MNLP_M2_document_encoder / README.md

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Add new SentenceTransformer model

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metadata

tags:
  - sentence-transformers
  - sentence-similarity
  - feature-extraction
  - generated_from_trainer
  - dataset_size:28050
  - loss:MultipleNegativesRankingLoss
base_model: BAAI/bge-base-en-v1.5
widget:
  - source_sentence: What helps an insectivorous plant attract and digest insects?
    sentences:
      - >-
        This investigation examined the accuracy of several generalizable
        anthropometric (ANTHRO) and bioelectrical impedance (BIA) regression
        equations to estimate % body fat (%BF) in women with either upper body
        (UB) or lower body (LB) fat distribution patterns.
      - >-
        Bacteria can also be chemotrophs. Chemosynthetic bacteria, or
        chemotrophs , obtain energy by breaking down chemical compounds in their
        environment. An example of one of these chemicals broken down by
        bacteria is nitrogen-containing ammonia. These bacteria are important
        because they help cycle nitrogen through the environment for other
        living things to use. Nitrogen cannot be made by living organisms, so it
        must be continually recycled. Organisms need nitrogen to make organic
        compounds, such as DNA.
      - >-
        Insectivorous Plants An insectivorous plant has specialized leaves to
        attract and digest insects. The Venus flytrap is popularly known for its
        insectivorous mode of nutrition, and has leaves that work as traps
        (Figure 31.16). The minerals it obtains from prey compensate for those
        lacking in the boggy (low pH) soil of its native North Carolina coastal
        plains. There are three sensitive hairs in the center of each half of
        each leaf. The edges of each leaf are covered with long spines. Nectar
        secreted by the plant attracts flies to the leaf. When a fly touches the
        sensory hairs, the leaf immediately closes. Next, fluids and enzymes
        break down the prey and minerals are absorbed by the leaf. Since this
        plant is popular in the horticultural trade, it is threatened in its
        original habitat.
  - source_sentence: >-
      When carbon atoms are not bonded to as many hydrogen atoms as possible,
      what kind of hydrocarbon results?
    sentences:
      - >-
        Unsaturated hydrocarbons have at least one double or triple bond between
        carbon atoms, so the carbon atoms are not bonded to as many hydrogen
        atoms as possible. In other words, they are unsaturated with hydrogen
        atoms.
      - >-
        Endoscopic radiofrequency ablation (RFA) is a promising new treatment of
        Barrett's esophagus (BE). Adjunctive intra-esophageal pH control with
        proton pump inhibitors and/or anti-reflux surgery is generally
        recommended to optimize squamous re-epithelialization after ablation.
      - >-
        The cell wall is located outside the cell membrane. It consists mainly
        of cellulose and may also contain lignin, which makes it more rigid. The
        cell wall shapes, supports, and protects the cell. It prevents the cell
        from absorbing too much water and bursting. It also keeps large,
        damaging molecules out of the cell.
  - source_sentence: >-
      Do comparison of ambulance dispatch protocols for nontraumatic abdominal
      pain?
    sentences:
      - >-
        KIOM-79, a combination of four plant extracts, has a preventive effect
        on diabetic nephropathy and retinopathy in diabetic animal models. In
        this study, we have investigated the inhibitory effects of KIOM-79 on
        diabetic cataractogenesis.
      - >-
        To compare rates of undertriage and overtriage of six ambulance dispatch
        protocols for the presenting complaint of nontraumatic abdominal pain,
        and to identify the optimal protocol.
      - a flower is a source of nectar
  - source_sentence: >-
      Does altered fractalkine cleavage potentially promote local inflammation
      in NOD salivary gland?
    sentences:
      - >-
        In France, when physicians in ambulances take care of patients, they
        report medical status to the dispatch centre. Then the dispatching
        physician search for the available and appropriate hospital service to
        agree in directly receiving the patient. We attempted to evaluate this
        direct admission dispatch, in a urban area, with many health care
        facilities.
      - >-
        Despite the high prevalence of cannabis use in schizophrenia, few
        studies have examined the potential relationship between cannabis
        exposure and brain structural abnormalities in schizophrenia.
      - >-
        In the nonobese diabetic (NOD) mouse model of Sjögren's syndrome,
        lymphocytic infiltration is preceded by an accumulation of dendritic
        cells in the submandibular glands (SMGs). NOD mice also exhibit an
        increased frequency of mature, fractalkine receptor (CX3C chemokine
        receptor [CX3CR]1) expressing monocytes, which are considered to be
        precursors for tissue dendritic cells. To unravel further the role
        played by fractalkine-CX3CR1 interactions in the salivary gland
        inflammation, we studied the expression of fractalkine in NOD SMGs.
  - source_sentence: The smallest cyclic ether is called what?
    sentences:
      - >-
        Most human traits have more complex modes of inheritance than simple
        Mendelian inheritance. For example, the traits may be controlled by
        multiple alleles or multiple genes.
      - >-
        Neonatal stress impairs postnatal bone mineralization. Evidence suggests
        that mechanical tactile stimulation (MTS) in early life decreases stress
        hormones and improves bone mineralization. Insulin-like growth factor
        (IGF1) is impacted by stress and essential to bone development. We
        hypothesized that MTS administered during neonatal stress would improve
        bone phenotype in later life. We also predicted an increase in bone
        specific mRNA expression of IGF1 related pathways.
      - The smallest cyclic ether is called an epoxide. Draw its structure.
pipeline_tag: sentence-similarity
library_name: sentence-transformers

SentenceTransformer based on BAAI/bge-base-en-v1.5

This is a sentence-transformers model finetuned from 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
Maximum Sequence Length: 512 tokens
Output Dimensionality: 768 dimensions
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': 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:

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("danthepol/mcqa_embedder_v2")
# Run inference
sentences = [
    'The smallest cyclic ether is called what?',
    'The smallest cyclic ether is called an epoxide. Draw its structure.',
    'Neonatal stress impairs postnatal bone mineralization. Evidence suggests that mechanical tactile stimulation (MTS) in early life decreases stress hormones and improves bone mineralization. Insulin-like growth factor (IGF1) is impacted by stress and essential to bone development. We hypothesized that MTS administered during neonatal stress would improve bone phenotype in later life. We also predicted an increase in bone specific mRNA expression of IGF1 related pathways.',
]
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]

Training Details

Training Dataset

Unnamed Dataset

Size: 28,050 training samples
Columns: sentence_0 and sentence_1
Approximate statistics based on the first 1000 samples:
sentence_0 sentence_1
type string string
details
min: 6 tokens
mean: 23.02 tokens
max: 63 tokens

min: 5 tokens
mean: 81.53 tokens
max: 512 tokens

	sentence_0	sentence_1
type	string	string
details	min: 6 tokens mean: 23.02 tokens max: 63 tokens	min: 5 tokens mean: 81.53 tokens max: 512 tokens

Samples:

sentence_0	sentence_1
`Ectotherms undergo a variety of changes at the cellular level to acclimatize to shifts in what?`	There are 44 autosomes and 2 sex chromosomes in the human genome, for a total of 46 chromosomes (23 pairs). Sex chromosomes specify an organism's genetic sex. Humans can have two different sex chromosomes, one called X and the other Y. Normal females possess two X chromosomes and normal males one X and one Y. An autosome is any chromosome other than a sex chromosome. The Figure below shows a representation of the 24 different human chromosomes. Figure below shows a karyotype of the human genome. A karyotype depicts, usually in a photograph, the chromosomal complement of an individual, including the number of chromosomes and any large chromosomal abnormalities. Karyotypes use chromosomes from the metaphase stage of mitosis.
`All polar compounds contain what type of bonds?`	Polar compounds, such as water, are compounds that have a partial negative charge on one side of each molecule and a partial positive charge on the other side. All polar compounds contain polar bonds (although not all compounds that contain polar bonds are polar. ) In a polar bond, two atoms share electrons unequally. One atom attracts the shared electrons more strongly, so it has a partial negative charge. The other atom attracts the shared electrons less strongly, so it is has a partial positive charge. In a water molecule, the oxygen atom attracts the shared electrons more strongly than the hydrogen atoms do. This explains why the oxygen side of the water molecule has a partial negative charge and the hydrogen side of the molecule has a partial positive charge.
`Do lateral cephalometric radiograph for the planning of maxillary implant reconstruction?`	`To present a simple and objective method for the planning of maxillary implant reconstruction with autogenous bone graft in maxilla atrophy.`

Loss: MultipleNegativesRankingLoss with these parameters:

{
    "scale": 20.0,
    "similarity_fct": "cos_sim"
}

Training Hyperparameters

Non-Default Hyperparameters

per_device_train_batch_size: 32
per_device_eval_batch_size: 32
multi_dataset_batch_sampler: round_robin

All Hyperparameters

Click to expand

overwrite_output_dir: False
do_predict: False
eval_strategy: no
prediction_loss_only: True
per_device_train_batch_size: 32
per_device_eval_batch_size: 32
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: 5e-05
weight_decay: 0.0
adam_beta1: 0.9
adam_beta2: 0.999
adam_epsilon: 1e-08
max_grad_norm: 1
num_train_epochs: 3
max_steps: -1
lr_scheduler_type: linear
lr_scheduler_kwargs: {}
warmup_ratio: 0.0
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: False
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}
tp_size: 0
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: None
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
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
average_tokens_across_devices: False
prompts: None
batch_sampler: batch_sampler
multi_dataset_batch_sampler: round_robin

Training Logs

Epoch	Step	Training Loss
0.5701	500	0.064
1.1403	1000	0.0455
1.7104	1500	0.0254
2.2805	2000	0.0189
2.8506	2500	0.0155

Framework Versions

Python: 3.12.8
Sentence Transformers: 3.4.1
Transformers: 4.51.3
PyTorch: 2.3.0+cu121
Accelerate: 1.3.0
Datasets: 3.6.0
Tokenizers: 0.21.1

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",
}

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}
}