trove | Weakly supervised medical named entity classification | Natural Language Processing library
kandi X-RAY | trove Summary
kandi X-RAY | trove Summary
Trove is a research framework for building weakly supervised (bio)medical named entity recognition (NER) and other entity attribute classifiers without hand-labeled training data. The COVID-19 pandemic has underlined the need for faster, more flexible ways of building and sharing state-of-the-art NLP/NLU tools to analyze electronic health records, scientific literature, and social media. Likewise, recent research into language modeling and the dangers of uncurated, "unfathomably" large-scale training data underlines the broader need to approach training set creation itself with more transparency and rigour. Trove provides tools for combining freely available supervision sources such as medical ontologies from the Unified Medical Language System (UMLS), common text heuristics, and other noisy labeling sources for use as entity labelers in weak supervision frameworks such as Snorkel, FlyingSquid and others. Technical details are available in our manuscript. Trove has been used as part of several COVID-19 reseach efforts at Stanford.
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Top functions reviewed by kandi - BETA
- Compute the LFs for a given set of train sentences
- Tokenize a text
- Build a word graph from a dictionary
- Compile the matrix
- Perform grid search
- Prints the scores for the given counts
- Compute the score for each candidate
- Compute the LFs for the given train sentences
- Add gold and predicates
- Build token match regex pattern
- Load Terminologies
- Get the annotations for the training set
- Load the ARAM database
- Loads the words from the file
- Return the LF text for the given span
- Return the contextual context for a given span
- Compile matrices
- Tag a document
- Load a json - formatted text dataset
- Applies filter filters
- Perform a grid search over a network
- Compute the LFs of train_sentences
- Convert annotations to a list of spans
- Convert a list of entities to tags
- Computes the ctbd rules from a docstring
- Tag a given document
- Return whether a label is in the given span
trove Key Features
trove Examples and Code Snippets
Lines of Code : 9License : Permissive (Apache-2.0)
Copy@article{fries2021trove,
title={Ontology-driven weak supervision for clinical entity classification in electronic health records},
author={Fries, Jason A and Steinberg, Ethan and Khattar, Saelig and Fleming, Scott L and Posada, Jose and Callahan, Community Discussions
Trending Discussions on trove
QUESTION
currently I am working on a java project that uses the repast java library (repast.jar, colt.jar and trove.jar). The project works fine with jdk-11, but currently, I am trying to migrate to jdk-17 and I am not able to run the project because of the next exception:
...ANSWER
Answered 2021-Dec-25 at 00:33Yea ...
The Tea / Trove project is ancient code that hasn't been maintained by the original developers (Disney Corp!). There is fork on Github at https://github.com/teatrove/teatrove ... but that has had no activity since 2013 either. Not promising.
As to your problem. Well it seems that the original designers decided to make the org.teatrove.trove.classfile.Modifiers a subclass of java.lang.reflect.Modifier.
The problem is that Modifier used to have a default public constructor ... but in Java 14 they deprecated this constructor (javadoc). In Java 17 there is now a private no-args constructor. That means that when Trove attempts to create a Modifiers instance on Java 17, it fails with a binary compatibility error.
One way to solve this would be to modify Trove so that Modifiers is no longer a subclass of Modifier. I don't know how feasible that would be. The feasibility will depend on whether the codebase makes use of the fact that Modifiers is a subtype of Modifier. That would be for you to investigate ...
If you take this approach, be a good citizen and submit your changes as a pull request against the "TeaTrove" codebase on Github.
Another approach would be to look for a replacement for the Trove dependency in your application. Again, without knowing how / why you are using Trove, it is difficult to suggest an alternative.
Your application's dependency may be due to your using an old version of Repast. I can't find any information on old Repast versions ... but this suggests another approach would be to upgrade to a newer Repast version that (hopefully1) avoids the Trove dependency.
Finally, given that the Repast developers still recommend Java 11 for the most recent versions of Repast, you could just stick with that.
1 - The Repast codebase doesn't use a modern build tool like Maven or Gradle that take a declarative approach to dependencies2. Instead they have snarfed copies of the dependency JARs and put them into their source repo. This makes dependency analysis difficult.
2 - See https://github.com/Repast/repast.simphony/issues/4
QUESTION
I seem to be having an intermittent issue with Android Studio upon carrying out a Gradle Sync.
I am running Android Studio 4.1.3 with Gradle 6.8.3 on Windows. Changing the Gradle version seems to make no difference.
In the Sync output window, the following appears:
Unable to load class 'org.jetbrains.kotlin.gradle.KotlinDslScriptModelProvider'. This is an unexpected error. Please file a bug containing the idea.log file.
Pressing the Gradle Sync button multiple times sometimes causes the class name to change, I have noticed the following class names appear:
org.jetbrains.kotlin.noarg.ide.NoArgModelorg.jetbrains.kotlin.gradle.KotlinMPPGradleModelorg.jetbrains.kotlin.samWithReceiver.ide.SamWithReceiverModelorg.jetbrains.kotlin.allopen.ide.AllOpenModelorg.jetbrains.kotlin.gradle.KotlinGradleModel
I have attempted multiple things to attempt to rectify this, including attempting to completely re-install Android Studio.
I have included the last sync from the "idea.log" file.
Many Thanks.
...ANSWER
Answered 2021-Apr-21 at 12:26Running Android Studio as an Administrator seems to have fixed this issue for the time being, I'm assuming there must be some extra required permissions that seem to be granted by using an administrator session.
Thanks.
QUESTION
I'm working on a text-based game where the player had to find 6 items in different rooms before running into the boss or they die. I have the items set in the dict with the rooms but I don't know how to pull from it as the player moves around. What I have currently have has the player able to add things to the inventory but then it's stuck in a permanent loop. I am very new at this and I am having trouble connecting things together. Here is the whole thing with comments.
...ANSWER
Answered 2020-Dec-06 at 04:19If each room only has one item, I think that the following line in the game() function should be removed
QUESTION
So thanks to another person here I got the movement working but now I'm not sure how to incorporate the items I put into the dictionary into a way where the player can see that the item is in the room and can get it. Or check the final room that has the boss. if they get to the final room before having all 6 items then they die! Here is the code and how would I go about doing it?
...ANSWER
Answered 2020-Dec-06 at 02:19i think you just need to browse the dic like this:
QUESTION
I have to make a text based game for a final project. The goal is to pick up 6 items and to move from room to room. I'm still very new at this and would like some help! I can't seem to call the functions and I don't know how to add an inventory. Here is my current code:
...ANSWER
Answered 2020-Dec-04 at 23:14This is not the final answer but I wanted to show you the changes you can make to the code to get the program to work.
This is just restructuring your code. It is not the solution. Once we understand what the problem is, I can help add to this to solve for it.
QUESTION
I'm using python3 on Ubuntu 20.04.
I have a trove of files with naive datetime strings in them, dating back more than 20 years. I know that all of these datetimes are in the Pacific Timezone. I would like to convert them all to UTC datetimes.
However, whether they are relative to PDT or PST is a bigger question. Since when PDT/PST changes has changed over the last 20 years, it's not just a matter of doing a simple date/month threshold to figure out whether to apply the pdt or pst timezone. Is there an elegant way to make this determination and apply it?
...ANSWER
Answered 2020-Jun-26 at 07:02Here's what you can to do set the timezone and convert to UTC. dateutil will take DST changes from the IANA database.
QUESTION
I am creating a python 3.7.2 package that I am then installing in different location, inside a virtualenv to use in an application. My package has multiple modules with dependencies (imports) between them. I can't figure out how to get the package to load correctly so that I can use the dependent modules in the package.
Package directory
...ANSWER
Answered 2020-Mar-10 at 19:51Please try to import it as below ...
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