har1/HealthScribe-Clinical_Note_Generator

HealthScribe (A Clinical Note Generator)

This model is a fine-tuned version of facebook/bart-large-cnn on a modified version of MTS-Dialog Dataset dataset.

Model description

The model was developed for the project HealthScirbe. This model is integrated with a Flask web application. The project is a web application that allows users to generate clinical notes from transcribed ASR(Automatic Speech Recognition) data of conversations between doctors and patients.

TEST DATA Sample For Inference (More given in test.txt)

You can refer test.txt for further examples of conversations.

"Doctor: Hi there, I love that dress, very pretty! 
Patient: Thank you for complementing a seventy-two-year-old patient.
Doctor: No, I mean it, seriously. Okay, so you were admitted here in May two thousand nine. You have a history of hypertension, and on June eighteenth two thousand nine you had bad abdominal pain diarrhea and cramps.
Patient: Yes, they told me I might have C Diff? They did a CT of my abdomen and that is when they thought I got the infection.
Doctor: Yes, it showed evidence of diffuse colitis, so I believe they gave you IV antibiotics?
Patient: Yes they did. 
Doctor: Yeah I see here, Flagyl and Levaquin. They started IV Reglan as well for your vomiting.
Patient: Yes, I was very nauseous. Vomited as well.
Doctor: After all this I still see your white blood cells high. Are you still nauseous? 
Patient: No, I do not have any nausea or vomiting, but still have diarrhea. Due to all that diarrhea I feel very weak.
Doctor: Okay. Anything else any other symptoms?
Patient: Actually no. Everything's well.
Doctor: Great.
Patient: Yeah."

Intended uses & limitations

The model is used to generate clinical notes from doctor-patient conversation data(ASR). This model has certain limitations like :

• N/A output generation is low. Sometimes None is produced
• When the input data is composed of very minimal character tokens or if input is very large it starts to hallucinate.

Training Metrics

Training and evaluation data

The model achieves the following results on the evaluation set:

• Loss: 0.1562
• Rouge1: 54.3238
• Rouge2: 34.2678
• Rougel: 46.5847
• Rougelsum: 51.2214
• Generation Length: 77.04

Training procedure

The model was trained on 1201 training samples and 100 validation samples of the modified MTS-Dialog

Training hyperparameters

The following hyperparameters were used during training:

• learning_rate: 2e-05
• train_batch_size: 1
• eval_batch_size: 1
• seed: 42
• gradient_accumulation_steps: 2
• total_train_batch_size: 2
• optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
• lr_scheduler_type: linear
• num_epochs: 3
• mixed_precision_training: Native AMP

Training results

Training Loss	Epoch	Step	Validation Loss	Rouge1	Rouge2	Rougel	Rougelsum	Gen Len
0.4426	1.0	600	0.1588	52.8864	33.253	44.9089	50.5072	69.38
0.1137	2.0	1201	0.1517	56.8499	35.309	48.2171	53.6983	72.74
0.0796	3.0	1800	0.1562	54.3238	34.2678	46.5847	51.2214	77.04

Framework versions

• Transformers 4.39.2
• Pytorch 2.2.1+cu121
• Datasets 2.18.0
• Tokenizers 0.15.2