results and model added

1_Pooling/config.json

@@ -0,0 +1,10 @@
+{
+  "word_embedding_dimension": 768,
+  "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
+}

Patient_Text_sbert_model.joblib

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7a205a5233e5d95eaec46769cb82c283adcc9ad23f22cf86a2bf1a18f9772d22
+size 438524577

README.md

@@ -1,3 +1,198 @@
 ---
 license: cc-by-nc-4.0
+language:
+- en
+metrics:
+- precision
+- recall
+- brier_score
+- f1
+- matthews_correlation
+base_model:
+- sentence-transformers/all-mpnet-base-v2
+tags:
+- IBD
+- cohort_identification
+- case_finding
 ---
+# Model Card for BioClinicalBERT IBD
+
+The model classifies documents as either IBD or Not IBD
+
+## Model Details
+
+### Model Description
+
+As above. This is a model trained to detect IBD patients from clinical text
+
+- **Developed by:** Matt Stammers
+- **Funded by:** University Hospital Foundation NHS Trust
+- **Shared by:** Matt Stammers - SETT Data and AI Clinical Lead
+- **Model type:** BERT Transformer
+- **Language(s) (NLP):** English
+- **License:** cc-by-nc-4.0
+- **Finetuned from model:** sentence-transformers/all-mpnet-base-v2
+
+### Model Sources
+
+- **Repository:** https://huggingface.co/MattStammers/SBERT_IBD
+- **Paper:** Arxiv (Pending)
+- **Demo:** https://huggingface.co/spaces/MattStammers/IBD_Cohort_Identification
+
+## Uses
+
+For document classification tasks to differentiate between documents likely to be diagnostic of IBD and those unlikely to be diagnostic of IBD. 
+
+### Direct Use
+
+This model can be used directly at [Cohort Identification Demo](https://huggingface.co/spaces/MattStammers/IBD_Cohort_Identification)
+
+### Downstream Use 
+
+Others can build on this model and improve it but only for non-commercial purposes.
+
+### Out-of-Scope Use
+
+This model is less powerful (in terms of F1 Score) when making predictions at the patient level by 1-2%. It can be used for this purpose but with care.
+
+## Bias, Risks, and Limitations
+
+This model contains substantial biases and is known to be biased against older patients and non-white patients so use with care. 
+
+### Recommendations
+
+It will work best in a predominantly younger caucasian population.
+
+## How to Get Started with the Model
+
+Use the code below to get started with the model.
+
+The model is best used with the transformers library.
+
+## Training Details
+
+### Training Data
+
+The model was trained on fully pseudonymised clinical information at UHSFT which was carefully labelled by a consultant (attending) physician and evaluated against a randomly selected internal holdout set.
+
+### Training Procedure
+
+See the paper for more information on the training procedure
+
+#### Training Hyperparameters
+
+- **Training regime:** fp32
+
+#### Speeds, Sizes, Times 
+
+This model (part of a set of models) took 213.55 minutes to train
+
+## Evaluation
+
+The model was internally validated against a holdout set
+
+### Testing Data, Factors & Metrics
+
+#### Testing Data
+
+The testing data cannot be revealed due to IG regulations and to remain compliant with GDPR, only the resulting model can be
+
+#### Factors
+
+IBD vs Not-IBD
+
+#### Metrics
+
+Full evaluation metrics are available in the paper with a summary below
+
+### Results
+
+| Model | Doc Coverage     | Accuracy                          | Precision                         | Recall                            | Specificity                      | NPV                              | F1 Score                         | MCC                               |
+|-------|------------------|-----------------------------------|-----------------------------------|-----------------------------------|----------------------------------|----------------------------------|----------------------------------|------------------------------------|
+| SBERT | 768 (100.00%)    | 89.67% (CI: 86.64% - 92.08%)      | 88.81% (CI: 85.44% - 91.48%)      | 99.20% (CI: 97.68% - 99.73%)      | 56.48% (CI: 47.07% - 65.45%)     | 95.31% (CI: 87.10% - 98.39%)     | 93.72% (CI: 92.50% - 94.90%)     | 0.6844 (CI: 0.6120 - 0.7545)        |
+
+
+#### Summary
+
+Overall performance of the model is high with an F1 Score of >94% on our internal holdout set.
+
+## Environmental Impact
+
+Training the model used 2.01kWh of energy emmitting 416.73 grams of CO2
+
+- **Hardware Type:** L40S
+- **Hours used:** 2
+- **Carbon Emitted:** 0.230 Kg CO2
+
+## Citation
+
+Arxiv (Pending)
+
+## Glossary
+
+| Term                                | Description |
+|-------------------------------------|-------------|
+| **Accuracy**                        | The percentage of results that were correct among all results from the system. Calc: (TP + TN) / (TP + FP + TN + FN). |
+| **Precision (PPV)**                 | Also called positive predictive value (PPV), it is the percentage of true positive results among all results that the system flagged as positive. Calc: TP / (TP + FP). |
+| **Negative Predictive Value (NPV)** | The percentage of results that were true negative (TN) among all results that the system flagged as negative. Calc: TN / (TN + FN). |
+| **Recall**                          | Also called sensitivity. The percentage of results flagged positive among all results that should have been obtained. Calc: TP / (TP + FN). |
+| **Specificity**                     | The percentage of results that were flagged negative among all negative results. Calc: TN / (TN + FP). |
+| **F1-Score**                        | The harmonic mean of PPV/precision and sensitivity/recall. Calc: 2 × (Precision × Recall) / (Precision + Recall). Moderately useful in the context of class imbalance. |
+| **Matthews’ Correlation Coefficient (MCC)** | A statistical measure used to evaluate the quality of binary classifications. Unlike other metrics, MCC considers all four categories of a confusion matrix. Calc: (TP × TN − FP × FN) / √((TP + FP)(TP + FN)(TN + FP)(TN + FN)). |
+| **Precision / Recall AUC**         | Represents the area under the Precision-Recall curve, which plots Precision against Recall at various threshold settings. It is more resistant to class imbalance than alternatives like AUROC. |
+| **Demographic Parity (DP)**        | Demographic Parity, also known as Statistical Parity, requires that the probability of a positive prediction is the same across different demographic groups. Calc: DP = P(Ŷ=1∣A=a) = P(Ŷ=1∣A=b). This figure is given as an absolute difference where positive values suggest the more privileged group gains and negative values the reverse. |
+| **Equal Opportunity (EO)**         | Equal Opportunity focuses on equalising the true positive rates across groups. Among those who truly belong to the positive class, the model should predict positive outcomes at equal rates across groups. Calc: EO = P(Ŷ=1∣Y=1, A=a) = P(Ŷ=1∣Y=1, A=b). A higher value indicates a bias against the more vulnerable group. |
+| **Disparate Impact (DI)**          | Divides the protected group’s positive prediction rate by that of the most-favoured group. If the ratio is below 0.8 or above 1.25, disparate impact is considered present. Calc: DI = P(Ŷ=1∣A=unfavoured) / P(Ŷ=1∣A=favoured). Values outside 0.8–1.25 range suggest bias. |
+| **Execution Time / Energy / CO₂ Emissions** | Measured in minutes and total energy consumption in kilowatt-hours (kWh), which is then converted to CO₂ emissions using a factor of 0.20705 Kg CO₂e per kWh. |
+
+## Model Card Authors
+
+Matt Stammers - Computational Gastroenterologist
+
+## Model Card Contact
+
+[email protected]
+
+## Base Training Data for the Model
+
+#### Training data
+
+We use the concatenation from multiple datasets to fine-tune our model. The total number of sentence pairs is above 1 billion sentences.
+We sampled each dataset given a weighted probability which configuration is detailed in the `data_config.json` file.
+
+
+| Dataset                                                  | Paper                                    | Number of training tuples  |
+|--------------------------------------------------------|:----------------------------------------:|:--------------------------:|
+| [Reddit comments (2015-2018)](https://github.com/PolyAI-LDN/conversational-datasets/tree/master/reddit) | [paper](https://arxiv.org/abs/1904.06472) | 726,484,430 |
+| [S2ORC](https://github.com/allenai/s2orc) Citation pairs (Abstracts) | [paper](https://aclanthology.org/2020.acl-main.447/) | 116,288,806 |
+| [WikiAnswers](https://github.com/afader/oqa#wikianswers-corpus) Duplicate question pairs | [paper](https://doi.org/10.1145/2623330.2623677) | 77,427,422 |
+| [PAQ](https://github.com/facebookresearch/PAQ) (Question, Answer) pairs | [paper](https://arxiv.org/abs/2102.07033) | 64,371,441 |
+| [S2ORC](https://github.com/allenai/s2orc) Citation pairs (Titles) | [paper](https://aclanthology.org/2020.acl-main.447/) | 52,603,982 |
+| [S2ORC](https://github.com/allenai/s2orc) (Title, Abstract) | [paper](https://aclanthology.org/2020.acl-main.447/) | 41,769,185 |
+| [Stack Exchange](https://huggingface.co/datasets/flax-sentence-embeddings/stackexchange_xml) (Title, Body) pairs  | - | 25,316,456 |
+| [Stack Exchange](https://huggingface.co/datasets/flax-sentence-embeddings/stackexchange_xml) (Title+Body, Answer) pairs  | - | 21,396,559 |
+| [Stack Exchange](https://huggingface.co/datasets/flax-sentence-embeddings/stackexchange_xml) (Title, Answer) pairs  | - | 21,396,559 |
+| [MS MARCO](https://microsoft.github.io/msmarco/) triplets | [paper](https://doi.org/10.1145/3404835.3462804) | 9,144,553 |
+| [GOOAQ: Open Question Answering with Diverse Answer Types](https://github.com/allenai/gooaq) | [paper](https://arxiv.org/pdf/2104.08727.pdf) | 3,012,496 |
+| [Yahoo Answers](https://www.kaggle.com/soumikrakshit/yahoo-answers-dataset) (Title, Answer) | [paper](https://proceedings.neurips.cc/paper/2015/hash/250cf8b51c773f3f8dc8b4be867a9a02-Abstract.html) | 1,198,260 |
+| [Code Search](https://huggingface.co/datasets/code_search_net) | - | 1,151,414 |
+| [COCO](https://cocodataset.org/#home) Image captions | [paper](https://link.springer.com/chapter/10.1007%2F978-3-319-10602-1_48) | 828,395|
+| [SPECTER](https://github.com/allenai/specter) citation triplets | [paper](https://doi.org/10.18653/v1/2020.acl-main.207) | 684,100 |
+| [Yahoo Answers](https://www.kaggle.com/soumikrakshit/yahoo-answers-dataset) (Question, Answer) | [paper](https://proceedings.neurips.cc/paper/2015/hash/250cf8b51c773f3f8dc8b4be867a9a02-Abstract.html) | 681,164 |
+| [Yahoo Answers](https://www.kaggle.com/soumikrakshit/yahoo-answers-dataset) (Title, Question) | [paper](https://proceedings.neurips.cc/paper/2015/hash/250cf8b51c773f3f8dc8b4be867a9a02-Abstract.html) | 659,896 |
+| [SearchQA](https://huggingface.co/datasets/search_qa) | [paper](https://arxiv.org/abs/1704.05179) | 582,261 |
+| [Eli5](https://huggingface.co/datasets/eli5) | [paper](https://doi.org/10.18653/v1/p19-1346) | 325,475 |
+| [Flickr 30k](https://shannon.cs.illinois.edu/DenotationGraph/) | [paper](https://transacl.org/ojs/index.php/tacl/article/view/229/33) | 317,695 |
+| [Stack Exchange](https://huggingface.co/datasets/flax-sentence-embeddings/stackexchange_xml) Duplicate questions (titles) | | 304,525 |
+| AllNLI ([SNLI](https://nlp.stanford.edu/projects/snli/) and [MultiNLI](https://cims.nyu.edu/~sbowman/multinli/) | [paper SNLI](https://doi.org/10.18653/v1/d15-1075), [paper MultiNLI](https://doi.org/10.18653/v1/n18-1101) | 277,230 | 
+| [Stack Exchange](https://huggingface.co/datasets/flax-sentence-embeddings/stackexchange_xml) Duplicate questions (bodies) | | 250,519 |
+| [Stack Exchange](https://huggingface.co/datasets/flax-sentence-embeddings/stackexchange_xml) Duplicate questions (titles+bodies) | | 250,460 |
+| [Sentence Compression](https://github.com/google-research-datasets/sentence-compression) | [paper](https://www.aclweb.org/anthology/D13-1155/) | 180,000 |
+| [Wikihow](https://github.com/pvl/wikihow_pairs_dataset) | [paper](https://arxiv.org/abs/1810.09305) | 128,542 |
+| [Altlex](https://github.com/chridey/altlex/) | [paper](https://aclanthology.org/P16-1135.pdf) | 112,696 |
+| [Quora Question Triplets](https://quoradata.quora.com/First-Quora-Dataset-Release-Question-Pairs) | - | 103,663 |
+| [Simple Wikipedia](https://cs.pomona.edu/~dkauchak/simplification/) | [paper](https://www.aclweb.org/anthology/P11-2117/) | 102,225 |
+| [Natural Questions (NQ)](https://ai.google.com/research/NaturalQuestions) | [paper](https://transacl.org/ojs/index.php/tacl/article/view/1455) | 100,231 |
+| [SQuAD2.0](https://rajpurkar.github.io/SQuAD-explorer/) | [paper](https://aclanthology.org/P18-2124.pdf) | 87,599 |
+| [TriviaQA](https://huggingface.co/datasets/trivia_qa) | - | 73,346 |
+| **Total** | | **1,170,060,424** |

config.json

@@ -0,0 +1,24 @@
+{
+  "_name_or_path": "sentence-transformers/all-mpnet-base-v2",
+  "architectures": [
+    "MPNetModel"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "bos_token_id": 0,
+  "eos_token_id": 2,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "layer_norm_eps": 1e-05,
+  "max_position_embeddings": 514,
+  "model_type": "mpnet",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 1,
+  "relative_attention_num_buckets": 32,
+  "torch_dtype": "float32",
+  "transformers_version": "4.49.0",
+  "vocab_size": 30527
+}

config_sentence_transformers.json

@@ -0,0 +1,10 @@
+{
+  "__version__": {
+    "sentence_transformers": "3.4.1",
+    "transformers": "4.49.0",
+    "pytorch": "2.5.1+cu121"
+  },
+  "prompts": {},
+  "default_prompt_name": null,
+  "similarity_fn_name": "cosine"
+}

logreg.onnx

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:230d0aefb15e70adfb0ba47d1570b1b960c11cf62c21b35db2d07a35ec72f296
+size 8303

model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0b3c8c717335c801abb15983036a6f1df4b6943fd6b93717969efd96d22eeec6
+size 437967672

modules.json

@@ -0,0 +1,20 @@
+[
+  {
+    "idx": 0,
+    "name": "0",
+    "path": "",
+    "type": "sentence_transformers.models.Transformer"
+  },
+  {
+    "idx": 1,
+    "name": "1",
+    "path": "1_Pooling",
+    "type": "sentence_transformers.models.Pooling"
+  },
+  {
+    "idx": 2,
+    "name": "2",
+    "path": "2_Normalize",
+    "type": "sentence_transformers.models.Normalize"
+  }
+]

sentence_bert_config.json

@@ -0,0 +1,4 @@
+{
+  "max_seq_length": 384,
+  "do_lower_case": false
+}

special_tokens_map.json

@@ -0,0 +1,51 @@
+{
+  "bos_token": {
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "cls_token": {
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "eos_token": {
+    "content": "</s>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "mask_token": {
+    "content": "<mask>",
+    "lstrip": true,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "pad_token": {
+    "content": "<pad>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "sep_token": {
+    "content": "</s>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "unk_token": {
+    "content": "[UNK]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  }
+}

tokenizer_config.json

@@ -0,0 +1,73 @@
+{
+  "added_tokens_decoder": {
+    "0": {
+      "content": "<s>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "1": {
+      "content": "<pad>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "2": {
+      "content": "</s>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "3": {
+      "content": "<unk>",
+      "lstrip": false,
+      "normalized": true,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "104": {
+      "content": "[UNK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "30526": {
+      "content": "<mask>",
+      "lstrip": true,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "bos_token": "<s>",
+  "clean_up_tokenization_spaces": false,
+  "cls_token": "<s>",
+  "do_lower_case": true,
+  "eos_token": "</s>",
+  "extra_special_tokens": {},
+  "mask_token": "<mask>",
+  "max_length": 128,
+  "model_max_length": 384,
+  "pad_to_multiple_of": null,
+  "pad_token": "<pad>",
+  "pad_token_type_id": 0,
+  "padding_side": "right",
+  "sep_token": "</s>",
+  "stride": 0,
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "MPNetTokenizer",
+  "truncation_side": "right",
+  "truncation_strategy": "longest_first",
+  "unk_token": "[UNK]"
+}