LitDD_crossencoder / README.md

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metadata

tags:
  - sentence-transformers
  - cross-encoder
  - reranker
  - generated_from_trainer
  - dataset_size:35474
  - loss:BinaryCrossEntropyLoss
base_model: ncbi/MedCPT-Cross-Encoder
pipeline_tag: text-ranking
library_name: sentence-transformers
metrics:
  - accuracy
  - accuracy_threshold
  - f1
  - f1_threshold
  - precision
  - recall
  - average_precision
model-index:
  - name: CrossEncoder based on ncbi/MedCPT-Cross-Encoder
    results:
      - task:
          type: cross-encoder-classification
          name: Cross Encoder Classification
        dataset:
          name: anno test
          type: anno_test
        metrics:
          - type: accuracy
            value: 0.824009900990099
            name: Accuracy
          - type: accuracy_threshold
            value: 0.9996383786201477
            name: Accuracy Threshold
          - type: f1
            value: 0.3841536614645858
            name: F1
          - type: f1_threshold
            value: 0.9992461800575256
            name: F1 Threshold
          - type: precision
            value: 0.26981450252951095
            name: Precision
          - type: recall
            value: 0.6666666666666666
            name: Recall
          - type: average_precision
            value: 0.3289533283996273
            name: Average Precision

CrossEncoder based on ncbi/MedCPT-Cross-Encoder

This is a Cross Encoder model finetuned from ncbi/MedCPT-Cross-Encoder using the sentence-transformers library. It computes scores for pairs of texts, which can be used for text reranking and semantic search.

Model Details

Model Description

Model Type: Cross Encoder
Base model: ncbi/MedCPT-Cross-Encoder
Maximum Sequence Length: 512 tokens
Number of Output Labels: 1 label

Model Sources

Documentation: Sentence Transformers Documentation
Documentation: Cross Encoder Documentation
Repository: Sentence Transformers on GitHub
Hugging Face: Cross Encoders on Hugging Face

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 CrossEncoder

# Download from the 🤗 Hub
model = CrossEncoder("cross_encoder_model_id")
# Get scores for pairs of texts
pairs = [
    ['Its8, a fission yeast homolog of Mcd4 and Pig-n, is involved in GPI anchor synthesis and shares an essential function with calcineurin in cytokinesis. In fission yeast, calcineurin is required for cytokinesis and ion homeostasis; however, most of its physiological roles remain obscure. To identify genes that share an essential function with calcineurin, we screened for mutations that confer sensitivity to the calcineurin inhibitor FK506 and high temperature and isolated the mutant its8-1. its8(+) encodes a homolog of the budding yeast MCD4 and human Pig-n that are involved in glycosylphosphatidylinositol (GPI) anchor synthesis. Consistently, reduced inositol labeling of proteins suggested impaired GPI anchor synthesis in its8-1 mutants. The temperature upshift induced a further decrease in inositol labeling and caused dramatic increases in the frequency of septation in its8-1 mutants. BE49385A, an inhibitor of MCD4 and Pig-n, also increased the septation index of the wild-type cell. Osmotic stabilization suppressed these morphological defects, indicating that cell wall weakness caused by impaired GPI anchor synthesis resulted in abnormal cytokinesis. Furthermore, calcineurin-deleted cells exhibited hypersensitivity to BE49385A, and FK506 exacerbated the cytokinesis defects of the its8-1 mutant. Thus, calcineurin and Its8 may share an essential function in cytokinesis and cell viability through the regulation of cell wall integrity.', 'G2P01414 - PIGN - 606097.0 - HGNC:8967 - MCD4; PIG-N - PIGN-related multiple congenital anomalies-hypotonia-seizures syndrome - 614080 - nan - biallelic_autosomal - nan - definitive - absent gene product; altered gene product structure - inframe_insertion; missense_variant; inframe_deletion - undetermined - inferred'],
    ['Its8, a fission yeast homolog of Mcd4 and Pig-n, is involved in GPI anchor synthesis and shares an essential function with calcineurin in cytokinesis. In fission yeast, calcineurin is required for cytokinesis and ion homeostasis; however, most of its physiological roles remain obscure. To identify genes that share an essential function with calcineurin, we screened for mutations that confer sensitivity to the calcineurin inhibitor FK506 and high temperature and isolated the mutant its8-1. its8(+) encodes a homolog of the budding yeast MCD4 and human Pig-n that are involved in glycosylphosphatidylinositol (GPI) anchor synthesis. Consistently, reduced inositol labeling of proteins suggested impaired GPI anchor synthesis in its8-1 mutants. The temperature upshift induced a further decrease in inositol labeling and caused dramatic increases in the frequency of septation in its8-1 mutants. BE49385A, an inhibitor of MCD4 and Pig-n, also increased the septation index of the wild-type cell. Osmotic stabilization suppressed these morphological defects, indicating that cell wall weakness caused by impaired GPI anchor synthesis resulted in abnormal cytokinesis. Furthermore, calcineurin-deleted cells exhibited hypersensitivity to BE49385A, and FK506 exacerbated the cytokinesis defects of the its8-1 mutant. Thus, calcineurin and Its8 may share an essential function in cytokinesis and cell viability through the regulation of cell wall integrity.', 'G2P02996 - MFF - 614785.0 - HGNC:24858 - C2ORF33; GL004 - MFF-related encephalopathy due to defective mitochondrial and peroxisomal fission - 617086 - nan - biallelic_autosomal - nan - definitive - absent gene product - nan - loss of function - inferred'],
    ['Its8, a fission yeast homolog of Mcd4 and Pig-n, is involved in GPI anchor synthesis and shares an essential function with calcineurin in cytokinesis. In fission yeast, calcineurin is required for cytokinesis and ion homeostasis; however, most of its physiological roles remain obscure. To identify genes that share an essential function with calcineurin, we screened for mutations that confer sensitivity to the calcineurin inhibitor FK506 and high temperature and isolated the mutant its8-1. its8(+) encodes a homolog of the budding yeast MCD4 and human Pig-n that are involved in glycosylphosphatidylinositol (GPI) anchor synthesis. Consistently, reduced inositol labeling of proteins suggested impaired GPI anchor synthesis in its8-1 mutants. The temperature upshift induced a further decrease in inositol labeling and caused dramatic increases in the frequency of septation in its8-1 mutants. BE49385A, an inhibitor of MCD4 and Pig-n, also increased the septation index of the wild-type cell. Osmotic stabilization suppressed these morphological defects, indicating that cell wall weakness caused by impaired GPI anchor synthesis resulted in abnormal cytokinesis. Furthermore, calcineurin-deleted cells exhibited hypersensitivity to BE49385A, and FK506 exacerbated the cytokinesis defects of the its8-1 mutant. Thus, calcineurin and Its8 may share an essential function in cytokinesis and cell viability through the regulation of cell wall integrity.', 'G2P01166 - CERT1 - 604677.0 - HGNC:2205 - CERT; COL4A3BP; GPBP; STARD11 - CERT1-related intellectual disability - 616351 - nan - monoallelic_autosomal - restricted mutation set - definitive - altered gene product structure - nan - gain of function - inferred'],
    ['Its8, a fission yeast homolog of Mcd4 and Pig-n, is involved in GPI anchor synthesis and shares an essential function with calcineurin in cytokinesis. In fission yeast, calcineurin is required for cytokinesis and ion homeostasis; however, most of its physiological roles remain obscure. To identify genes that share an essential function with calcineurin, we screened for mutations that confer sensitivity to the calcineurin inhibitor FK506 and high temperature and isolated the mutant its8-1. its8(+) encodes a homolog of the budding yeast MCD4 and human Pig-n that are involved in glycosylphosphatidylinositol (GPI) anchor synthesis. Consistently, reduced inositol labeling of proteins suggested impaired GPI anchor synthesis in its8-1 mutants. The temperature upshift induced a further decrease in inositol labeling and caused dramatic increases in the frequency of septation in its8-1 mutants. BE49385A, an inhibitor of MCD4 and Pig-n, also increased the septation index of the wild-type cell. Osmotic stabilization suppressed these morphological defects, indicating that cell wall weakness caused by impaired GPI anchor synthesis resulted in abnormal cytokinesis. Furthermore, calcineurin-deleted cells exhibited hypersensitivity to BE49385A, and FK506 exacerbated the cytokinesis defects of the its8-1 mutant. Thus, calcineurin and Its8 may share an essential function in cytokinesis and cell viability through the regulation of cell wall integrity.', 'G2P01646 - STAT2 - 600556.0 - HGNC:11363 - STAT113 - STAT2-related viral induced severe multiorgan dysfunction related with impaired mitochondrial fission - nan - nan - biallelic_autosomal - nan - limited - absent gene product - nan - loss of function - inferred'],
    ['Its8, a fission yeast homolog of Mcd4 and Pig-n, is involved in GPI anchor synthesis and shares an essential function with calcineurin in cytokinesis. In fission yeast, calcineurin is required for cytokinesis and ion homeostasis; however, most of its physiological roles remain obscure. To identify genes that share an essential function with calcineurin, we screened for mutations that confer sensitivity to the calcineurin inhibitor FK506 and high temperature and isolated the mutant its8-1. its8(+) encodes a homolog of the budding yeast MCD4 and human Pig-n that are involved in glycosylphosphatidylinositol (GPI) anchor synthesis. Consistently, reduced inositol labeling of proteins suggested impaired GPI anchor synthesis in its8-1 mutants. The temperature upshift induced a further decrease in inositol labeling and caused dramatic increases in the frequency of septation in its8-1 mutants. BE49385A, an inhibitor of MCD4 and Pig-n, also increased the septation index of the wild-type cell. Osmotic stabilization suppressed these morphological defects, indicating that cell wall weakness caused by impaired GPI anchor synthesis resulted in abnormal cytokinesis. Furthermore, calcineurin-deleted cells exhibited hypersensitivity to BE49385A, and FK506 exacerbated the cytokinesis defects of the its8-1 mutant. Thus, calcineurin and Its8 may share an essential function in cytokinesis and cell viability through the regulation of cell wall integrity.', 'G2P03036 - NDUFA8 - 603359.0 - HGNC:7692 - MGC793; PGIV - NDUFA8-related developmental disorder - nan - nan - biallelic_autosomal - nan - strong - absent gene product - nan - loss of function - inferred'],
]
scores = model.predict(pairs)
print(scores.shape)
# (5,)

# Or rank different texts based on similarity to a single text
ranks = model.rank(
    'Its8, a fission yeast homolog of Mcd4 and Pig-n, is involved in GPI anchor synthesis and shares an essential function with calcineurin in cytokinesis. In fission yeast, calcineurin is required for cytokinesis and ion homeostasis; however, most of its physiological roles remain obscure. To identify genes that share an essential function with calcineurin, we screened for mutations that confer sensitivity to the calcineurin inhibitor FK506 and high temperature and isolated the mutant its8-1. its8(+) encodes a homolog of the budding yeast MCD4 and human Pig-n that are involved in glycosylphosphatidylinositol (GPI) anchor synthesis. Consistently, reduced inositol labeling of proteins suggested impaired GPI anchor synthesis in its8-1 mutants. The temperature upshift induced a further decrease in inositol labeling and caused dramatic increases in the frequency of septation in its8-1 mutants. BE49385A, an inhibitor of MCD4 and Pig-n, also increased the septation index of the wild-type cell. Osmotic stabilization suppressed these morphological defects, indicating that cell wall weakness caused by impaired GPI anchor synthesis resulted in abnormal cytokinesis. Furthermore, calcineurin-deleted cells exhibited hypersensitivity to BE49385A, and FK506 exacerbated the cytokinesis defects of the its8-1 mutant. Thus, calcineurin and Its8 may share an essential function in cytokinesis and cell viability through the regulation of cell wall integrity.',
    [
        'G2P01414 - PIGN - 606097.0 - HGNC:8967 - MCD4; PIG-N - PIGN-related multiple congenital anomalies-hypotonia-seizures syndrome - 614080 - nan - biallelic_autosomal - nan - definitive - absent gene product; altered gene product structure - inframe_insertion; missense_variant; inframe_deletion - undetermined - inferred',
        'G2P02996 - MFF - 614785.0 - HGNC:24858 - C2ORF33; GL004 - MFF-related encephalopathy due to defective mitochondrial and peroxisomal fission - 617086 - nan - biallelic_autosomal - nan - definitive - absent gene product - nan - loss of function - inferred',
        'G2P01166 - CERT1 - 604677.0 - HGNC:2205 - CERT; COL4A3BP; GPBP; STARD11 - CERT1-related intellectual disability - 616351 - nan - monoallelic_autosomal - restricted mutation set - definitive - altered gene product structure - nan - gain of function - inferred',
        'G2P01646 - STAT2 - 600556.0 - HGNC:11363 - STAT113 - STAT2-related viral induced severe multiorgan dysfunction related with impaired mitochondrial fission - nan - nan - biallelic_autosomal - nan - limited - absent gene product - nan - loss of function - inferred',
        'G2P03036 - NDUFA8 - 603359.0 - HGNC:7692 - MGC793; PGIV - NDUFA8-related developmental disorder - nan - nan - biallelic_autosomal - nan - strong - absent gene product - nan - loss of function - inferred',
    ]
)
# [{'corpus_id': ..., 'score': ...}, {'corpus_id': ..., 'score': ...}, ...]

Evaluation

Metrics

Cross Encoder Classification

Dataset: anno_test
Evaluated with CrossEncoderClassificationEvaluator

Metric	Value
accuracy	0.824
accuracy_threshold	0.9996
f1	0.3842
f1_threshold	0.9992
precision	0.2698
recall	0.6667
average_precision	0.329

Training Details

Training Dataset

Unnamed Dataset

Size: 35,474 training samples
Columns: tiab, g2p_lgmde, and label

Approximate statistics based on the first 1000 samples:

	tiab	g2p_lgmde	label
type	string	string	int
details	min: 30 characters mean: 1348.52 characters max: 2802 characters	min: 177 characters mean: 258.9 characters max: 407 characters	0: ~72.90% 1: ~27.10%

Samples:

tiab	g2p_lgmde	label
Its8, a fission yeast homolog of Mcd4 and Pig-n, is involved in GPI anchor synthesis and shares an essential function with calcineurin in cytokinesis. In fission yeast, calcineurin is required for cytokinesis and ion homeostasis; however, most of its physiological roles remain obscure. To identify genes that share an essential function with calcineurin, we screened for mutations that confer sensitivity to the calcineurin inhibitor FK506 and high temperature and isolated the mutant its8-1. its8(+) encodes a homolog of the budding yeast MCD4 and human Pig-n that are involved in glycosylphosphatidylinositol (GPI) anchor synthesis. Consistently, reduced inositol labeling of proteins suggested impaired GPI anchor synthesis in its8-1 mutants. The temperature upshift induced a further decrease in inositol labeling and caused dramatic increases in the frequency of septation in its8-1 mutants. BE49385A, an inhibitor of MCD4 and Pig-n, also increased the septation index of the wild-type cell. Os...	`G2P01414 - PIGN - 606097.0 - HGNC:8967 - MCD4; PIG-N - PIGN-related multiple congenital anomalies-hypotonia-seizures syndrome - 614080 - nan - biallelic_autosomal - nan - definitive - absent gene product; altered gene product structure - inframe_insertion; missense_variant; inframe_deletion - undetermined - inferred`	`1`
Its8, a fission yeast homolog of Mcd4 and Pig-n, is involved in GPI anchor synthesis and shares an essential function with calcineurin in cytokinesis. In fission yeast, calcineurin is required for cytokinesis and ion homeostasis; however, most of its physiological roles remain obscure. To identify genes that share an essential function with calcineurin, we screened for mutations that confer sensitivity to the calcineurin inhibitor FK506 and high temperature and isolated the mutant its8-1. its8(+) encodes a homolog of the budding yeast MCD4 and human Pig-n that are involved in glycosylphosphatidylinositol (GPI) anchor synthesis. Consistently, reduced inositol labeling of proteins suggested impaired GPI anchor synthesis in its8-1 mutants. The temperature upshift induced a further decrease in inositol labeling and caused dramatic increases in the frequency of septation in its8-1 mutants. BE49385A, an inhibitor of MCD4 and Pig-n, also increased the septation index of the wild-type cell. Os...	`G2P02996 - MFF - 614785.0 - HGNC:24858 - C2ORF33; GL004 - MFF-related encephalopathy due to defective mitochondrial and peroxisomal fission - 617086 - nan - biallelic_autosomal - nan - definitive - absent gene product - nan - loss of function - inferred`	`0`
Its8, a fission yeast homolog of Mcd4 and Pig-n, is involved in GPI anchor synthesis and shares an essential function with calcineurin in cytokinesis. In fission yeast, calcineurin is required for cytokinesis and ion homeostasis; however, most of its physiological roles remain obscure. To identify genes that share an essential function with calcineurin, we screened for mutations that confer sensitivity to the calcineurin inhibitor FK506 and high temperature and isolated the mutant its8-1. its8(+) encodes a homolog of the budding yeast MCD4 and human Pig-n that are involved in glycosylphosphatidylinositol (GPI) anchor synthesis. Consistently, reduced inositol labeling of proteins suggested impaired GPI anchor synthesis in its8-1 mutants. The temperature upshift induced a further decrease in inositol labeling and caused dramatic increases in the frequency of septation in its8-1 mutants. BE49385A, an inhibitor of MCD4 and Pig-n, also increased the septation index of the wild-type cell. Os...	`G2P01166 - CERT1 - 604677.0 - HGNC:2205 - CERT; COL4A3BP; GPBP; STARD11 - CERT1-related intellectual disability - 616351 - nan - monoallelic_autosomal - restricted mutation set - definitive - altered gene product structure - nan - gain of function - inferred`	`0`

Loss: BinaryCrossEntropyLoss with these parameters:

{
    "activation_fn": "torch.nn.modules.linear.Identity",
    "pos_weight": null
}

Training Hyperparameters

Non-Default Hyperparameters

per_device_train_batch_size: 16
per_device_eval_batch_size: 16
learning_rate: 3.879271032713091e-05
num_train_epochs: 2
warmup_ratio: 0.1

All Hyperparameters

Click to expand

overwrite_output_dir: False
do_predict: False
eval_strategy: no
prediction_loss_only: True
per_device_train_batch_size: 16
per_device_eval_batch_size: 16
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: 3.879271032713091e-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: 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}
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
hub_revision: None
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
liger_kernel_config: None
eval_use_gather_object: False
average_tokens_across_devices: False
prompts: None
batch_sampler: batch_sampler
multi_dataset_batch_sampler: proportional
router_mapping: {}
learning_rate_mapping: {}

Training Logs

Epoch	Step	Training Loss	anno_test_average_precision
-1	-1	-	0.6910
0.2254	500	0.0908	-
0.4509	1000	0.0266	-
0.6763	1500	0.0207	-
0.9017	2000	0.0126	-
1.1271	2500	0.0082	-
1.3526	3000	0.0098	-
1.5780	3500	0.0072	-
1.8034	4000	0.0098	-
-1	-1	-	0.3290

Framework Versions

Python: 3.10.12
Sentence Transformers: 5.1.0
Transformers: 4.55.0
PyTorch: 2.7.1+cu126
Accelerate: 1.10.0
Datasets: 4.0.0
Tokenizers: 0.21.4

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",
}