This is a sentence-transformers model finetuned from intfloat/multilingual-e5-large-instruct. It maps sentences & paragraphs to a 1024-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: intfloat/multilingual-e5-large-instruct
Maximum Sequence Length: 512 tokens
Output Dimensionality: 1024 tokens
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: XLMRobertaModel 
  (1): Pooling({'word_embedding_dimension': 1024, '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})
  (2): 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.

python

from sentence_transformers import SentenceTransformer

# Download from the 🤗 Hub
model = SentenceTransformer("FareedKhan/just_for_testing_model")
# Run inference
sentences = [
    '\n\nThe gene in question appears to have a multifaceted role and involvement in various biological processes, diseases, and anatomical structures, with implications for both physiology and pathology. Here is a summary of its characteristics:\n\n### Function and Interactions\n- **Name**: mTORC1, a component of the mammalian target of rapamycin complex 1.\n- **Role**: Involved in regulation of membrane potential',
    'Identify genes or proteins that interact with KCNMB1 and share an associated phenotype or effect.',
    'Which solid-state medications specifically engage with the METAP2 gene/protein through direct interaction?',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 1024]

# 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

Metric	Value
cosine_accuracy@1	0.401
cosine_accuracy@3	0.4604
cosine_accuracy@5	0.4901
cosine_accuracy@10	0.5446
cosine_precision@1	0.401
cosine_precision@3	0.1535
cosine_precision@5	0.098
cosine_precision@10	0.0545
cosine_recall@1	0.401
cosine_recall@3	0.4604
cosine_recall@5	0.4901
cosine_recall@10	0.5446
cosine_ndcg@10	0.465
cosine_mrr@10	0.4406
cosine_map@100	0.4488

Training Details

Training Dataset

Unnamed Dataset

Size: 1,814 training samples
Columns: positive and anchor
Approximate statistics based on the first 1000 samples:
positive anchor
type string string
details
min: 3 tokens
mean: 270.4 tokens
max: 512 tokens
min: 15 tokens
mean: 39.58 tokens
max: 127 tokens

Samples:

positive	anchor
[object Object]Racecadotril, a drug from the Antidiarrheals and Intestinal Antiinflammatory/antiinfective Agents therapeutic group, targets the treatment of acute diarrhea and acute gastroenteritis. This drug falls under Alimentary Tract and Metabolism (ATC Classification) and is related to other antidiarrheals (ATC Specificity Class). Its chemical and functional group is classified under other antidiarrheals, reflecting its role in gastrointestinal health. With a molecular weight of 385.48 grams, and a topological polar surface area of 72.47, Racecadotril demonstrates specific properties that contribute to its effectiveness. The drug's inclusion in the investigational group suggests ongoing research to further validate its efficacy and safety in managing acute diarrhea. Racecadotril's diverse chemical nature, including amino acids, peptides, and sulfur-compound-based inhibitors, highlights its broad mechanism of action, which is crucial for addressing the multifaceted causes of acute diarrhea.	`Could you suggest some effective medications for acute diarrhea?`
[object Object]The gene KCNJ6, also known as potassium inwardly rectifying channel subfamily J member 6, is responsible for encoding a member of the G protein-coupled inwardly-rectifying potassium channel family. This type of potassium channel allows for a greater flow of potassium into the cell than out, playing a critical role in various physiological processes. The KCNJ6 gene modulates functions in cardiac cells and neuronal cells through G-protein coupled receptor stimulation. Mutations in KCNJ6 can lead to Keppen-Lubinsky Syndrome, a rare condition characterized by severe developmental delay, facial dysmorphism, and intellectual disability. [object Object][object Object]In terms of its expression, the KCNJ6 gene is notably absent in the mucosal tissues of the mouth and the small intestine as indicated by its 'expression_absent' attribute. The absence of KCNJ6 in these specific anatomical areas might imply a tailored physiological function or evolutionary adaptation distinct from that in other organs where it is expressed. The gene's absence in the small intestine and mouth tissues might be crucial for ensuring optimal functionality within those specific environments, emphasizing the importance of precise gene expression in various parts of the body. Overall, the gene plays a vital role in cellular and physiological activities and its absence from certain tissues like the mucosal surfaces of the mouth and small intestine is indicative of tailored biological functions within these areas.	`Which gene or protein is consistently not expressed in the mucosal tissues of the mouth and the small intestine?`
[object Object]The term you're referring to seems to describe a wide range of biological entities or contexts, possibly within the framework of a scientific study or database that categorizes anatomical locations, tissues, or organs in the human body. Here's a breakdown of the classification:[object Object][object Object]1. [object Object]: [object Object] - [object Object]: Refers to the large intestine (colon) and small intestine, parts of the digestive system.[object Object] - [object Object]: Includes both the adult kidney and metanephros, an embryonic kidney stage.[object Object] - [object Object]: Part of the endocrine system related to metabolism, stress response, and more.[object Object] - [object Object]: A primary organ involved in detoxification and metabolism.[object Object] - [object Object]: Produces digestive enzymes and hormones such as insulin.[object Object] - [object Object]: Tiny filtration units in the kidney.[object Object] - [object Object]: Refers to a classification of skeletal, smooth, and cardiac muscles, each serving different bodily functions.[object Object] - [object Object]: Includes bones, regions like the spinal cord, and structures like the heart, aorta, etc.[object Object][object Object]2. [object Object]: [object Object] - [object Object]: A cluster of neurons in the spinal cord.[object Object] - [object Object]: Outer layers of the brain responsible for higher functions.[object Object] - [object Object]: Describes entities like the embryonic kidney (metanephros) and placenta, which are crucial during fetal development.[object Object] - [object Object]: Such as the uterus, vagina, and mammary gland, highlighting the female reproductive system.[object Object][object Object]3. [object Object]: [object Object] - [object Object]: Includes bones, the meninges, and fat.[object Object] - [object Object]: Found in various organs and is involved in energy storage and insulation.[object Object][object Object]4. [object Object]: The mention of "blood" might indicate the interest in studying the effects of environmental	`Which genes or proteins exhibit interactions with HNRNPU, share an association with its related disease(s), and participate in the peroxisomal beta-oxidation process of fatty acid metabolism?`

Loss: MatryoshkaLoss with these parameters:
json
1{ 2 "loss": "MultipleNegativesRankingLoss", 3 "matryoshka_dims": [ 4 768 5 ], 6 "matryoshka_weights": [ 7 1 8 ], 9 "n_dims_per_step": -1 10}

Training Hyperparameters

Non-Default Hyperparameters

eval_strategy: epoch
per_device_train_batch_size: 2
learning_rate: 1e-05
num_train_epochs: 2
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: 2
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: 2
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
eval_use_gather_object: False
batch_sampler: batch_sampler
multi_dataset_batch_sampler: proportional

Training Logs

Epoch	Step	Training Loss	dim_768_cosine_map@100
0	0	-	0.2774
0.0220	10	0.7928	-
0.0441	20	0.7435	-
0.0661	30	0.6181	-
0.0881	40	0.5851	-
0.1101	50	0.4896	-
0.1322	60	0.5216	-
0.1542	70	0.3562	-
0.1762	80	0.4002	-
0.1982	90	0.286	-
0.2203	100	0.3835	-
0.2423	110	0.3237	-
0.2643	120	0.5041	-
0.2863	130	0.4061	-
0.3084	140	0.3758	-
0.3304	150	0.4442	-
0.3524	160	0.3714	-
0.3744	170	0.4349	-
0.3965	180	0.3492	-
0.4185	190	0.1045	-
0.4405	200	0.2965	-
0.4626	210	0.1913	-
0.4846	220	0.4259	-
0.5066	230	0.4671	-
0.5286	240	0.4812	-
0.5507	250	0.2442	-
0.5727	260	0.157	-
0.5947	270	0.4386	-
0.6167	280	0.0979	-
0.6388	290	0.7879	-
0.6608	300	0.073	-
0.6828	310	0.252	-
0.7048	320	0.3913	-
0.7269	330	0.1331	-
0.7489	340	0.1311	-
0.7709	350	0.3487	-
0.7930	360	0.2204	-
0.8150	370	0.1718	-
0.8370	380	0.4277	-
0.8590	390	0.4798	-
0.8811	400	0.1381	-
0.9031	410	0.4986	-
0.9251	420	0.2379	-
0.9471	430	0.2717	-
0.9692	440	0.5997	-
0.9912	450	0.2738	-
1.0	454	-	0.4476
1.0132	460	0.0649	-
1.0352	470	0.1113	-
1.0573	480	0.0916	-
1.0793	490	0.0866	-
1.1013	500	0.1341	-
1.1233	510	0.1591	-
1.1454	520	0.0737	-
1.1674	530	0.2395	-
1.1894	540	0.051	-
1.2115	550	0.1838	-
1.2335	560	0.0741	-
1.2555	570	0.2529	-
1.2775	580	0.1624	-
1.2996	590	0.1957	-
1.3216	600	0.1015	-
1.3436	610	0.056	-
1.3656	620	0.0592	-
1.3877	630	0.2027	-
1.4097	640	0.0874	-
1.4317	650	0.144	-
1.4537	660	0.2371	-
1.4758	670	0.083	-
1.4978	680	0.1608	-
1.5198	690	0.1924	-
1.5419	700	0.1765	-
1.5639	710	0.0068	-
1.5859	720	0.1316	-
1.6079	730	0.1538	-
1.6300	740	0.1136	-
1.6520	750	0.1216	-
1.6740	760	0.2417	-
1.6960	770	0.1868	-
1.7181	780	0.2164	-
1.7401	790	0.1186	-
1.7621	800	0.0155	-
1.7841	810	0.033	-
1.8062	820	0.024	-
1.8282	830	0.2094	-
1.8502	840	0.0761	-
1.8722	850	0.0876	-
1.8943	860	0.308	-
1.9163	870	0.0557	-
1.9383	880	0.2808	-
1.9604	890	0.0886	-
1.9824	900	0.2489	-
2.0	908	-	0.4488

The bold row denotes the saved checkpoint.

Framework Versions

Python: 3.10.10
Sentence Transformers: 3.0.1
Transformers: 4.43.4
PyTorch: 2.4.0+cu121
Accelerate: 0.33.0
Datasets: 2.21.0
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}
}

	positive	anchor
type	string	string
details	min: 3 tokens mean: 270.4 tokens max: 512 tokens	min: 15 tokens mean: 39.58 tokens max: 127 tokens