metadata

base_model: TaylorAI/bge-micro-v2
library_name: sentence-transformers
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
pipeline_tag: sentence-similarity
tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - generated_from_trainer
  - dataset_size:1814
  - loss:MatryoshkaLoss
  - loss:MultipleNegativesRankingLoss
widget:
  - source_sentence: >-

      The list you've provided contains a variety of medications, including
      antidepressants, antihistamines, anxiolytics, and more. Here's a breakdown
      by category:


      ### Antidepressants

      - **Amphetamine**

      - **Cevimeline**

      - **Esmolol**

      - **Bortezomib**

      - **
    sentences:
      - >-
        Which body parts are associated with the expression of genes or proteins
        that impact the transporter responsible for the movement of Cycloserine?
      - >-
        Identify genes or proteins that interact with a protein threonine
        kinase, participate in the mitotic centrosome proteins and complexes
        recruitment pathway, and engage in protein-protein interactions with
        CCT2.
      - >-
        Which medication is effective against simple Plasmodium falciparum
        infections and functions by engaging with genes or proteins that
        interact with the minor groove of DNA rich in adenine and thymine?
  - source_sentence: >-

      RNASE6, also known by aliases such as RAD1, RNS6, and RNasek6, functions
      as a member of the ribonuclease A superfamily. Specifically identified via
      the NCBI gene/protein database, this protein is related to the
      antimicrobial peptides pathway, showcasing broad-spectrum antimicrobial
      activity against pathogenic bacteria in the urinary tract. The provided
      gene summary emphasizes its role in the urinary tract, highlighting its
      enzymatic function and broad antimicrobial capability.


      With a genomic position spanning from 20781268 to 20782467 on chromosome
      14, the RNASE6 gene encodes a protein named ribonuclease A family member
      k6. The protein's interactions with cellular and molecular functions are
      integral to its role, including its interaction with molecular functions
      like ribonuclease activity and endonuclease activity, as well as its
      involvement in nucleic acid binding.


      RNASE6's involvement in biological
    sentences:
      - >-
        Identify genes or proteins linked to encephalopathy that are involved in
        the Antimicrobial peptides pathway and have interactions with molecular
        functions associated with ribonuclease activity.
      - >-
        Identify genes or proteins that exhibit interaction with COMMD1 and
        share an associated phenotype or effect.
      - >-
        What medical conditions are associated with severe combined
        immunodeficiency and also cause muscle pain and weakness?
  - source_sentence: >-


      The gene in question is likely involved in multiple biological processes,
      including:


      1. **Transmembrane transport**: It facilitates the entry of substances
      into or out of a cell through the cell membrane, which is crucial for
      maintaining cellular homeostasis and responding to environmental stimuli.
      This includes organic anion and carboxylic acid transport.


      2. **ABC-family proteins mediated transport**: ABC (or ATP-binding
      cassette) proteins are responsible for a variety of transport processes,
      such as drug efflux, nutrient uptake, and xenobiotic detoxification.


      3. **Response to drug**: It likely plays a role in how cells interact with
      and respond to medication or other foreign substances they encounter. This
      is important in pharmacology and toxicology.


      4. **Regulation of chloride transport**: Chloride ions are crucial for
      maintaining electrolyte balance and are involved in multiple physiological
      processes. This gene likely helps regulate their transport in and out of
      the cell.


      5. **Export across plasma membrane**: It is part of pathways that help in
      the removal of substances from the cell, such as efflux of drug
      metabolites or other waste products.


      ### Expression Contexts:


      - **Present**: This gene is expressed in many parts of the body,
      indicating a broad role. It shows presence in tissues like the islet of
      Langerhans (involved in insulin regulation), zones of the skin, and
      various brain regions. It's also active in organs such as the heart,
      kidney, and lungs, and in the digestive tract, including the stomach,
      esophagus, and intestines.


      - **Absent or Reduced**: The gene's expression is notably absent or less
      pronounced in tissues like the nasal cavity epithelium, suggesting it may
      not play a significant role in this specific tissue type.


      The gene's multifaceted expression and roles suggest a key function in
      biological activities related to:

      - **Chemical
    sentences:
      - >-
        Could you supply a selection of medications used to treat acute myeloid
        leukemia with minimal differentiation that have a potential side effect
        of arrhythmias and work by intercalating DNA and inhibiting
        topoisomerase II?
      - >-
        Is the ABCB1 protein responsible for the translocation of
        pharmaceuticals that exhibit synergistic effects when combined with
        ferric ions?
      - >-
        What potential conditions could I have that are associated with
        oophoritis and involve ovarian complications?
  - source_sentence: >-


      The list you provided seems to be a collection of various chemical
      compounds, pharmaceuticals, and their synonyms. They span across various
      categories:


      1. **Pharmaceuticals & Synthetic Drug Analogs**:
          - **Antibiotics** (Ceftazidime, Azithromycin, Ceftodipen, etc.)
          - **Analgesics** (Fentanyl, Ketorolac, etc.)
          - **Cephalosporins** (Ceftazidime, Ceftazidime-avibactam, etc.)
          - **Blood Thinners/Synthetic Anticoagulants** (Enoxaparin, Edoxaban, Rivaroxaban, etc.)
          - **Analgesic/Aspirin Analogues** (Mefenamic Acid, Indometacin, etc.)
          - **Adrenergic Agonists** (Isoprenaline, Dopamine, etc.)
          - **Antiviral Drugs** (Adefovir, Idelalisib, etc.)
          - **Antibiotic Resistance Modifiers** (Sulbactam, Tazobactam, etc.)
          - **Calcium Channel Blockers** (Verapamil, Nicardipine, etc.)
          - **Nutraceuticals/Herbal Extracts** (Ginsenoside, Phloretin, etc.)
         
      2. **Diagnostic Agents**:
          - **Radiopharmaceuticals** (F-Fluorodeoxyglucose, Ga-68 DOTATOC, etc.)
          - **MRI Contrasts** (Gadolinium chelates, etc.)
          - **CT Contrast Agents** (Iodinated contrast agents, etc.)
         
      3. **Ingredients in Drugs**:
          - **Excipients** (Hydroxypropylmethylcellulose, Lactose, etc.)
          - **Antifungal Drugs** (Itraconazole, Terconazole, etc.)
          - **Anticoagulants** (Warfarin, Heparin, etc.)
              
      This list represents a broad spectrum of modern medicine, from antibiotics
      to chemicals used in diagnostic imaging techniques, and from dietary
      supplements to drug excipients. Each compound typically serves a specific
      therapeutic purpose in the human body.
    sentences:
      - >-
        Which investigational compound in solid form that aims at altering
        membrane lipids, specifically phospholipids and glycerophospholipids,
        has the additional property of interacting with genes or proteins
        involved in ubiquitin-specific protease binding?
      - >-
        Could you provide a list of medications that exhibit synergistic effects
        when used in combination with Choline magnesium trisalicylate to treat
        the same condition and that also selectively target COX-2 enzymes to
        alleviate inflammation?
      - >-
        Identify pathways associated with the interaction between TNFs and their
        physiological receptors that concurrently influence the same gene or
        protein.
  - source_sentence: >-


      Diarrhea, a condition characterized by the passage of loose, watery, and
      often more than five times a day, is a common ailment affecting
      individuals of all ages. It is typically acute when it lasts for a few
      days to a week or recurrent when it persists for more than four weeks.
      While acute diarrhea often resolves on its own and is usually not a cause
      for concern, recurrent or chronic forms require medical attention due to
      the risk of dehydration and nutrient deficiencies. 


      ### Causes


      Diarrhea can be caused by various factors, including:


      1. **Viral
    sentences:
      - >-
        Could you describe the specific effects or phenotypes associated with
        acute hydrops in patients with the subtype of keratoconus?
      - >-
        What is the disease associated with the CPT2 gene that causes severe
        fasting intolerance leading to metabolic disturbances such as
        hypoketotic hypoglycemia, risking coma and seizures, and can lead to
        hepatic encephalopathy and liver failure, and also affects the heart and
        skeletal muscles, increasing the risk of potentially fatal cardiac
        arrhythmias?
      - >-
        Could you assist in identifying a condition linked to congenital
        secretory diarrhea, similar to intractable diarrhea of infancy, given my
        symptoms of persistent, salty watery diarrhea, hyponatremia, abnormal
        body pH, and reliance on parenteral nutrition due to chronic
        dehydration?
model-index:
  - name: SentenceTransformer based on TaylorAI/bge-micro-v2
    results:
      - task:
          type: information-retrieval
          name: Information Retrieval
        dataset:
          name: dim 384
          type: dim_384
        metrics:
          - type: cosine_accuracy@1
            value: 0.36633663366336633
            name: Cosine Accuracy@1
          - type: cosine_accuracy@3
            value: 0.45544554455445546
            name: Cosine Accuracy@3
          - type: cosine_accuracy@5
            value: 0.4801980198019802
            name: Cosine Accuracy@5
          - type: cosine_accuracy@10
            value: 0.504950495049505
            name: Cosine Accuracy@10
          - type: cosine_precision@1
            value: 0.36633663366336633
            name: Cosine Precision@1
          - type: cosine_precision@3
            value: 0.1518151815181518
            name: Cosine Precision@3
          - type: cosine_precision@5
            value: 0.09603960396039603
            name: Cosine Precision@5
          - type: cosine_precision@10
            value: 0.05049504950495049
            name: Cosine Precision@10
          - type: cosine_recall@1
            value: 0.36633663366336633
            name: Cosine Recall@1
          - type: cosine_recall@3
            value: 0.45544554455445546
            name: Cosine Recall@3
          - type: cosine_recall@5
            value: 0.4801980198019802
            name: Cosine Recall@5
          - type: cosine_recall@10
            value: 0.504950495049505
            name: Cosine Recall@10
          - type: cosine_ndcg@10
            value: 0.4371640266541694
            name: Cosine Ndcg@10
          - type: cosine_mrr@10
            value: 0.4153524280999529
            name: Cosine Mrr@10
          - type: cosine_map@100
            value: 0.42164032403755497
            name: Cosine Map@100

SentenceTransformer based on TaylorAI/bge-micro-v2

This is a sentence-transformers model finetuned from TaylorAI/bge-micro-v2 on the json dataset. 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: TaylorAI/bge-micro-v2
Maximum Sequence Length: 512 tokens
Output Dimensionality: 384 tokens
Similarity Function: Cosine Similarity
Training Dataset:
- json

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: 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("FareedKhan/TaylorAI_bge-micro-v2_FareedKhan_prime_synthetic_data_2k_10_64")
# Run inference
sentences = [
    '\n\nDiarrhea, a condition characterized by the passage of loose, watery, and often more than five times a day, is a common ailment affecting individuals of all ages. It is typically acute when it lasts for a few days to a week or recurrent when it persists for more than four weeks. While acute diarrhea often resolves on its own and is usually not a cause for concern, recurrent or chronic forms require medical attention due to the risk of dehydration and nutrient deficiencies. \n\n### Causes\n\nDiarrhea can be caused by various factors, including:\n\n1. **Viral',
    'Could you assist in identifying a condition linked to congenital secretory diarrhea, similar to intractable diarrhea of infancy, given my symptoms of persistent, salty watery diarrhea, hyponatremia, abnormal body pH, and reliance on parenteral nutrition due to chronic dehydration?',
    'Could you describe the specific effects or phenotypes associated with acute hydrops in patients with the subtype of keratoconus?',
]
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

Information Retrieval

Dataset: dim_384
Evaluated with InformationRetrievalEvaluator

Metric	Value
cosine_accuracy@1	0.3663
cosine_accuracy@3	0.4554
cosine_accuracy@5	0.4802
cosine_accuracy@10	0.505
cosine_precision@1	0.3663
cosine_precision@3	0.1518
cosine_precision@5	0.096
cosine_precision@10	0.0505
cosine_recall@1	0.3663
cosine_recall@3	0.4554
cosine_recall@5	0.4802
cosine_recall@10	0.505
cosine_ndcg@10	0.4372
cosine_mrr@10	0.4154
cosine_map@100	0.4216

Training Details

Training Dataset

json

Dataset: json
Size: 1,814 training samples
Columns: positive and anchor
Approximate statistics based on the first 1000 samples:
positive anchor
type string string
details
min: 2 tokens
mean: 249.7 tokens
max: 512 tokens

min: 13 tokens
mean: 35.54 tokens
max: 135 tokens

	positive	anchor
type	string	string
details	min: 2 tokens mean: 249.7 tokens max: 512 tokens	min: 13 tokens mean: 35.54 tokens max: 135 tokens

Samples:

positive	anchor
The list you provided appears to be a collection of various substances and medications, each with its own unique properties and uses. Here's a brief overview of each: 1. Abacavir - Used in HIV treatment, it inhibits reverse transcriptase. 2. Abate - Often refers to fenpyroximate, used as an insecticide. 3. Abidaquine - An antimalarial drug used to treat and prevent malaria. 4. Abiraterone - Used in treating prostate cancer, specifically to block the production of testosterone. 5. Abiraterone alfa - Similar to abiraterone, used in prostate cancer treatment. 6. Abiraterone acetate - An active form of abiraterone. 7. Abiraterone citrate - Another form of abiraterone. 8. Acelprozil - A medication commonly used as an anti-epileptic drug. 9. Acenocoumarol - Used as a blood thinner, also known as a vitamin K antagonist. 10. Acenocoumarol citrate - Same as acenocoumarol but with citrate, functioning similarly as a	`Which pharmacological agents with antioxidant properties have the potential to disrupt the PCSK9-LDLR interaction by affecting the gene or protein players in this pathway?`
Bartholin duct cyst is a gynecological condition characterized by the distension of Bartholin glands due to mucus accumulation within the ducts, typically resulting from an obstructed orifice. This issue, categorized under women's reproductive health, falls directly under the umbrella of both integumentary system diseases and female reproductive system diseases. Originating from the Bartholin glands, which play a pivotal role in lubrication and arousal of the vulva during intercourse, the blockage or obstruction leads to cyst formation, affecting the overall female reproductive health landscape.	`What is the name of the gynecological condition that arises due to blocked Bartholin's glands and involves cyst formation, falling under the broader category of women's reproductive health issues?`
Neuralgia, as defined by the MONDO ontology, refers to a pain disorder characterized by pain in the distribution of a nerve or nerves. This condition could be associated with the use of Capsaicin cream, given its known capability to alleviate symptoms by causing a temporary sensation of pain that interferes with the perception of more severe pain. Peripheral neuropathy, another symptom, is often manifest in cases where nerve damage occurs, frequently affecting multiple nerves. This condition can result in symptoms similar to sciatica, which is characterized by pain that starts in the lower back, often radiating down the leg, a common route for the sciatic nerve. The document indicates that diseases related to neuralgia include pudendal neuralgia, peripheral neuropathy, disorders involving pain, cranial neuralgia, post-infectious neuralgia, and sciatica. Furthermore, the document mentions several drugs that can be used for the purpose of managing symptoms related to neuralgia, including Lidocaine, as well as a wide array of off-label uses for treatments like Phenytoin, Morphine, Amitriptyline, Imipramine, Oxycodone, Nortriptyline, Lamotrigine, Maprotiline, Desipramine, Gabapentin, Carbamazepine, Phenobarbital, Tramadol, Venlafaxine, Trimipramine, Desvenlafaxine, Primidone, and Naltrexone.	`What condition could be associated with the use of Capsaicin cream, peripheral neuropathy, and symptoms similar to sciatica?`

Loss: MatryoshkaLoss with these parameters:

{
    "loss": "MultipleNegativesRankingLoss",
    "matryoshka_dims": [
        384
    ],
    "matryoshka_weights": [
        1
    ],
    "n_dims_per_step": -1
}

Training Hyperparameters

Non-Default Hyperparameters

eval_strategy: epoch
per_device_train_batch_size: 64
learning_rate: 1e-05
num_train_epochs: 10
warmup_ratio: 0.1
bf16: True
tf32: False
load_best_model_at_end: True

All Hyperparameters

Click to expand

overwrite_output_dir: False
do_predict: False
eval_strategy: epoch
prediction_loss_only: True
per_device_train_batch_size: 64
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: 1e-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: 10
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: True
fp16: False
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
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
eval_on_start: False
use_liger_kernel: False
eval_use_gather_object: False
batch_sampler: batch_sampler
multi_dataset_batch_sampler: proportional

Training Logs

Epoch	Step	Training Loss	dim_384_cosine_map@100
0	0	-	0.3737
0.3448	10	2.4936	-
0.6897	20	2.4873	-
1.0	29	-	0.3917
1.0345	30	2.1624	-
1.3793	40	2.0774	-
1.7241	50	1.973	-
2.0	58	-	0.4065
2.0690	60	1.8545	-
2.4138	70	1.8635	-
2.7586	80	1.8483	-
3.0	87	-	0.4167
3.1034	90	1.764	-
3.4483	100	1.744	-
3.7931	110	1.8287	-
4.0	116	-	0.4212
4.1379	120	1.574	-
4.4828	130	1.6807	-
4.8276	140	1.7146	-
5.0	145	-	0.4222
5.1724	150	1.5898	-
5.5172	160	1.6352	-
5.8621	170	1.6344	-
6.0	174	-	0.4183
6.2069	180	1.5556	-
6.5517	190	1.6743	-
6.8966	200	1.5934	-
7.0	203	-	0.4199
7.2414	210	1.4956	-
7.5862	220	1.5644	-
7.9310	230	1.5856	-
8.0	232	-	0.4215
8.2759	240	1.4328	-
8.6207	250	1.6208	-
8.9655	260	1.57	-
9.0	261	-	0.4216
9.3103	270	1.6354	-
9.6552	280	1.5414	-
10.0	290	1.3757	0.4216

The bold row denotes the saved checkpoint.

Framework Versions

Python: 3.10.10
Sentence Transformers: 3.1.1
Transformers: 4.45.1
PyTorch: 2.2.1+cu121
Accelerate: 0.34.2
Datasets: 3.0.1
Tokenizers: 0.20.0

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",
}

MatryoshkaLoss

@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

@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}
}