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app.py
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> `TransCheX` model consists of vision, language, and mixed-modality transformer layers for processing chest X-ray and their corresponding radiological reports within a unified framework.
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I modified the architecture by varying the number of vision, language and mixed-modality layers and customizing the classification head. In addition, I added image preprocessing and more language processing modules.
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Finally, the model is pre-trained on the Open-I dataset and fine-tuned on modified and relabeled [SIIM-FISABIO-RSNA COVID-19 Detection](https://www.kaggle.com/competitions/siim-covid19-detection/data) and [VinBigData Chest X-ray Abnormalities Detection ](https://www.kaggle.com/competitions/vinbigdata-chest-xray-abnormalities-detection/data).
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## Components
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- [scikit-image: Image processing in Python](https://scikit-image.org/): is a collection of algorithms for image processing. I used this module for all the image preprocessing.
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- [gradio](https://github.com/gradio-app/gradio): is an open-source Python library that is used to build machine learning and data science demos and web applications. This demo is created by gradio.
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- [Modal](https://modal.com/): is a end to end stack for cloud compute. This is used to deploy the model-service for subsequent fine-tuning on more datasets.
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## Dataset
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The Open-I dataset provides a collection of 3,996 radiology reports with 8,121 associated images in PA, AP and lateral views. The 14 finding categories in this work include Atelectasis, Cardiomegaly, Consolidation, Edema, Enlarged-Cardiomediastinum, Fracture, Lung-Lesion, Lung-Opacity, No-Finding, Pleural-Effusion, Pleural-Other, Pneumonia, Pneumothorax and Support-Devices. More information can be found in this [link](https://openi.nlm.nih.gov/faq)
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model_predict,
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cache_examples=True,
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)
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iface.launch()
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> `TransCheX` model consists of vision, language, and mixed-modality transformer layers for processing chest X-ray and their corresponding radiological reports within a unified framework.
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I modified the architecture by varying the number of vision, language and mixed-modality layers and customizing the classification head. In addition, I added image preprocessing and more language processing modules.
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Finally, the model is pre-trained on the Open-I dataset and fine-tuned on modified and relabeled [SIIM-FISABIO-RSNA COVID-19 Detection](https://www.kaggle.com/competitions/siim-covid19-detection/data) and [VinBigData Chest X-ray Abnormalities Detection ](https://www.kaggle.com/competitions/vinbigdata-chest-xray-abnormalities-detection/data).
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## Components
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- [scikit-image: Image processing in Python](https://scikit-image.org/): is a collection of algorithms for image processing. I used this module for all the image preprocessing.
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- [gradio](https://github.com/gradio-app/gradio): is an open-source Python library that is used to build machine learning and data science demos and web applications. This demo is created by gradio.
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- [Modal](https://modal.com/): is a end to end stack for cloud compute. This is used to deploy the model-service for subsequent fine-tuning on more datasets.
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- [mage-ai/mage-ai: 🧙 A modern replacement for Airflow.](https://github.com/mage-ai/mage-ai) is a tool to build real-time and batch pipelines to **transform** data using Python, SQL, and R. Run, monitor, and **orchestrate** thousands of pipelines without losing sleep. I'm using this tool to build an online data processing pipeline.
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## Dataset
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The Open-I dataset provides a collection of 3,996 radiology reports with 8,121 associated images in PA, AP and lateral views. The 14 finding categories in this work include Atelectasis, Cardiomegaly, Consolidation, Edema, Enlarged-Cardiomediastinum, Fracture, Lung-Lesion, Lung-Opacity, No-Finding, Pleural-Effusion, Pleural-Other, Pneumonia, Pneumothorax and Support-Devices. More information can be found in this [link](https://openi.nlm.nih.gov/faq)
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model_predict,
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cache_examples=True,
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)
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gr.Markdown(
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"""## Todo/Doing
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- TODO -- Fine-tuning on more datasets
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- Doing -- Add the object detection model, plan to use yolov5
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- Doing -- Build an online machine learning pipeline
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"""
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)
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iface.launch()
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