ChemSpot | named entity recognition tool | Natural Language Processing library

 by   rockt Java Version: v2.0 License: Non-SPDX

kandi X-RAY | ChemSpot Summary

kandi X-RAY | ChemSpot Summary

ChemSpot is a Java library typically used in Artificial Intelligence, Natural Language Processing applications. ChemSpot has build file available and it has low support. However ChemSpot has 45 bugs, it has 2 vulnerabilities and it has a Non-SPDX License. You can download it from GitHub.

ChemSpot 2.0 is a set of tools for named entity recognition and classification of chemicals in natural language texts, including trivial names, abbreviations, molecular formulas and IUPAC entities. Since the different classes of relevant entities have rather different naming characteristics, ChemSpot uses a combined approach of employing a Conditional Random Field and a dictionary, as well as pattern-based recognition, a classifier model and several methods for consolidating all annotations. ChemSpot also performs named entity normalization by assigning identifiers from several chemical databases. It achieves an F1 measure of 79.0% on the SCAI corpus. ChemSpot is released under the Common Public License 1.0 (see LICENSE). The warning message "Couldn't open cc.mallet.util.MalletLogger resources/logging.properties file." can be ignored.
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            kandi-support Support

              ChemSpot has a low active ecosystem.
              It has 40 star(s) with 9 fork(s). There are 4 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 12 open issues and 20 have been closed. On average issues are closed in 59 days. There are 2 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of ChemSpot is v2.0

            kandi-Quality Quality

              OutlinedDot
              ChemSpot has 45 bugs (26 blocker, 7 critical, 5 major, 7 minor) and 5400 code smells.

            kandi-Security Security

              ChemSpot has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              OutlinedDot
              ChemSpot code analysis shows 2 unresolved vulnerabilities (2 blocker, 0 critical, 0 major, 0 minor).
              There are 43 security hotspots that need review.

            kandi-License License

              ChemSpot has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              ChemSpot releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.
              ChemSpot saves you 18237 person hours of effort in developing the same functionality from scratch.
              It has 36089 lines of code, 3496 functions and 752 files.
              It has medium code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed ChemSpot and discovered the below as its top functions. This is intended to give you an instant insight into ChemSpot implemented functionality, and help decide if they suit your requirements.
            • Performs the processing of a JCas annotation
            • Converts a list of chemical entities to chemical objects
            • Checks if the last entity crosses the last entity
            • Checks if an abbreviation matches an abbreviation
            • Starts the ChemSpotAgent
            • Find mentions in a given JCas object
            • Gets the sentence list
            • Tag collection
            • Converts a cas into training example
            • Load the chebi data
            • Initialize the normalizer
            • Process a CAS
            • Initializes the resources
            • Performs the comparison
            • Initialize the reader
            • Process a JCas object
            • Get the pubmed document from the input
            • Gets the next
            • Process a JCas
            • Writes the prefix and suffix lists
            • Get the source document information
            • Get next document
            • Expands entities
            • Performs the analysis on a JCas
            • Gets the next collection
            • Processes the given JCas object
            Get all kandi verified functions for this library.

            ChemSpot Key Features

            No Key Features are available at this moment for ChemSpot.

            ChemSpot Examples and Code Snippets

            ChemSpot,Using ChemSpot in your Code
            Javadot img1Lines of Code : 10dot img1License : Non-SPDX (NOASSERTION)
            copy iconCopy
            ChemSpot tagger = ChemSpotFactory.createChemSpot("dict.zip", "ids.zip", "multiclass.bin");
            String text = "The abilities of LHRH and a potent LHRH agonist ([D-Ser-(But),6, " +
              "des-Gly-NH210]LHRH ethylamide) inhibit FSH responses by rat " +
              "granu  
            ChemSpot,Running ChemSpot:
            Javadot img2Lines of Code : 6dot img2License : Non-SPDX (NOASSERTION)
            copy iconCopy
            unzip chemspot.zip
            
            java -Xmx16G -jar chemspot.jar -t sample.txt -o predict.txt
            
            java -Xmx5G -jar chemspot.jar -u
            
            java -Xmx12G -jar chemspot.jar -t sample.txt -o predict.txt -i ""
            
            java -Xmx7G -jar chemspot.jar -t sample.txt -o predict.txt -i "" -d   
            ChemSpot,Reproducing our Results
            Javadot img3Lines of Code : 1dot img3License : Non-SPDX (NOASSERTION)
            copy iconCopy
            java -Xmx16G -jar chemspot.jar -c chemicals-test-corpus-27-04-2009-v3.iob.gz -o predict.txt -e
              

            Community Discussions

            QUESTION

            number of matches for keywords in specified categories
            Asked 2022-Apr-14 at 13:32

            For a large scale text analysis problem, I have a data frame containing words that fall into different categories, and a data frame containing a column with strings and (empty) counting columns for each category. I now want to take each individual string, check which of the defined words appear, and count them within the appropriate category.

            As a simplified example, given the two data frames below, i want to count how many of each animal type appear in the text cell.

            ...

            ANSWER

            Answered 2022-Apr-14 at 13:32

            Here's a way do to it in the tidyverse. First look at whether strings in df_texts$text contain animals, then count them and sum by text and type.

            Source https://stackoverflow.com/questions/71871613

            QUESTION

            Apple's Natural Language API returns unexpected results
            Asked 2022-Apr-01 at 20:30

            I'm trying to figure out why Apple's Natural Language API returns unexpected results.

            What am I doing wrong? Is it a grammar issue?

            I have the following four strings, and I want to extract each word's "stem form."

            ...

            ANSWER

            Answered 2022-Apr-01 at 20:30

            As for why the tagger doesn't find "accredit" from "accreditation", this is because the scheme .lemma finds the lemma of words, not actually the stems. See the difference between stem and lemma on Wikipedia.

            The stem is the part of the word that never changes even when morphologically inflected; a lemma is the base form of the word. For example, from "produced", the lemma is "produce", but the stem is "produc-". This is because there are words such as production and producing In linguistic analysis, the stem is defined more generally as the analyzed base form from which all inflected forms can be formed.

            The documentation uses the word "stem", but I do think that the lemma is what is intended here, and getting "accreditation" is the expected behaviour. See the Usage section of the Wikipedia article for "Word stem" for more info. The lemma is the dictionary form of a word, and "accreditation" has a dictionary entry, whereas something like "accredited" doesn't. Whatever you call these things, the point is that there are two distinct concepts, and the tagger gets you one of them, but you are expecting the other one.

            As for why the order of the words matters, this is because the tagger tries to analyse your words as "natural language", rather than each one individually. Naturally, word order matters. If you use .lexicalClass, you'll see that it thinks the third word in text2 is an adjective, which explains why it doesn't think its dictionary form is "accredit", because adjectives don't conjugate like that. Note that accredited is an adjective in the dictionary. So "is it a grammar issue?" Exactly.

            Source https://stackoverflow.com/questions/71711847

            QUESTION

            Tokenize text but keep compund hyphenated words together
            Asked 2022-Mar-29 at 09:16

            I am trying to clean up text using a pre-processing function. I want to remove all non-alpha characters such as punctuation and digits, but I would like to retain compound words that use a dash without splitting them (e.g. pre-tender, pre-construction).

            ...

            ANSWER

            Answered 2022-Mar-29 at 09:14

            To remove all non-alpha characters but - between letters, you can use

            Source https://stackoverflow.com/questions/71659125

            QUESTION

            Create new boolean fields based on specific bigrams appearing in a tokenized pandas dataframe
            Asked 2022-Feb-16 at 20:47

            Looping over a list of bigrams to search for, I need to create a boolean field for each bigram according to whether or not it is present in a tokenized pandas series. And I'd appreciate an upvote if you think this is a good question!

            List of bigrams:

            ...

            ANSWER

            Answered 2022-Feb-16 at 20:28

            You could use a regex and extractall:

            Source https://stackoverflow.com/questions/71147799

            QUESTION

            ModuleNotFoundError: No module named 'milvus'
            Asked 2022-Feb-15 at 19:23

            Goal: to run this Auto Labelling Notebook on AWS SageMaker Jupyter Labs.

            Kernels tried: conda_pytorch_p36, conda_python3, conda_amazonei_mxnet_p27.

            ...

            ANSWER

            Answered 2022-Feb-03 at 09:29

            I would recommend to downgrade your milvus version to a version before the 2.0 release just a week ago. Here is a discussion on that topic: https://github.com/deepset-ai/haystack/issues/2081

            Source https://stackoverflow.com/questions/70954157

            QUESTION

            Which model/technique to use for specific sentence extraction?
            Asked 2022-Feb-08 at 18:35

            I have a dataset of tens of thousands of dialogues / conversations between a customer and customer support. These dialogues, which could be forum posts, or long-winded email conversations, have been hand-annotated to highlight the sentence containing the customers problem. For example:

            Dear agent, I am writing to you because I have a very annoying problem with my washing machine. I bought it three weeks ago and was very happy with it. However, this morning the door does not lock properly. Please help

            Dear customer.... etc

            The highlighted sentence would be:

            However, this morning the door does not lock properly.

            1. What approaches can I take to model this, so that in future I can automatically extract the customers problem? The domain of the datasets are broad, but within the hardware space, so it could be appliances, gadgets, machinery etc.
            2. What is this type of problem called? I thought this might be called "intent recognition", but most guides seem to refer to multiclass classification. The sentence either is or isn't the customers problem. I considered analysing each sentence and performing binary classification, but I'd like to explore options that take into account the context of the rest of the conversation if possible.
            3. What resources are available to research how to implement this in Python (using tensorflow or pytorch)

            I found a model on HuggingFace which has been pre-trained with customer dialogues, and have read the research paper, so I was considering fine-tuning this as a starting point, but I only have experience with text (multiclass/multilabel) classification when it comes to transformers.

            ...

            ANSWER

            Answered 2022-Feb-07 at 10:21

            This type of problem where you want to extract the customer problem from the original text is called Extractive Summarization and this type of task is solved by Sequence2Sequence models.

            The main reason for this type of model being called Sequence2Sequence is because the input and the output of this model would both be text.

            I recommend you to use a transformers model called Pegasus which has been pre-trained to predict a masked text, but its main application is to be fine-tuned for text summarization (extractive or abstractive).

            This Pegasus model is listed on Transformers library, which provides you with a simple but powerful way of fine-tuning transformers with custom datasets. I think this notebook will be extremely useful as guidance and for understanding how to fine-tune this Pegasus model.

            Source https://stackoverflow.com/questions/70990722

            QUESTION

            Assigning True/False if a token is present in a data-frame
            Asked 2022-Jan-06 at 12:38

            My current data-frame is:

            ...

            ANSWER

            Answered 2022-Jan-06 at 12:13

            QUESTION

            How to calculate perplexity of a sentence using huggingface masked language models?
            Asked 2021-Dec-25 at 21:51

            I have several masked language models (mainly Bert, Roberta, Albert, Electra). I also have a dataset of sentences. How can I get the perplexity of each sentence?

            From the huggingface documentation here they mentioned that perplexity "is not well defined for masked language models like BERT", though I still see people somehow calculate it.

            For example in this SO question they calculated it using the function

            ...

            ANSWER

            Answered 2021-Dec-25 at 21:51

            There is a paper Masked Language Model Scoring that explores pseudo-perplexity from masked language models and shows that pseudo-perplexity, while not being theoretically well justified, still performs well for comparing "naturalness" of texts.

            As for the code, your snippet is perfectly correct but for one detail: in recent implementations of Huggingface BERT, masked_lm_labels are renamed to simply labels, to make interfaces of various models more compatible. I have also replaced the hard-coded 103 with the generic tokenizer.mask_token_id. So the snippet below should work:

            Source https://stackoverflow.com/questions/70464428

            QUESTION

            Mapping values from a dictionary's list to a string in Python
            Asked 2021-Dec-21 at 16:45

            I am working on some sentence formation like this:

            ...

            ANSWER

            Answered 2021-Dec-12 at 17:53

            You can first replace the dictionary keys in sentence to {} so that you can easily format a string in loop. Then you can use itertools.product to create the Cartesian product of dictionary.values(), so you can simply loop over it to create your desired sentences.

            Source https://stackoverflow.com/questions/70325758

            QUESTION

            What are differences between AutoModelForSequenceClassification vs AutoModel
            Asked 2021-Dec-05 at 09:07

            We can create a model from AutoModel(TFAutoModel) function:

            ...

            ANSWER

            Answered 2021-Dec-05 at 09:07

            The difference between AutoModel and AutoModelForSequenceClassification model is that AutoModelForSequenceClassification has a classification head on top of the model outputs which can be easily trained with the base model

            Source https://stackoverflow.com/questions/69907682

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install ChemSpot

            You can download it from GitHub.
            You can use ChemSpot like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the ChemSpot component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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