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Medical Transcription Analysis (MTA) demonstrates how the integration of Amazon Comprehend Medical and Amazon Transcribe Medical can be used to transcribe audio data, extract key medical components and tag the data to their corresponding entities. Automating the medical transcription and comprehension process makes it easier for health care professionals to focus on patient care.

License: MIT No Attribution

HTML 0.57% CSS 8.39% JavaScript 48.79% TypeScript 6.59% Shell 0.07% Python 28.21% SCSS 7.38%

aws healthcare amazon-transcribe amazon-comprehend-medical

medical-transcription-analysis's Introduction

Medical Transcription Analysis

Medical Transcription Analysis (MTA) is a simple solution that leverages the powers of Amazon Transcribe Medical and Amazon Comprehend Medical to provide medical notes transcription and comprehension. The solution opens a WebSocket between the client (browser) and Amazon Transcribe Medical. This WebSocket is used to send the audio from the client to Amazon Transcribe Medical and retrieve real time transcription which is then rendered on the UI. The transcribed results are then sent to Amazon Comprehend Medical which returns an analysis of the transcription.

Checkout our AWS Blog here : https://aws.amazon.com/blogs/machine-learning/performing-medical-transcription-analysis-with-amazon-transcribe-medical-and-amazon-comprehend-medical/

To run the solution, clone/download the project. To deploy the solution follow the steps below:

Deployment

The instructions below cover installation on Unix-based Operating systems like macOS and Linux. You can use an AWS Cloud9 enviornment or EC2 instance (recommended: t3.large or higher on Amazon Linux platform) to deploy the solution

Requirements

yarn (You can install yarn by following instructions here)
node 10+ (You can install nodejs by following the instructions here)
aws cli (You can install aws cli by following the instructions here)
tsc (npm install typescript)
Google Chrome web browser

If you have not already, configure the aws cli to interact with AWS services using aws configure . To deploy using this approach, you must first set a few values inside the package.json file in the app folder.

Set your AWS deployment region in the stack->region property, replacing "%%REGION%%".

Note MTA is supported in AWS Regions where Amazon Transcribe Medical and Amazon Comprehend Medical are available. For more information, check out the AWS Region Table

Enter your email into the email property, replacing "%%USER_EMAIL%%"

Now switch to the app directory, and use yarn to deploy the solution:

cd ./app

yarn && yarn deploy

Note:

This deployment creates 2 S3 buckets that will have to be deleted manually when the stack is destroyed. (Cloudformation does not delete them, in order to avoid data loss).

1 for the client bucket
1 for CDK toolkit (if this is your first time using CDK)

Deploy Commands

yarn deploy:backend: deploys the backend app
yarn deploy:client: deploys or updates the client web app
yarn build-app: builds the react app
yarn start: allows development of the web app locally.
yarn destroy: destroys the backend and client stacks

Additional Notes

Sample Data

MTA has pre-loaded audio sample files. These samples were synthesized using data from MTSamples.com

Offline Mode

MTA comes with an offline mode built in. This mode is useful for cases when presenting the capabilities of Amazon Transcribe Medical and Amazon Comprehend Medical in situations with internet connectivity issues. To display offline mode options, press the Shift key thrice while on the webpage.

Amazon Transcribe Medical Demo

This solution was built over components from the amazon-transcribe-medical-demo

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medical-transcription-analysis's Issues

NodeJS12.x no longer supported

Resource handler returned message: "The runtime parameter of nodejs12.x is no longer supported for creating or updating AWS Lambda functions. We recommend you use the new runtime (nodejs18.x) while creating or updating functions. (Service: Lambda, Status Code: 400, Request ID: a69c7ccc-989d-4881-9aa1-af558e228efe)" (RequestToken: 864b2930-449b-c86b-d064-c4472350398b, HandlerErrorCode: InvalidRequest)

How to fix the code to upgrade to 18x? Tried updating all the places where 12x to 19x but MTAStack still creates a template as 12x.

4:04 AM MTAStack failed: Error: The stack named MTAStack failed creation, it may need to be manually deleted from the AWS console: ROLLBACK_COMPLETE

@alexchirayath Even after updating the nodejs to the latest version still getting the following issue/error, Please help

MTAStack failed: Error: The stack named MTAStack failed creation, it may need to be manually deleted from the AWS console: ROLLBACK_COMPLETE
at Object.waitForStackDeploy (/home/fawad/medical-transcription-analysis/app/node_modules/aws-cdk/lib/api/util/cloudformation.ts:307:11)
at processTicksAndRejections (node:internal/process/task_queues:96:5)
at prepareAndExecuteChangeSet (/home/fawad/medical-transcription-analysis/app/node_modules/aws-cdk/lib/api/deploy-stack.ts:337:26)
at CdkToolkit.deploy (/home/fawad/medical-transcription-analysis/app/node_modules/aws-cdk/lib/cdk-toolkit.ts:194:24)
at initCommandLine (/home/fawad/medical-transcription-analysis/app/node_modules/aws-cdk/bin/cdk.ts:267:9)
The stack named MTAStack failed creation, it may need to be manually deleted from the AWS console: ROLLBACK_COMPLETE
Error: The stack named MTAStack failed creation, it may need to be manually deleted from the AWS console: ROLLBACK_COMPLETE
at Object.waitForStackDeploy (/home/fawad/medical-transcription-analysis/app/node_modules/aws-cdk/lib/api/util/cloudformation.ts:307:11)
at processTicksAndRejections (node:internal/process/task_queues:96:5)
at prepareAndExecuteChangeSet (/home/fawad/medical-transcription-analysis/app/node_modules/aws-cdk/lib/api/deploy-stack.ts:337:26)
at CdkToolkit.deploy (/home/fawad/medical-transcription-analysis/app/node_modules/aws-cdk/lib/cdk-toolkit.ts:194:24)
at initCommandLine (/home/fawad/medical-transcription-analysis/app/node_modules/aws-cdk/bin/cdk.ts:267:9)
error Command failed with exit code 1.
info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command.

yarn deploy error

Encountered below error when running below command in mac as well as cloud9
yarn && yarn deploy

no credentials

I recently depolyed this but did not get an email with credentials. Any solution?

Stack fails to create due to Lambda runtime error

The stack includes a Lambda function with Node 10x, which is no longer supported for new functions. See https://docs.aws.amazon.com/lambda/latest/dg/runtime-support-policy.html. The error received when deploying the stack is The runtime parameter of nodejs10.x is no longer supported for creating or updating AWS Lambda functions. We recommend you use the new runtime (nodejs14.x) while creating or updating functions

Module not found: Error: Can't resolve 'fs' in ...

Encountered below error while trying to deploy it

Getting the error "ERROR Request has expired"

[Deprecation] The ScriptProcessorNode is deprecated. Use AudioWorkletNode instead. (https://bit.ly/audio-worklet)

ERROR Request has expired

When I click on "Automated note-taking", I am getting error as

[Deprecation] The ScriptProcessorNode is deprecated. Use AudioWorkletNode instead. (https://bit.ly/audio-worklet)

ERROR Request has expired

The stack is getting installed properly.

When I am using existing MT samples it does not analyze the data. Please have a look at the below screenshot.

Please let me know what wrong I am doing. Thank you.