SentenceTransformer

This is a sentence-transformers model trained. 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
  • Maximum Sequence Length: 1024 tokens
  • Output Dimensionality: 384 tokens
  • Similarity Function: Cosine Similarity

Model Sources

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 1024, 'do_lower_case': False}) with Transformer model: BertModel 
  (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("pankajrajdeo/2812371_bioformer_16L")
# Run inference
sentences = [
    'Albendazol',
    'SKF-92058',
    'C0130494',
]
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]

Training Details

Training Dataset

Unnamed Dataset

  • Size: 187,491,593 training samples
  • Columns: anchor, positive, negative_id, positive_id, and negative
  • Approximate statistics based on the first 1000 samples:
    anchor positive negative_id positive_id negative
    type string string string string string
    details
    • min: 3 tokens
    • mean: 13.27 tokens
    • max: 247 tokens
    • min: 3 tokens
    • mean: 12.25 tokens
    • max: 157 tokens
    • min: 5 tokens
    • mean: 6.27 tokens
    • max: 7 tokens
    • min: 5 tokens
    • mean: 6.49 tokens
    • max: 7 tokens
    • min: 3 tokens
    • mean: 13.53 tokens
    • max: 118 tokens
  • Samples:
    anchor positive negative_id positive_id negative
    Zaburzenie metabolizmu minerałów Distúrbio não especificado do metabolismo de minerais C2887914 C0154260 Acute alcoholic hepatic failure
    testy funkčnosti placenty Metoder som brukes til å vurdere morkakefunksjon. C2350391 C0032049 Hjärtmuskelscintigrafi
    Tsefapiriin:Susc:Pt:Is:OrdQn cefapirina:susceptibilidad:punto en el tiempo:cepa clínica:ordinal o cuantitativo: C0942365 C0801894 2 proyecciones:hallazgo:punto en el tiempo:tobillo.izquierdo:Narrativo:radiografía
  • Loss: main.CustomTripletLoss with these parameters:
    {
        "distance_metric": "TripletDistanceMetric.EUCLIDEAN",
        "triplet_margin": 5
    }
    

Training Hyperparameters

Non-Default Hyperparameters

  • per_device_train_batch_size: 50
  • learning_rate: 2e-05
  • num_train_epochs: 5
  • warmup_ratio: 0.1
  • fp16: True

All Hyperparameters

Click to expand
  • overwrite_output_dir: False
  • do_predict: False
  • eval_strategy: no
  • prediction_loss_only: True
  • per_device_train_batch_size: 50
  • per_device_eval_batch_size: 8
  • 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: False
  • 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
  • batch_sampler: batch_sampler
  • multi_dataset_batch_sampler: proportional

Training Logs

Click to expand
Epoch Step Training Loss
0.5000 1875000 0.1053
0.5003 1876000 0.0899
0.5006 1877000 0.0978
0.5008 1878000 0.0928
0.5011 1879000 0.0887
0.5014 1880000 0.0921
0.5016 1881000 0.0908
0.5019 1882000 0.0925
0.5022 1883000 0.0886
0.5024 1884000 0.0924
0.5027 1885000 0.0932
0.5030 1886000 0.0938
0.5032 1887000 0.0976
0.5035 1888000 0.087
0.5038 1889000 0.0882
0.5040 1890000 0.0955
0.5043 1891000 0.0927
0.5046 1892000 0.0922
0.5048 1893000 0.086
0.5051 1894000 0.0899
0.5054 1895000 0.0941
0.5056 1896000 0.0924
0.5059 1897000 0.0941
0.5062 1898000 0.0904
0.5064 1899000 0.09
0.5067 1900000 0.0928
0.5070 1901000 0.088
0.5072 1902000 0.0924
0.5075 1903000 0.0927
0.5078 1904000 0.0912
0.5080 1905000 0.0971
0.5083 1906000 0.0973
0.5086 1907000 0.0932
0.5088 1908000 0.092
0.5091 1909000 0.0894
0.5094 1910000 0.0866
0.5096 1911000 0.0951
0.5099 1912000 0.0924
0.5102 1913000 0.0913
0.5104 1914000 0.0921
0.5107 1915000 0.0915
0.5110 1916000 0.0897
0.5112 1917000 0.0932
0.5115 1918000 0.0871
0.5118 1919000 0.0872
0.5120 1920000 0.0962
0.5123 1921000 0.0902
0.5126 1922000 0.0939
0.5128 1923000 0.0873
0.5131 1924000 0.0841
0.5134 1925000 0.0863
0.5136 1926000 0.0941
0.5139 1927000 0.0905
0.5142 1928000 0.0876
0.5144 1929000 0.0866
0.5147 1930000 0.0921
0.5150 1931000 0.0973
0.5152 1932000 0.0937
0.5155 1933000 0.0899
0.5158 1934000 0.0965
0.5160 1935000 0.0942
0.5163 1936000 0.0927
0.5166 1937000 0.0897
0.5168 1938000 0.094
0.5171 1939000 0.0874
0.5174 1940000 0.0954
0.5176 1941000 0.0904
0.5179 1942000 0.0913
0.5182 1943000 0.0891
0.5184 1944000 0.0941
0.5187 1945000 0.0908
0.5190 1946000 0.0903
0.5192 1947000 0.0957
0.5195 1948000 0.0875
0.5198 1949000 0.0895
0.5200 1950000 0.0883
0.5203 1951000 0.0942
0.5206 1952000 0.091
0.5208 1953000 0.0874
0.5211 1954000 0.0921
0.5214 1955000 0.0967
0.5216 1956000 0.0962
0.5219 1957000 0.0942
0.5222 1958000 0.0818
0.5224 1959000 0.0861
0.5227 1960000 0.0849
0.5230 1961000 0.0894
0.5232 1962000 0.101
0.5235 1963000 0.0832
0.5238 1964000 0.0901
0.5240 1965000 0.0949
0.5243 1966000 0.0942
0.5246 1967000 0.0897
0.5248 1968000 0.0894
0.5251 1969000 0.0846
0.5254 1970000 0.087
0.5256 1971000 0.086
0.5259 1972000 0.086
0.5262 1973000 0.0913
0.5264 1974000 0.0916
0.5267 1975000 0.0867
0.5270 1976000 0.085
0.5272 1977000 0.0863
0.5275 1978000 0.0927
0.5278 1979000 0.0866
0.5280 1980000 0.0865
0.5283 1981000 0.0898
0.5286 1982000 0.0917
0.5288 1983000 0.0864
0.5291 1984000 0.0937
0.5294 1985000 0.0916
0.5296 1986000 0.0913
0.5299 1987000 0.0927
0.5302 1988000 0.0947
0.5304 1989000 0.0939
0.5307 1990000 0.0864
0.5310 1991000 0.0816
0.5312 1992000 0.0931
0.5315 1993000 0.0906
0.5318 1994000 0.0907
0.5320 1995000 0.0895
0.5323 1996000 0.0913
0.5326 1997000 0.0915
0.5328 1998000 0.0909
0.5331 1999000 0.0917
0.5334 2000000 0.0828
0.5336 2001000 0.0865
0.5339 2002000 0.0864
0.5342 2003000 0.0887
0.5344 2004000 0.0871
0.5347 2005000 0.0903
0.5350 2006000 0.092
0.5352 2007000 0.083
0.5355 2008000 0.0934
0.5358 2009000 0.0885
0.5360 2010000 0.0841
0.5363 2011000 0.0919
0.5366 2012000 0.0909
0.5368 2013000 0.0899
0.5371 2014000 0.0905
0.5374 2015000 0.0917
0.5376 2016000 0.0936
0.5379 2017000 0.0926
0.5382 2018000 0.0884
0.5384 2019000 0.0909
0.5387 2020000 0.0858
0.5390 2021000 0.0927
0.5392 2022000 0.0908
0.5395 2023000 0.0936
0.5398 2024000 0.0896
0.5400 2025000 0.0948
0.5403 2026000 0.091
0.5406 2027000 0.0917
0.5408 2028000 0.0866
0.5411 2029000 0.0925
0.5414 2030000 0.0846
0.5416 2031000 0.0878
0.5419 2032000 0.0792
0.5422 2033000 0.0872
0.5424 2034000 0.088
0.5427 2035000 0.0972
0.5430 2036000 0.081
0.5432 2037000 0.0901
0.5435 2038000 0.092
0.5438 2039000 0.0902
0.5440 2040000 0.091
0.5443 2041000 0.0876
0.5446 2042000 0.0799
0.5448 2043000 0.0921
0.5451 2044000 0.0823
0.5454 2045000 0.0846
0.5456 2046000 0.0863
0.5459 2047000 0.0893
0.5462 2048000 0.0829
0.5464 2049000 0.0913
0.5467 2050000 0.0956
0.5470 2051000 0.0879
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0.5478 2054000 0.0822
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0.5488 2058000 0.0868
0.5491 2059000 0.0918
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0.5502 2063000 0.0906
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0.5520 2070000 0.0879
0.5523 2071000 0.0867
0.5526 2072000 0.0868
0.5528 2073000 0.0911
0.5531 2074000 0.0869
0.5534 2075000 0.0858
0.5536 2076000 0.0882
0.5539 2077000 0.086
0.5542 2078000 0.0868
0.5544 2079000 0.0879
0.5547 2080000 0.0847
0.5550 2081000 0.0907
0.5552 2082000 0.0897
0.5555 2083000 0.0894
0.5558 2084000 0.0939
0.5560 2085000 0.0878
0.5563 2086000 0.0885
0.5566 2087000 0.0905
0.5568 2088000 0.092
0.5571 2089000 0.0845
0.5574 2090000 0.0854
0.5576 2091000 0.0896
0.5579 2092000 0.0858
0.5582 2093000 0.0881
0.5584 2094000 0.0891
0.5587 2095000 0.0872
0.5590 2096000 0.09
0.5592 2097000 0.0835
0.5595 2098000 0.0911
0.5598 2099000 0.0909
0.5600 2100000 0.087
0.5603 2101000 0.099
0.5606 2102000 0.0855
0.5608 2103000 0.0883
0.5611 2104000 0.0919
0.5614 2105000 0.0906
0.5616 2106000 0.0925
0.5619 2107000 0.0874
0.5622 2108000 0.0901
0.5624 2109000 0.0839
0.5627 2110000 0.0882
0.5630 2111000 0.0851
0.5632 2112000 0.0902
0.5635 2113000 0.0874
0.5638 2114000 0.0875
0.5640 2115000 0.0866
0.5643 2116000 0.0909
0.5646 2117000 0.0905
0.5648 2118000 0.0915
0.5651 2119000 0.0871
0.5654 2120000 0.0823
0.5656 2121000 0.0923
0.5659 2122000 0.0886
0.5662 2123000 0.0824
0.5664 2124000 0.0871
0.5667 2125000 0.0808
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0.5672 2127000 0.0862
0.5675 2128000 0.0896
0.5678 2129000 0.09
0.5680 2130000 0.092
0.5683 2131000 0.0875
0.5686 2132000 0.0844
0.5688 2133000 0.0838
0.5691 2134000 0.0871
0.5694 2135000 0.0812
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0.5702 2138000 0.0862
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0.5707 2140000 0.0881
0.5710 2141000 0.0854
0.5712 2142000 0.0852
0.5715 2143000 0.0825
0.5718 2144000 0.0893
0.5720 2145000 0.0884
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0.5728 2148000 0.0869
0.5731 2149000 0.0831
0.5734 2150000 0.0852
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0.5750 2156000 0.0868
0.5752 2157000 0.0835
0.5755 2158000 0.0832
0.5758 2159000 0.0896
0.5760 2160000 0.0856
0.5763 2161000 0.0857
0.5766 2162000 0.093
0.5768 2163000 0.0933
0.5771 2164000 0.0863
0.5774 2165000 0.0857
0.5776 2166000 0.0894
0.5779 2167000 0.0836
0.5782 2168000 0.0893
0.5784 2169000 0.0803
0.5787 2170000 0.081
0.5790 2171000 0.089
0.5792 2172000 0.0829
0.5795 2173000 0.0884
0.5798 2174000 0.0852
0.5800 2175000 0.0798
0.5803 2176000 0.0752
0.5806 2177000 0.0828
0.5808 2178000 0.0848
0.5811 2179000 0.0895
0.5814 2180000 0.0846
0.5816 2181000 0.0841
0.5819 2182000 0.0868
0.5822 2183000 0.0885
0.5824 2184000 0.0874
0.5827 2185000 0.0865
0.5830 2186000 0.0838
0.5832 2187000 0.081
0.5835 2188000 0.0829
0.5838 2189000 0.0801
0.5840 2190000 0.0861
0.5843 2191000 0.08
0.5846 2192000 0.0842
0.5848 2193000 0.0831
0.5851 2194000 0.0842
0.5854 2195000 0.0836
0.5856 2196000 0.0811
0.5859 2197000 0.0851
0.5862 2198000 0.0854
0.5864 2199000 0.0857
0.5867 2200000 0.089
0.5870 2201000 0.0794
0.5872 2202000 0.0908
0.5875 2203000 0.0852
0.5878 2204000 0.0866
0.5880 2205000 0.085
0.5883 2206000 0.0895
0.5886 2207000 0.089
0.5888 2208000 0.087
0.5891 2209000 0.0822
0.5894 2210000 0.09
0.5896 2211000 0.0858
0.5899 2212000 0.0836
0.5902 2213000 0.0837
0.5904 2214000 0.0881
0.5907 2215000 0.0789
0.5910 2216000 0.0796
0.5912 2217000 0.0834
0.5915 2218000 0.0839
0.5918 2219000 0.0787
0.5920 2220000 0.0825
0.5923 2221000 0.0863
0.5926 2222000 0.0862
0.5928 2223000 0.0837
0.5931 2224000 0.0781
0.5934 2225000 0.0867
0.5936 2226000 0.0897
0.5939 2227000 0.0825
0.5942 2228000 0.0798
0.5944 2229000 0.086
0.5947 2230000 0.0807
0.5950 2231000 0.0788
0.5952 2232000 0.0851
0.5955 2233000 0.0844
0.5958 2234000 0.0779
0.5960 2235000 0.0804
0.5963 2236000 0.0799
0.5966 2237000 0.0843
0.5968 2238000 0.0794
0.5971 2239000 0.0848
0.5974 2240000 0.0854
0.5976 2241000 0.0906
0.5979 2242000 0.0855
0.5982 2243000 0.0793
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0.5990 2246000 0.0868
0.5992 2247000 0.0867
0.5995 2248000 0.0869
0.5998 2249000 0.0853
0.6000 2250000 0.0844
0.6003 2251000 0.089
0.6006 2252000 0.0789
0.6008 2253000 0.0808
0.6011 2254000 0.0854
0.6014 2255000 0.0856
0.6016 2256000 0.0874
0.6019 2257000 0.0893
0.6022 2258000 0.0772
0.6024 2259000 0.0804
0.6027 2260000 0.0903
0.6030 2261000 0.0883
0.6032 2262000 0.0841
0.6035 2263000 0.0862
0.6038 2264000 0.0806
0.6040 2265000 0.0839
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0.6046 2267000 0.0851
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0.6051 2269000 0.0815
0.6054 2270000 0.0875
0.6056 2271000 0.0813
0.6059 2272000 0.085
0.6062 2273000 0.0818
0.6064 2274000 0.0833
0.6067 2275000 0.0891
0.6070 2276000 0.0869
0.6072 2277000 0.0818
0.6075 2278000 0.0874
0.6078 2279000 0.0787
0.6080 2280000 0.0782
0.6083 2281000 0.0809
0.6086 2282000 0.083
0.6088 2283000 0.082
0.6091 2284000 0.0872
0.6094 2285000 0.0851
0.6096 2286000 0.087
0.6099 2287000 0.0848
0.6102 2288000 0.0821
0.6104 2289000 0.085
0.6107 2290000 0.0838
0.6110 2291000 0.081
0.6112 2292000 0.0809
0.6115 2293000 0.0781
0.6118 2294000 0.0796
0.6120 2295000 0.0828
0.6123 2296000 0.0833
0.6126 2297000 0.0859
0.6128 2298000 0.0824
0.6131 2299000 0.0825
0.6134 2300000 0.0909
0.6136 2301000 0.0856
0.6139 2302000 0.0827
0.6142 2303000 0.0842
0.6144 2304000 0.0798
0.6147 2305000 0.0797
0.6150 2306000 0.0812
0.6152 2307000 0.0812
0.6155 2308000 0.0897
0.6158 2309000 0.0833
0.6160 2310000 0.0835
0.6163 2311000 0.0848
0.6166 2312000 0.0858
0.6168 2313000 0.0738
0.6171 2314000 0.08
0.6174 2315000 0.0784
0.6176 2316000 0.0797
0.6179 2317000 0.0791
0.6182 2318000 0.0873
0.6184 2319000 0.0825
0.6187 2320000 0.0883
0.6190 2321000 0.084
0.6192 2322000 0.0801
0.6195 2323000 0.0856
0.6198 2324000 0.0764
0.6200 2325000 0.088
0.6203 2326000 0.0814
0.6206 2327000 0.0857
0.6208 2328000 0.0873
0.6211 2329000 0.0846
0.6214 2330000 0.0871
0.6216 2331000 0.0798
0.6219 2332000 0.0908
0.6222 2333000 0.0799
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Framework Versions

  • Python: 3.12.2
  • Sentence Transformers: 3.2.1
  • Transformers: 4.46.1
  • PyTorch: 2.5.0
  • Accelerate: 1.0.1
  • Datasets: 3.0.2
  • Tokenizers: 0.20.1

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",
}

CustomTripletLoss

@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}
}
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