--- language: - en license: apache-2.0 library_name: sentence-transformers tags: - sentence-transformers - sentence-similarity - feature-extraction - generated_from_trainer - dataset_size:4247 - loss:MatryoshkaLoss - loss:MultipleNegativesRankingLoss base_model: BAAI/bge-base-en-v1.5 datasets: [] metrics: - cosine_accuracy@1 - cosine_accuracy@3 - cosine_accuracy@5 - cosine_accuracy@10 - cosine_precision@1 - cosine_precision@3 - cosine_precision@5 - cosine_precision@10 - cosine_recall@1 - cosine_recall@3 - cosine_recall@5 - cosine_recall@10 - cosine_ndcg@10 - cosine_mrr@10 - cosine_map@100 widget: - source_sentence: Perry syndrome is a familial parkinsonism associated with central hypoventilation, mental depression, and weight loss. sentences: - List features of the Perry syndrome. - Which is the main abnormality that arises with Sox9 locus duplication? - Was modafinil tested for schizophrenia treatment? - source_sentence: Yes. HDAC1 is required for GATA-1 transcription activity, global chromatin occupancy and hematopoiesis. sentences: - Is HDAC1 required for GATA-1 transcriptional activity? - Which cells are affected in radiation-induced leukemias? - Is phospholamban phosphorylated by Protein kinase A? - source_sentence: Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, the expression of 285 lncRNAs was systematically knocked down in human dermal fibroblasts. Cellular growth, morphological changes, and transcriptomic responses were quantified using Capped Analysis of Gene Expression (CAGE).The functional annotation of the mammalian genome 6 (FANTOM6) project aims to systematically map all human long noncoding RNAs (lncRNAs) in a gene-dependent manner through dedicated efforts from national and international teams sentences: - What delivery system is used for the Fluzone Intradermal vaccine? - What is dovitinib? - Which class of genomic elements was assessed as part of the FANTOM6 project? - source_sentence: ' The proband had normal molecular analysis of the glypican 6 gene (GPC6), which was recently reported as a candidate for autosomal recessive omodysplasiaThe proband had normal molecular analysis of the glypican 6 gene (GPC6), which was recently reported as a candidate for autosomal recessive omodysplasiaThe glypican 6 gene (GPC6), which was recently reported as a candidate for autosomal recessive omodysplasia.Omodysplasia is a rare autosomal recessive disorder with a frequency of 1 in 50,000 newborn, and is associated with mutations in the GPC6 gene on chromosome 13.' sentences: - What is the effect of ivabradine in heart failure with preserved ejection fraction? - What rare disease is associated with a mutation in the GPC6 gene on chromosome 13? - What is the effect of rHDL-apoE3 on endothelial cell migration? - source_sentence: Yes, numerous whole exome sequencing studies of ALzheimer patients have been conducted. sentences: - Is muscle regeneration possible in mdx mice with the use of induced mesenchymal stem cells? - Has whole exome sequencing been performed in Alzheimer patients? - How is connected "isolated Non-compaction cardiomyopathy" with dilated cardiomyopathy? pipeline_tag: sentence-similarity model-index: - name: BGE base BioASQ Matryoshka results: - task: type: information-retrieval name: Information Retrieval dataset: name: dim 768 type: dim_768 metrics: - type: cosine_accuracy@1 value: 0.8516949152542372 name: Cosine Accuracy@1 - type: cosine_accuracy@3 value: 0.940677966101695 name: Cosine Accuracy@3 - type: cosine_accuracy@5 value: 0.9576271186440678 name: Cosine Accuracy@5 - type: cosine_accuracy@10 value: 0.961864406779661 name: Cosine Accuracy@10 - type: cosine_precision@1 value: 0.8516949152542372 name: Cosine Precision@1 - type: cosine_precision@3 value: 0.31355932203389825 name: Cosine Precision@3 - type: cosine_precision@5 value: 0.19152542372881357 name: Cosine Precision@5 - type: cosine_precision@10 value: 0.09618644067796611 name: Cosine Precision@10 - type: cosine_recall@1 value: 0.8516949152542372 name: Cosine Recall@1 - type: cosine_recall@3 value: 0.940677966101695 name: Cosine Recall@3 - type: cosine_recall@5 value: 0.9576271186440678 name: Cosine Recall@5 - type: cosine_recall@10 value: 0.961864406779661 name: Cosine Recall@10 - type: cosine_ndcg@10 value: 0.9149563623470877 name: Cosine Ndcg@10 - type: cosine_mrr@10 value: 0.8990348399246703 name: Cosine Mrr@10 - type: cosine_map@100 value: 0.8999167242053622 name: Cosine Map@100 - task: type: information-retrieval name: Information Retrieval dataset: name: dim 512 type: dim_512 metrics: - type: cosine_accuracy@1 value: 0.8516949152542372 name: Cosine Accuracy@1 - type: cosine_accuracy@3 value: 0.9449152542372882 name: Cosine Accuracy@3 - type: cosine_accuracy@5 value: 0.9555084745762712 name: Cosine Accuracy@5 - type: cosine_accuracy@10 value: 0.9597457627118644 name: Cosine Accuracy@10 - type: cosine_precision@1 value: 0.8516949152542372 name: Cosine Precision@1 - type: cosine_precision@3 value: 0.3149717514124293 name: Cosine Precision@3 - type: cosine_precision@5 value: 0.19110169491525428 name: Cosine Precision@5 - type: cosine_precision@10 value: 0.09597457627118645 name: Cosine Precision@10 - type: cosine_recall@1 value: 0.8516949152542372 name: Cosine Recall@1 - type: cosine_recall@3 value: 0.9449152542372882 name: Cosine Recall@3 - type: cosine_recall@5 value: 0.9555084745762712 name: Cosine Recall@5 - type: cosine_recall@10 value: 0.9597457627118644 name: Cosine Recall@10 - type: cosine_ndcg@10 value: 0.9136223756024043 name: Cosine Ndcg@10 - type: cosine_mrr@10 value: 0.8979166666666664 name: Cosine Mrr@10 - type: cosine_map@100 value: 0.8990624087448101 name: Cosine Map@100 - task: type: information-retrieval name: Information Retrieval dataset: name: dim 256 type: dim_256 metrics: - type: cosine_accuracy@1 value: 0.8389830508474576 name: Cosine Accuracy@1 - type: cosine_accuracy@3 value: 0.934322033898305 name: Cosine Accuracy@3 - type: cosine_accuracy@5 value: 0.9470338983050848 name: Cosine Accuracy@5 - type: cosine_accuracy@10 value: 0.9597457627118644 name: Cosine Accuracy@10 - type: cosine_precision@1 value: 0.8389830508474576 name: Cosine Precision@1 - type: cosine_precision@3 value: 0.3114406779661017 name: Cosine Precision@3 - type: cosine_precision@5 value: 0.189406779661017 name: Cosine Precision@5 - type: cosine_precision@10 value: 0.09597457627118645 name: Cosine Precision@10 - type: cosine_recall@1 value: 0.8389830508474576 name: Cosine Recall@1 - type: cosine_recall@3 value: 0.934322033898305 name: Cosine Recall@3 - type: cosine_recall@5 value: 0.9470338983050848 name: Cosine Recall@5 - type: cosine_recall@10 value: 0.9597457627118644 name: Cosine Recall@10 - type: cosine_ndcg@10 value: 0.9053426368336166 name: Cosine Ndcg@10 - type: cosine_mrr@10 value: 0.8872721616895344 name: Cosine Mrr@10 - type: cosine_map@100 value: 0.8879933659912613 name: Cosine Map@100 - task: type: information-retrieval name: Information Retrieval dataset: name: dim 128 type: dim_128 metrics: - type: cosine_accuracy@1 value: 0.8241525423728814 name: Cosine Accuracy@1 - type: cosine_accuracy@3 value: 0.9110169491525424 name: Cosine Accuracy@3 - type: cosine_accuracy@5 value: 0.9322033898305084 name: Cosine Accuracy@5 - type: cosine_accuracy@10 value: 0.9470338983050848 name: Cosine Accuracy@10 - type: cosine_precision@1 value: 0.8241525423728814 name: Cosine Precision@1 - type: cosine_precision@3 value: 0.30367231638418074 name: Cosine Precision@3 - type: cosine_precision@5 value: 0.1864406779661017 name: Cosine Precision@5 - type: cosine_precision@10 value: 0.09470338983050848 name: Cosine Precision@10 - type: cosine_recall@1 value: 0.8241525423728814 name: Cosine Recall@1 - type: cosine_recall@3 value: 0.9110169491525424 name: Cosine Recall@3 - type: cosine_recall@5 value: 0.9322033898305084 name: Cosine Recall@5 - type: cosine_recall@10 value: 0.9470338983050848 name: Cosine Recall@10 - type: cosine_ndcg@10 value: 0.8905411432220106 name: Cosine Ndcg@10 - type: cosine_mrr@10 value: 0.8719422585418346 name: Cosine Mrr@10 - type: cosine_map@100 value: 0.8732028981082185 name: Cosine Map@100 --- # BGE base BioASQ Matryoshka This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [BAAI/bge-base-en-v1.5](https://huggingface.co/BAAI/bge-base-en-v1.5). It maps sentences & paragraphs to a 768-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:** [BAAI/bge-base-en-v1.5](https://huggingface.co/BAAI/bge-base-en-v1.5) - **Maximum Sequence Length:** 512 tokens - **Output Dimensionality:** 768 tokens - **Similarity Function:** Cosine Similarity - **Language:** en - **License:** apache-2.0 ### Model Sources - **Documentation:** [Sentence Transformers Documentation](https://sbert.net) - **Repository:** [Sentence Transformers on GitHub](https://github.com/UKPLab/sentence-transformers) - **Hugging Face:** [Sentence Transformers on Hugging Face](https://huggingface.co/models?library=sentence-transformers) ### Full Model Architecture ``` SentenceTransformer( (0): Transformer({'max_seq_length': 512, 'do_lower_case': True}) with Transformer model: BertModel (1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': True, 'pooling_mode_mean_tokens': False, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True}) (2): Normalize() ) ``` ## Usage ### Direct Usage (Sentence Transformers) First install the Sentence Transformers library: ```bash pip install -U sentence-transformers ``` Then you can load this model and run inference. ```python from sentence_transformers import SentenceTransformer # Download from the 🤗 Hub model = SentenceTransformer("pavanmantha/bge-base-en-bioembed") # Run inference sentences = [ 'Yes, numerous whole exome sequencing studies of ALzheimer patients have been conducted.', 'Has whole exome sequencing been performed in Alzheimer patients?', 'How is connected "isolated Non-compaction cardiomyopathy" with dilated cardiomyopathy?', ] embeddings = model.encode(sentences) print(embeddings.shape) # [3, 768] # Get the similarity scores for the embeddings similarities = model.similarity(embeddings, embeddings) print(similarities.shape) # [3, 3] ``` ## Evaluation ### Metrics #### Information Retrieval * Dataset: `dim_768` * Evaluated with [InformationRetrievalEvaluator](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator) | Metric | Value | |:--------------------|:-----------| | cosine_accuracy@1 | 0.8517 | | cosine_accuracy@3 | 0.9407 | | cosine_accuracy@5 | 0.9576 | | cosine_accuracy@10 | 0.9619 | | cosine_precision@1 | 0.8517 | | cosine_precision@3 | 0.3136 | | cosine_precision@5 | 0.1915 | | cosine_precision@10 | 0.0962 | | cosine_recall@1 | 0.8517 | | cosine_recall@3 | 0.9407 | | cosine_recall@5 | 0.9576 | | cosine_recall@10 | 0.9619 | | cosine_ndcg@10 | 0.915 | | cosine_mrr@10 | 0.899 | | **cosine_map@100** | **0.8999** | #### Information Retrieval * Dataset: `dim_512` * Evaluated with [InformationRetrievalEvaluator](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator) | Metric | Value | |:--------------------|:-----------| | cosine_accuracy@1 | 0.8517 | | cosine_accuracy@3 | 0.9449 | | cosine_accuracy@5 | 0.9555 | | cosine_accuracy@10 | 0.9597 | | cosine_precision@1 | 0.8517 | | cosine_precision@3 | 0.315 | | cosine_precision@5 | 0.1911 | | cosine_precision@10 | 0.096 | | cosine_recall@1 | 0.8517 | | cosine_recall@3 | 0.9449 | | cosine_recall@5 | 0.9555 | | cosine_recall@10 | 0.9597 | | cosine_ndcg@10 | 0.9136 | | cosine_mrr@10 | 0.8979 | | **cosine_map@100** | **0.8991** | #### Information Retrieval * Dataset: `dim_256` * Evaluated with [InformationRetrievalEvaluator](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator) | Metric | Value | |:--------------------|:----------| | cosine_accuracy@1 | 0.839 | | cosine_accuracy@3 | 0.9343 | | cosine_accuracy@5 | 0.947 | | cosine_accuracy@10 | 0.9597 | | cosine_precision@1 | 0.839 | | cosine_precision@3 | 0.3114 | | cosine_precision@5 | 0.1894 | | cosine_precision@10 | 0.096 | | cosine_recall@1 | 0.839 | | cosine_recall@3 | 0.9343 | | cosine_recall@5 | 0.947 | | cosine_recall@10 | 0.9597 | | cosine_ndcg@10 | 0.9053 | | cosine_mrr@10 | 0.8873 | | **cosine_map@100** | **0.888** | #### Information Retrieval * Dataset: `dim_128` * Evaluated with [InformationRetrievalEvaluator](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator) | Metric | Value | |:--------------------|:-----------| | cosine_accuracy@1 | 0.8242 | | cosine_accuracy@3 | 0.911 | | cosine_accuracy@5 | 0.9322 | | cosine_accuracy@10 | 0.947 | | cosine_precision@1 | 0.8242 | | cosine_precision@3 | 0.3037 | | cosine_precision@5 | 0.1864 | | cosine_precision@10 | 0.0947 | | cosine_recall@1 | 0.8242 | | cosine_recall@3 | 0.911 | | cosine_recall@5 | 0.9322 | | cosine_recall@10 | 0.947 | | cosine_ndcg@10 | 0.8905 | | cosine_mrr@10 | 0.8719 | | **cosine_map@100** | **0.8732** | ## Training Details ### Training Dataset #### Unnamed Dataset * Size: 4,247 training samples * Columns: positive and anchor * Approximate statistics based on the first 1000 samples: | | positive | anchor | |:--------|:------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------| | type | string | string | | details | | | * Samples: | positive | anchor | |:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------| | Yes, saracatinib is being studied as a treatment against Alzheimer's Disease. A clinical Phase Ib study has been completed, and a clinical Phase IIa study is ongoing. | Was saracatinib being considered as a treatment for Alzheimer's disease in November 2017? | | TREM2 variants have been found to be associated with early as well as with late onset Alzheimer's disease. | Is TREM2 associated with Alzheimer's disease in humans? | | Yes, siltuximab , a chimeric human-mouse monoclonal antibody to IL6, is approved for the treatment of patients with multicentric Castleman disease who are human immunodeficiency virus negative and human herpesvirus-8 negative. | Is siltuximab effective for Castleman disease? | * Loss: [MatryoshkaLoss](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#matryoshkaloss) with these parameters: ```json { "loss": "MultipleNegativesRankingLoss", "matryoshka_dims": [ 768, 512, 256, 128 ], "matryoshka_weights": [ 1, 1, 1, 1 ], "n_dims_per_step": -1 } ``` ### Training Hyperparameters #### Non-Default Hyperparameters - `eval_strategy`: epoch - `per_device_train_batch_size`: 32 - `per_device_eval_batch_size`: 16 - `gradient_accumulation_steps`: 16 - `learning_rate`: 2e-05 - `num_train_epochs`: 4 - `lr_scheduler_type`: cosine - `warmup_ratio`: 0.1 - `fp16`: True - `tf32`: False - `load_best_model_at_end`: True - `optim`: adamw_torch_fused - `batch_sampler`: no_duplicates #### All Hyperparameters
Click to expand - `overwrite_output_dir`: False - `do_predict`: False - `eval_strategy`: epoch - `prediction_loss_only`: True - `per_device_train_batch_size`: 32 - `per_device_eval_batch_size`: 16 - `per_gpu_train_batch_size`: None - `per_gpu_eval_batch_size`: None - `gradient_accumulation_steps`: 16 - `eval_accumulation_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`: 4 - `max_steps`: -1 - `lr_scheduler_type`: cosine - `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`: False - `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_fused - `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`: False - `hub_always_push`: False - `gradient_checkpointing`: False - `gradient_checkpointing_kwargs`: None - `include_inputs_for_metrics`: False - `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 - `batch_sampler`: no_duplicates - `multi_dataset_batch_sampler`: proportional
### Training Logs | Epoch | Step | Training Loss | dim_128_cosine_map@100 | dim_256_cosine_map@100 | dim_512_cosine_map@100 | dim_768_cosine_map@100 | |:----------:|:-----:|:-------------:|:----------------------:|:----------------------:|:----------------------:|:----------------------:| | **0.9624** | **8** | **-** | **0.8794** | **0.8937** | **0.9044** | **0.9018** | | 1.2030 | 10 | 1.1405 | - | - | - | - | | 1.9248 | 16 | - | 0.8739 | 0.8866 | 0.8998 | 0.8984 | | 2.4060 | 20 | 0.4328 | - | - | - | - | | 2.8872 | 24 | - | 0.8732 | 0.8876 | 0.8987 | 0.8998 | | 3.6090 | 30 | 0.312 | - | - | - | - | | 3.8496 | 32 | - | 0.8732 | 0.8880 | 0.8991 | 0.8999 | * The bold row denotes the saved checkpoint. ### Framework Versions - Python: 3.10.13 - Sentence Transformers: 3.0.1 - Transformers: 4.41.2 - PyTorch: 2.1.2 - Accelerate: 0.31.0 - Datasets: 2.19.1 - Tokenizers: 0.19.1 ## Citation ### BibTeX #### Sentence Transformers ```bibtex @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", } ``` #### MatryoshkaLoss ```bibtex @misc{kusupati2024matryoshka, title={Matryoshka Representation Learning}, author={Aditya Kusupati and Gantavya Bhatt and Aniket Rege and Matthew Wallingford and Aditya Sinha and Vivek Ramanujan and William Howard-Snyder and Kaifeng Chen and Sham Kakade and Prateek Jain and Ali Farhadi}, year={2024}, eprint={2205.13147}, archivePrefix={arXiv}, primaryClass={cs.LG} } ``` #### MultipleNegativesRankingLoss ```bibtex @misc{henderson2017efficient, title={Efficient Natural Language Response Suggestion for Smart Reply}, author={Matthew Henderson and Rami Al-Rfou and Brian Strope and Yun-hsuan Sung and Laszlo Lukacs and Ruiqi Guo and Sanjiv Kumar and Balint Miklos and Ray Kurzweil}, year={2017}, eprint={1705.00652}, archivePrefix={arXiv}, primaryClass={cs.CL} } ```