---
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](https://www.sbert.net/docs/cross_encoder/usage/usage.html) model finetuned from [ncbi/MedCPT-Cross-Encoder](https://huggingface.co/ncbi/MedCPT-Cross-Encoder) using the [sentence-transformers](https://www.SBERT.net) 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](https://huggingface.co/ncbi/MedCPT-Cross-Encoder)
- **Maximum Sequence Length:** 512 tokens
- **Number of Output Labels:** 1 label
### Model Sources
- **Documentation:** [Sentence Transformers Documentation](https://sbert.net)
- **Documentation:** [Cross Encoder Documentation](https://www.sbert.net/docs/cross_encoder/usage/usage.html)
- **Repository:** [Sentence Transformers on GitHub](https://github.com/UKPLab/sentence-transformers)
- **Hugging Face:** [Cross Encoders on Hugging Face](https://huggingface.co/models?library=sentence-transformers&other=cross-encoder)
## Usage
### Direct Usage (Sentence Transformers)
First install the Sentence Transformers library:
```bash
pip install -U sentence-transformers
```
Then you can load this model and run inference.
```python
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](https://sbert.net/docs/package_reference/cross_encoder/evaluation.html#sentence_transformers.cross_encoder.evaluation.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 |
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](https://sbert.net/docs/package_reference/cross_encoder/losses.html#binarycrossentropyloss) with these parameters:
```json
{
"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