cafierom/smiles_embedding_gemma_FT

SentenceTransformer based on google/embeddinggemma-300m

This is a sentence-transformers model finetuned from google/embeddinggemma-300m. It maps sentences & paragraphs to a 768-dimensional dense vector space and can be used for retrieval.

Model Details

Model Description

• Model Type: Sentence Transformer
• Base model: google/embeddinggemma-300m
• Maximum Sequence Length: 128 tokens
• Output Dimensionality: 768 dimensions
• Similarity Function: Cosine Similarity
• Supported Modality: Text

Model Sources

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

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'transformer_task': 'feature-extraction', 'modality_config': {'text': {'method': 'forward', 'method_output_name': 'last_hidden_state'}}, 'module_output_name': 'token_embeddings', 'architecture': 'Gemma3TextModel'})
  (1): Pooling({'embedding_dimension': 768, 'pooling_mode': 'mean', 'include_prompt': True})
  (2): Dense({'in_features': 768, 'out_features': 3072, 'bias': False, 'activation_function': 'torch.nn.modules.linear.Identity', 'module_input_name': 'sentence_embedding', 'module_output_name': 'sentence_embedding'})
  (3): Dense({'in_features': 3072, 'out_features': 768, 'bias': False, 'activation_function': 'torch.nn.modules.linear.Identity', 'module_input_name': 'sentence_embedding', 'module_output_name': 'sentence_embedding'})
  (4): Normalize({})
)

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("cafierom/smiles_embedding_gemma_FT")
# Run inference
queries = [
    'CCC(CC)(c1ccccc1)c1ccc(\\C=C\\[C@@H](O)C[C@@H](O)CC([O-])=O)c(c1)-c1ccccc1F',
]
documents = [
    'Cc1ccc(C(=C(\\C=C\\[C@@H](O)C[C@@H](O)CC([O-])=O)c2nnnn2C)c2ccc(C)cc2C)c(C)c1',
    'O[C@H](CCn1c(nc(c1-c1ccc(F)cc1)-c1ccc(F)cc1)C(F)(F)F)C[C@@H](O)CC([O-])=O',
    'CC(C)c1c(c(c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC([O-])=O)-c1ccccc1)S(=O)(=O)N(C)C',
]
query_embeddings = model.encode_query(queries)
document_embeddings = model.encode_document(documents)
print(query_embeddings.shape, document_embeddings.shape)
# [1, 768] [3, 768]

# Get the similarity scores for the embeddings
similarities = model.similarity(query_embeddings, document_embeddings)
print(similarities)
# tensor([[0.9356, 0.9019, 0.5159]])

Training Details

Training Dataset

Unnamed Dataset

• Size: 3,396 training samples
• Columns: premise, hypothesis, and label
• Approximate statistics based on the first 100 samples:

  	premise	hypothesis	label
  type	string	string	int
  modality	text	text
  details	min: 18 tokens mean: 58.11 tokens max: 117 tokens	min: 11 tokens mean: 54.91 tokens max: 119 tokens	0: ~55.77% 2: ~44.23%

• Samples:

  premise	hypothesis	label
  CCC@HC(=O)O[C@H]1CC@H\C=C\Cc1ccccc1	Cc1cc(-c2ccc(Cl)cc2)c(\C=C[C@@H]2CC@@HCC(=O)O2)c(C)n1	2
  CC(C)n1c(CCC@@HCC@@HCC([O-])=O)c(c(c1C(=O)Nc1ccccc1)-c1ccccc1)-c1ccc(F)cc1	CC(C)n1c(CCC@@HCC@@HCC([O-])=O)c(c(c1C(=O)NCc1ccccn1)-c1ccccc1)-c1ccc(F)cc1	0
  CC(C)n1c(CCC@@HCC@@HCC([O-])=O)c(c(c1C(=O)N(C)C)-c1ccccc1)-c1ccc(F)cc1	COc1ccc2ccccc2c1-c1ccc(C(C)C)n1CC[C@@H]1CC@@HCC(=O)O1	2

• Loss: SoftmaxLoss with these parameters:

  {
      "num_labels": 3,
      "concatenation_sent_rep": true,
      "concatenation_sent_difference": true,
      "concatenation_sent_multiplication": false
  }
  

Evaluation Dataset

Unnamed Dataset

• Size: 600 evaluation samples
• Columns: premise, hypothesis, and label
• Approximate statistics based on the first 100 samples:

  	premise	hypothesis	label
  type	string	string	int
  modality	text	text
  details	min: 11 tokens mean: 56.06 tokens max: 101 tokens	min: 12 tokens mean: 55.85 tokens max: 119 tokens	0: ~41.35% 2: ~58.65%

• Samples:

  premise	hypothesis	label
  CNc1cccc(c1)-c1nc(C(C)C)n(\C=C[C@@H](O)CC@@HCC([O-])=O)c1-c1ccc(F)cc1	CC(C)c1c(CCC@@HCC@@HCC([O-])=O)c(cn1-c1ccccc1)-c1ccc(F)cc1	0
  CC(C)c1nc(nc(-c2ccc(F)cc2)c1\C=C[C@@H]1CC@@HCC(OCC(Cl)(Cl)Cl)O1)N(C)S(C)(=O)=O	CC(C)c1nn(-c2nc3ccccc3s2)c(c1\C=C[C@@H](O)CC@@HCC([O-])=O)-c1ccc(F)cc1	2
  Cc1c(\C=C[C@H](O)CC@@HCC([O-])=O)c(cn1-c1ccccc1)-c1ccc(F)cc1	CC@H[C@H]1CC(=O)[C@@]2(C)C3=C(C(=O)C[C@]12C)[C@@]1(C)CCC(=O)C@@(COC(=O)CC@@(O)CC(O)=O)[C@@H]1CC3=O	2

• Loss: SoftmaxLoss with these parameters:

  {
      "num_labels": 3,
      "concatenation_sent_rep": true,
      "concatenation_sent_difference": true,
      "concatenation_sent_multiplication": false
  }
  

Training Hyperparameters

Non-Default Hyperparameters

• warmup_steps: 10
• optim: adafactor
• weight_decay: 0.01
• bf16: True
• load_best_model_at_end: True
• dataloader_pin_memory: False

All Hyperparameters

Click to expand

• per_device_train_batch_size: 8
• num_train_epochs: 3
• max_steps: -1
• learning_rate: 5e-05
• lr_scheduler_type: linear
• lr_scheduler_kwargs: None
• warmup_steps: 10
• optim: adafactor
• optim_args: None
• weight_decay: 0.01
• adam_beta1: 0.9
• adam_beta2: 0.999
• adam_epsilon: 1e-08
• optim_target_modules: None
• gradient_accumulation_steps: 1
• average_tokens_across_devices: True
• max_grad_norm: 1.0
• label_smoothing_factor: 0.0
• bf16: True
• fp16: False
• bf16_full_eval: False
• fp16_full_eval: False
• tf32: None
• gradient_checkpointing: False
• gradient_checkpointing_kwargs: None
• torch_compile: False
• torch_compile_backend: None
• torch_compile_mode: None
• use_liger_kernel: False
• liger_kernel_config: None
• use_cache: False
• neftune_noise_alpha: None
• torch_empty_cache_steps: None
• auto_find_batch_size: False
• log_on_each_node: True
• logging_nan_inf_filter: True
• include_num_input_tokens_seen: no
• log_level: passive
• log_level_replica: warning
• disable_tqdm: False
• project: huggingface
• trackio_space_id: None
• trackio_bucket_id: None
• trackio_static_space_id: None
• per_device_eval_batch_size: 8
• prediction_loss_only: True
• eval_on_start: False
• eval_do_concat_batches: True
• eval_use_gather_object: False
• eval_accumulation_steps: None
• include_for_metrics: []
• batch_eval_metrics: False
• save_only_model: False
• save_on_each_node: False
• enable_jit_checkpoint: False
• push_to_hub: False
• hub_private_repo: None
• hub_model_id: None
• hub_strategy: every_save
• hub_always_push: False
• hub_revision: None
• load_best_model_at_end: True
• ignore_data_skip: False
• restore_callback_states_from_checkpoint: False
• full_determinism: False
• seed: 42
• data_seed: None
• use_cpu: False
• accelerator_config: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}
• parallelism_config: None
• dataloader_drop_last: False
• dataloader_num_workers: 0
• dataloader_pin_memory: False
• dataloader_persistent_workers: False
• dataloader_prefetch_factor: None
• remove_unused_columns: True
• label_names: None
• train_sampling_strategy: random
• length_column_name: length
• ddp_find_unused_parameters: None
• ddp_bucket_cap_mb: None
• ddp_broadcast_buffers: False
• ddp_static_graph: None
• ddp_backend: None
• ddp_timeout: 1800
• fsdp: None
• fsdp_config: None
• deepspeed: None
• debug: []
• skip_memory_metrics: True
• do_predict: False
• resume_from_checkpoint: None
• warmup_ratio: None
• local_rank: -1
• prompts: None
• batch_sampler: batch_sampler
• multi_dataset_batch_sampler: proportional
• router_mapping: {}
• learning_rate_mapping: {}

Training Logs

Epoch	Step	Training Loss	Validation Loss
0.0471	20	0.9762	-
0.0941	40	0.8931	-
0.1176	50	-	0.8680
0.1412	60	0.8805	-
0.1882	80	0.8463	-
0.2353	100	0.8186	0.8070
0.2824	120	0.8125	-
0.3294	140	0.7831	-
0.3529	150	-	0.7607
0.3765	160	0.7789	-
0.4235	180	0.7543	-
0.4706	200	0.7119	0.7341
0.5176	220	0.7230	-
0.5647	240	0.7006	-
0.5882	250	-	0.6976
0.6118	260	0.6999	-
0.6588	280	0.6649	-
0.7059	300	0.6693	0.6542
0.7529	320	0.6768	-
0.8	340	0.6203	-
0.8235	350	-	0.6334
0.8471	360	0.6820	-
0.8941	380	0.6402	-
0.9412	400	0.6327	0.6568
0.9882	420	0.5882	-
1.0353	440	0.6258	-
1.0588	450	-	0.6009
1.0824	460	0.5778	-
1.1294	480	0.6016	-
1.1765	500	0.5251	0.5823
1.2235	520	0.5810	-
1.2706	540	0.5700	-
1.2941	550	-	0.5618
1.3176	560	0.5384	-
1.3647	580	0.6171	-
1.4118	600	0.5861	0.5493
1.4588	620	0.5898	-
1.5059	640	0.5139	-
1.5294	650	-	0.5250
1.5529	660	0.5235	-
1.6	680	0.4972	-
1.6471	700	0.5056	0.5538
1.6941	720	0.5550	-
1.7412	740	0.5275	-
1.7647	750	-	0.5268
1.7882	760	0.5224	-
1.8353	780	0.4965	-
1.8824	800	0.4768	0.5072
1.9294	820	0.5545	-
1.9765	840	0.5012	-
2.0	850	-	0.5041
2.0235	860	0.5343	-
2.0706	880	0.4404	-
2.1176	900	0.4679	0.4866
2.1647	920	0.5153	-
2.2118	940	0.4592	-
2.2353	950	-	0.4959
2.2588	960	0.4473	-
2.3059	980	0.5223	-
2.3529	1000	0.4917	0.4882
2.4	1020	0.4113	-
2.4471	1040	0.5266	-
2.4706	1050	-	0.4844
2.4941	1060	0.4752	-
2.5412	1080	0.4672	-
2.5882	1100	0.5019	0.4730
2.6353	1120	0.4282	-
2.6824	1140	0.3954	-
2.7059	1150	-	0.4660
2.7294	1160	0.4608	-
2.7765	1180	0.4770	-
2.8235	1200	0.4747	0.4630
2.8706	1220	0.5013	-
2.9176	1240	0.3948	-
2.9412	1250	-	0.4606
2.9647	1260	0.4259	-
3.0	1275	-	0.4595

• The bold row denotes the saved checkpoint.

Training Time

• Training: 31.9 minutes
• Evaluation: 19.4 minutes
• Total: 51.3 minutes

Framework Versions

• Python: 3.12.13
• Sentence Transformers: 5.6.1
• Transformers: 5.14.1
• PyTorch: 2.13.0
• Accelerate: 1.14.0
• Datasets: 5.0.1
• Tokenizers: 0.22.2

Citation

BibTeX

Sentence Transformers and SoftmaxLoss

@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",
}