_alpha: None
• optim_target_modules: None
• batch_eval_metrics: False
• eval_on_start: False
• use_liger_kernel: False
• liger_kernel_config: None
• eval_use_gather_object: False
• average_tokens_across_devices: False
• prompts: None
• batch_sampler: batch_sampler
• multi_dataset_batch_sampler: proportional
• router_mapping: {}
• learning_rate_mapping: {}

Training Logs

Epoch	Step	Training Loss	Validation Loss	val-sim_cosine_ap
7.2464	500	4.0383	5.2239	0.6972
14.4928	1000	3.5414	5.6988	0.6918
21.7391	1500	3.2672	5.3616	0.7147
28.9855	2000	2.885	5.7296	0.7240
36.2319	2500	2.7761	5.5717	0.7399
43.4783	3000	2.6489	5.8045	0.7371

• The bold row denotes the saved checkpoint.

Framework Versions

• Python: 3.9.23
• Sentence Transformers: 5.0.0
• Transformers: 4.53.3
• PyTorch: 2.5.0+cu118
• Accelerate: 1.9.0
• Datasets: 4.0.0
• Tokenizers: 0.21.2

Citation

BibTeX

Sentence Transformers

@inproceedings{reimers-2019-sentence-bert,
    title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
    author = "Reimers, Nils and Gurevych, Iryna",
    booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
    month = "11",
    year = "2019",
    publisher = "Association for Computational Linguistics",
    url = "https://arxiv.org/abs/1908.10084",
}

BatchAllTripletLoss

@misc{hermans2017defense,
    title={In Defense of the Triplet Loss for Person Re-Identification},
    author={Alexander Hermans and Lucas Beyer and Bastian Leibe},
    year={2017},
    eprint={1703.07737},
    archivePrefix={arXiv},
    primaryClass={cs.CV}
}