metadata

tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - generated_from_trainer
  - dataset_size:10000
  - loss:ContrastiveLoss
base_model: DeepChem/ChemBERTa-77M-MLM
widget:
  - source_sentence: CC(C)N=c1cc2n(-c3ccc(Cl)cc3)c3ccccc3nc-2cc1Nc1ccc(Cl)cc1
    sentences:
      - C[NH+]1CCC(=C2c3ccccc3CCn3c(C=O)c[nH+]c32)CC1
      - COc1ccc(C(=O)CC(=O)c2ccc(C(C)(C)C)cc2)cc1
      - CC1CNc2c(cccc2S(=O)(=O)NC(CCC[NH+]=C(N)N)C(=O)N2CCC(C)CC2C(=O)[O-])C1
  - source_sentence: CC(C)c1ccc2oc3nc(N)c(C(=O)[O-])cc3c(=O)c2c1
    sentences:
      - COC1=CC(=O)CC(C)C12Oc1c(Cl)c(OC)cc(OC)c1C2=O
      - CON=C(C(=O)NC1C(=O)N2C(C(=O)[O-])=C(C[N+]3(C)CCCC3)CSC12)c1csc(N)n1
      - >-
        CC1C=CC=CC=CC=CC=CC=CC=CC(OC2OC(C)C(O)C([NH3+])C2O)CC2OC(O)(CC(O)CC(O)C(O)CCC(O)CC(O)CC(=O)OC(C)C(C)C1O)CC(O)C2C(=O)[O-]
  - source_sentence: C[NH2+]C1CCc2[nH]c3ccc(C(N)=O)cc3c2C1
    sentences:
      - >-
        CC(OC(=O)c1ccccc1)C1=CCC23OCC[NH+](C)CC12CC(O)C12OC4(O)CCC1(C)C(CC=C32)C4
      - >-
        CC(=O)NC(Cc1ccc2ccccc2c1)C(=O)NC(Cc1ccc(Cl)cc1)C(=O)NC(Cc1cccnc1)C(=O)NC(CO)C(=O)NC(Cc1ccc(NC(=O)C2CC(=O)NC(=O)N2)cc1)C(=O)NC(Cc1ccc(NC(N)=O)cc1)C(=O)NC(CC(C)C)C(=O)NC(CCCC[NH2+]C(C)C)C(=O)N1CCCC1C(=O)NC(C)C(N)=O
      - C[NH+](C)CCOC(=O)C(c1ccccc1)C1(O)CCCC1
  - source_sentence: CC(C)n1c(C=CC(O)CC(O)CC(=O)[O-])c(-c2ccc(F)cc2)c2ccccc21
    sentences:
      - C#CC1(O)CCC2C3CCC4=C(CCC(=O)C4)C3CCC21C
      - CC(C=CC(C)C(C)(C)O)C1CCC2C(=CC=C3CC(O)CC(O)C3)CCCC21C
      - CC(C)CNCc1ccc(-c2ccccc2S(=O)(=O)N2CCCC2)cc1
  - source_sentence: CC#CCn1c(N2CCCC([NH3+])C2)nc2c1c(=O)n(Cc1nc(C)c3ccccc3n1)c(=O)n2C
    sentences:
      - C[N+]1(C)CCCC(OC(=O)C(O)(c2ccccc2)c2ccccc2)C1
      - CC(Cc1ccc(O)c(O)c1)C(C)Cc1ccc(O)c(O)c1
      - CC12CCC(=O)C=C1CCC1C2C(O)CC2(C)C1CCC2(O)C(=O)COC(=O)CCC1CCCC1
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
model-index:
  - name: SentenceTransformer based on DeepChem/ChemBERTa-77M-MLM
    results:
      - task:
          type: binary-classification
          name: Binary Classification
        dataset:
          name: all dev
          type: all-dev
        metrics:
          - type: cosine_accuracy
            value: 0.9066
            name: Cosine Accuracy
          - type: cosine_accuracy_threshold
            value: 0.5664876699447632
            name: Cosine Accuracy Threshold
          - type: cosine_f1
            value: 0.9510122731564041
            name: Cosine F1
          - type: cosine_f1_threshold
            value: 0.5664876699447632
            name: Cosine F1 Threshold
          - type: cosine_precision
            value: 0.9067813562712542
            name: Cosine Precision
          - type: cosine_recall
            value: 0.9997794441993825
            name: Cosine Recall
          - type: cosine_ap
            value: 0.9523113003188102
            name: Cosine Ap

SentenceTransformer based on DeepChem/ChemBERTa-77M-MLM

This is a sentence-transformers model finetuned from DeepChem/ChemBERTa-77M-MLM. 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: DeepChem/ChemBERTa-77M-MLM
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}) with Transformer model: 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("HassanCS/chemBERTa-tuned-on-ClinTox-3")
# Run inference
sentences = [
    'CC#CCn1c(N2CCCC([NH3+])C2)nc2c1c(=O)n(Cc1nc(C)c3ccccc3n1)c(=O)n2C',
    'CC12CCC(=O)C=C1CCC1C2C(O)CC2(C)C1CCC2(O)C(=O)COC(=O)CCC1CCCC1',
    'CC(Cc1ccc(O)c(O)c1)C(C)Cc1ccc(O)c(O)c1',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 384]

# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [3, 3]

Evaluation

Metrics

Binary Classification

Dataset: all-dev
Evaluated with BinaryClassificationEvaluator

Metric	Value
cosine_accuracy	0.9066
cosine_accuracy_threshold	0.5665
cosine_f1	0.951
cosine_f1_threshold	0.5665
cosine_precision	0.9068
cosine_recall	0.9998
cosine_ap	0.9523

Training Details

Training Dataset

Unnamed Dataset

Size: 10,000 training samples
Columns: smiles1, smiles2, and label
Approximate statistics based on the first 1000 samples:
smiles1 smiles2 label
type string string int
details
min: 3 tokens
mean: 40.69 tokens
max: 221 tokens

min: 4 tokens
mean: 51.43 tokens
max: 221 tokens

0: ~14.90%
1: ~85.10%

	smiles1	smiles2	label
type	string	string	int
details	min: 3 tokens mean: 40.69 tokens max: 221 tokens	min: 4 tokens mean: 51.43 tokens max: 221 tokens	0: ~14.90% 1: ~85.10%

Samples:

smiles1	smiles2	label
`Cn1c(=O)c2c(ncn2C)n(C)c1=O`	`Cc1cc2c(s1)=Nc1ccccc1NC=2N1CCNH+CC1`	`1`
`Oc1ccc(OCc2ccccc2)cc1`	`Oc1ccc(CCCC[NH2+]CC(O)c2ccc(O)c(O)c2)cc1`	`1`
`OCC(S)CS`	`CC12CCC(=O)C=C1CCC1C2C(O)CC2(C)C1CCC2(O)C(=O)CO`	`0`

Loss: ContrastiveLoss with these parameters:

{
    "distance_metric": "SiameseDistanceMetric.COSINE_DISTANCE",
    "margin": 0.5,
    "size_average": true
}

Evaluation Dataset

Unnamed Dataset

Size: 5,000 evaluation samples
Columns: smiles1, smiles2, and label
Approximate statistics based on the first 1000 samples:
smiles1 smiles2 label
type string string int
details
min: 18 tokens
mean: 56.96 tokens
max: 209 tokens

min: 18 tokens
mean: 61.21 tokens
max: 244 tokens

0: ~10.00%
1: ~90.00%

	smiles1	smiles2	label
type	string	string	int
details	min: 18 tokens mean: 56.96 tokens max: 209 tokens	min: 18 tokens mean: 61.21 tokens max: 244 tokens	0: ~10.00% 1: ~90.00%

Samples:

smiles1	smiles2	label
`CC(=CC(=O)OCCCCCCCCC(=O)[O-])CC1OCC(CC2OC2C(C)C(C)O)C(O)C1O`	`CC(C=CC(C)C(C)(C)O)C1CCC2C(=CC=C3CC(O)CC(O)C3)CCCC21C`	`1`
`C=C1c2cccc([O-])c2C(=O)C2=C([O-])C3(O)C(=O)C(C(N)=O)=C([O-])C(NH+C)C3C(O)C12`	`CC(c1ncncc1F)C(O)(Cn1cncn1)c1ccc(F)cc1F`	`1`
`CC(C)CC1C(=O)N2CCCC2C2(O)OC(NC(=O)C3C=C4c5cccc6[nH]c(Br)c(c56)CC4NH+C3)(C(C)C)C(=O)N12`	`CNH+CCC=C1c2ccccc2Sc2ccc(Cl)cc21`	`1`

Loss: ContrastiveLoss with these parameters:

{
    "distance_metric": "SiameseDistanceMetric.COSINE_DISTANCE",
    "margin": 0.5,
    "size_average": true
}

Training Hyperparameters

Non-Default Hyperparameters

eval_strategy: steps
per_device_train_batch_size: 16
per_device_eval_batch_size: 16
learning_rate: 2e-05
num_train_epochs: 5
warmup_ratio: 0.1
fp16: True
batch_sampler: no_duplicates

All Hyperparameters

Click to expand

overwrite_output_dir: False
do_predict: False
eval_strategy: steps
prediction_loss_only: True
per_device_train_batch_size: 16
per_device_eval_batch_size: 16
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: 2e-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: 5
max_steps: -1
lr_scheduler_type: linear
lr_scheduler_kwargs: {}
warmup_ratio: 0.1
warmup_steps: 0
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: True
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: False
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
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
dispatch_batches: None
split_batches: 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
eval_use_gather_object: False
average_tokens_across_devices: False
prompts: None
batch_sampler: no_duplicates
multi_dataset_batch_sampler: proportional

Training Logs

Epoch	Step	Training Loss	Validation Loss	all-dev_cosine_ap
0.8	500	0.0264	0.0112	0.9213
1.6	1000	0.0152	0.0122	0.9362
2.4	1500	0.0134	0.0128	0.9463
3.2	2000	0.0112	0.0134	0.9502
4.0	2500	0.01	0.0125	0.9513
4.8	3000	0.0097	0.0132	0.9523

Framework Versions

Python: 3.11.11
Sentence Transformers: 3.3.1
Transformers: 4.47.1
PyTorch: 2.5.1+cu124
Accelerate: 1.2.1
Datasets: 3.2.0
Tokenizers: 0.21.0

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",
}

ContrastiveLoss

@inproceedings{hadsell2006dimensionality,
    author={Hadsell, R. and Chopra, S. and LeCun, Y.},
    booktitle={2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'06)},
    title={Dimensionality Reduction by Learning an Invariant Mapping},
    year={2006},
    volume={2},
    number={},
    pages={1735-1742},
    doi={10.1109/CVPR.2006.100}
}