llsourcell/how-to-build-a-biomedical-startup

This is the code for "How to Build a Biomedical Startup" by Siraj Raval on Youtube

Overview

This is the code for this video on Youtube by Siraj Raval on how to build a biomedical startup. I basically saw these Colab demos of this BioBERT model answering medical questions pretty acurately and got hype. I thought, why not apply this type of interface to that as a backend, paywall it, and hey! You've got yourself a business, serving the underserved st scale at a very low cost. This app works, but there are still TODOs, i'll list them below.

Usage

Install flutter. Then, install all dependencies and run using these commands. I prefer running it using Android Studio, but terminal works too.

flutter packages get
flutter run

📺 Video demo

TODOs - Make a PR if you fix any

• Take the model here and integrate it into the app. My previous healthcare app nicely integrated tensorflow lite.
• Parse the input using keyword recognition. You can use an existing API like this to categorize words as symptoms, medications, or side effects. Train a new model on a health dataset for the most accuracy, have it learn to classify those 3 keywords from a given corpus. Once the input is parsed properly into those categories, it can be fed into the existing model.
• Finish Integrating Firebase
• Finish Integrating Payments

Credits

rxlabs and the Doc Product team. Also the Flutter team.

how-to-build-a-biomedical-startup's Issues

issue with converting the model from colab to tf.keras h5 model?

It seems alot of people have been struggling with this, so I am posting this here as well in case anyone had any luck with this.
re-search/DocProduct#6
I tried to save the model with this code:

`from docproduct.models import MedicalQAModelwithBert

medical_qa_model = MedicalQAModelwithBert(
config_file=os.path.join(
pretrained_path, 'bert_config.json'),
checkpoint_file=os.path.join(pretrained_path, 'biobert_model.ckpt'))

medical_qa_model.save("model.h5")`

i am getting this error which suggest save_weights but in this case it doesnt work since we cant convert it to tflite later.

NotImplementedError: The savemethod requires the model to be a Functional model or a Sequential model. It does not work for subclassed models, because such models are defined via the body of a Python method, which isn't safely serializable. Consider usingsave_weights, in order to save the weights of the model.

Any one managed to save the h5?

The model won't run on windows platform

I tried to run the model in original repository DocProduct on windows platform but the predict.py file has an import called faiss which isn't supported on windows right now. What can we do about it? Any ideas? Also if anyone can actually run the model then please shed some light! thanks.

Notebook is not loading

Could not find method google() for arguments [] on repository container.

Getting the following error when I download and run the project without any changes:

* Error running Gradle:
ProcessException: Process "/home/abhijeet/Documents/android/How-to-Build-a-Biomedical-Startup-master/android/gradlew" exited abnormally:
Starting a Gradle Daemon, 1 busy Daemon could not be reused, use --status for details
NDK is missing a "platforms" directory.
If you are using NDK, verify the ndk.dir is set to a valid NDK directory.  It is currently set to /home/abhijeet/Android/Sdk/ndk-bundle.
If you are not using NDK, unset the NDK variable from ANDROID_NDK_HOME or local.properties to remove this warning.


BUILD FAILED

Total time: 13.22 secs

Failed to notify ProjectEvaluationListener.afterEvaluate(), but primary configuration failure takes precedence.
java.lang.IllegalStateException: buildToolsVersion is not specified.
	at com.google.common.base.Preconditions.checkState(Preconditions.java:173)
	at com.android.build.gradle.BasePlugin.createAndroidTasks(BasePlugin.java:558)
	at com.android.build.gradle.BasePlugin.lambda$null$4(BasePlugin.java:526)
	at com.android.builder.profile.ThreadRecorder.record(ThreadRecorder.java:81)
	at com.android.build.gradle.BasePlugin.lambda$createTasks$5(BasePlugin.java:522)
	at org.gradle.internal.event.BroadcastDispatch$ActionInvocationHandler.dispatch(BroadcastDispatch.java:93)
	at org.gradle.internal.event.BroadcastDispatch$ActionInvocationHandler.dispatch(BroadcastDispatch.java:82)
	at org.gradle.internal.event.AbstractBroadcastDispatch.dispatch(AbstractBroadcastDispatch.java:44)
	at org.gradle.internal.event.BroadcastDispatch.dispatch(BroadcastDispatch.java:79)
	at org.gradle.internal.event.BroadcastDispatch.dispatch(BroadcastDispatch.java:30)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)
	at com.sun.proxy.$Proxy15.afterEvaluate(Unknown Source)
	at org.gradle.configuration.project.LifecycleProjectEvaluator.notifyAfterEvaluate(LifecycleProjectEvaluator.java:82)
	at org.gradle.configuration.project.LifecycleProjectEvaluator.doConfigure(LifecycleProjectEvaluator.java:76)
	at org.gradle.configuration.project.LifecycleProjectEvaluator.access$000(LifecycleProjectEvaluator.java:33)
	at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:53)
	at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:50)
	at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:61)
	at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:50)
	at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:628)
	at org.gradle.api.internal.project.DefaultProject.evaluationDependsOn(DefaultProject.java:699)
	at org.gradle.api.internal.project.DefaultProject.evaluationDependsOn(DefaultProject.java:691)
	at org.gradle.api.Project$evaluationDependsOn.call(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
	at build_8p2bt6iwt7p7payeevg09dhee$_run_closure2.doCall(/home/abhijeet/Documents/android/How-to-Build-a-Biomedical-Startup-master/android/build.gradle:20)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
	at groovy.lang.Closure.call(Closure.java:414)
	at groovy.lang.Closure.call(Closure.java:430)
	at org.gradle.api.internal.ClosureBackedAction.execute(ClosureBackedAction.java:70)
	at org.gradle.util.ConfigureUtil.configureTarget(ConfigureUtil.java:160)
	at org.gradle.util.ConfigureUtil.configure(ConfigureUtil.java:106)
	at org.gradle.api.internal.project.DefaultProject.configure(DefaultProject.java:983)
	at org.gradle.api.internal.project.DefaultProject.configure(DefaultProject.java:988)
	at org.gradle.api.internal.project.DefaultProject.subprojects(DefaultProject.java:971)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at org.gradle.internal.metaobject.BeanDynamicObject$MetaClassAdapter.invokeMethod(BeanDynamicObject.java:382)
	at org.gradle.internal.metaobject.BeanDynamicObject.invokeMethod(BeanDynamicObject.java:170)
	at org.gradle.internal.metaobject.CompositeDynamicObject.invokeMethod(CompositeDynamicObject.java:96)
	at org.gradle.internal.metaobject.MixInClosurePropertiesAsMethodsDynamicObject.invokeMethod(MixInClosurePropertiesAsMethodsDynamicObject.java:30)
	at org.gradle.internal.metaobject.AbstractDynamicObject.invokeMethod(AbstractDynamicObject.java:163)
	at org.gradle.groovy.scripts.BasicScript.methodMissing(BasicScript.java:83)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaClassImpl.invokeMissingMethod(MetaClassImpl.java:941)
	at groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1264)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1217)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at build_8p2bt6iwt7p7payeevg09dhee.run(/home/abhijeet/Documents/android/How-to-Build-a-Biomedical-Startup-master/android/build.gradle:18)
	at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90)
	at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl$2.run(DefaultScriptPluginFactory.java:176)
	at org.gradle.configuration.ProjectScriptTarget.addConfiguration(ProjectScriptTarget.java:77)
	at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.apply(DefaultScriptPluginFactory.java:181)
	at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:39)
	at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:26)
	at org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:34)
	at org.gradle.configuration.project.LifecycleProjectEvaluator.doConfigure(LifecycleProjectEvaluator.java:70)
	at org.gradle.configuration.project.LifecycleProjectEvaluator.access$000(LifecycleProjectEvaluator.java:33)
	at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:53)
	at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:50)
	at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:61)
	at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:50)
	at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:628)
	at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:129)
	at org.gradle.execution.TaskPathProjectEvaluator.configure(TaskPathProjectEvaluator.java:35)
	at org.gradle.execution.TaskPathProjectEvaluator.configureHierarchy(TaskPathProjectEvaluator.java:60)
	at org.gradle.configuration.DefaultBuildConfigurer.configure(DefaultBuildConfigurer.java:38)
	at org.gradle.initialization.DefaultGradleLauncher$1.execute(DefaultGradleLauncher.java:161)
	at org.gradle.initialization.DefaultGradleLauncher$1.execute(DefaultGradleLauncher.java:158)
	at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
	at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:56)
	at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:158)
	at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:119)
	at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:102)
	at org.gradle.launcher.exec.GradleBuildController.run(GradleBuildController.java:71)
	at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
Finished with error: Please review your Gradle project setup in the android/ folder.
	at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
	at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:41)
	at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:26)
	at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:75)
	at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:49)
	at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:44)
	at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:29)
	at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67)
	at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
	at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:47)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
	at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
	at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
	at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74)
	at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72)
	at org.gradle.util.Swapper.swap(Swapper.java:38)
	at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
	at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:55)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
	at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:60)
	at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
	at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:72)
	at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
	at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
	at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50)
	at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:297)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
	at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

FAILURE: Build failed with an exception.

* Where:
Script '/home/abhijeet/softwares/flutter/packages/flutter_tools/gradle/flutter.gradle' line: 27

* What went wrong:
A problem occurred evaluating script.
> Could not find method google() for arguments [] on repository container.

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
  Command: /home/abhijeet/Documents/android/How-to-Build-a-Biomedical-Startup-master/android/gradlew app:properties

I believe it might be related to an old Flutter version as discussed in this issue.

@llSourcell This guide indicates that the project files might be outdated and regenerating them may fix the issue, but custom changes will be lost and need to be reapplied. I tried that and that app ran but the voice button is not working. Can you please list out the custom changes to be added in the android folder?

This issue seems to be originating from the base repo. I've raised an issue there too with the same error.

Software

• Flutter 1.9.1+hotfix.2
• Dart 2.5.0
• Java(TM) SE Runtime Environment (build 9.0.4+11)

Dependencies Error

I keep getting this error when I try to run this project: "Cannot change dependencies of configuration ':app:debugCompile' after it has been included in dependency resolution."

How to integrate Colab DotProduct model into Fultter app