SurfinPy | Thermodynamic Phase Diagram Generator | Topic Modeling library

 by   symmy596 Python Version: 2.0.2 License: MIT

kandi X-RAY | SurfinPy Summary

kandi X-RAY | SurfinPy Summary

SurfinPy is a Python library typically used in Manufacturing, Utilities, Energy, Utilities, Artificial Intelligence, Topic Modeling applications. SurfinPy has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install SurfinPy' or download it from GitHub, PyPI.

This is the documentation for the open-source Python project - surfinpy. A library designed to facilitate the generation of publication ready phase diagrams from ab initio calculations for both surface and bulk materials. surfinpy is built on existing Python packages that those in the solid state physics/chemistry community should already be familiar with. It is hoped that this tool will bring some benfits to the solid state community and facilitate the generation of publication ready phase diagrams (powered by Matplotlib.).
Support
    Quality
      Security
        License
          Reuse

            kandi-support Support

              SurfinPy has a low active ecosystem.
              It has 19 star(s) with 12 fork(s). There are 1 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 5 open issues and 4 have been closed. On average issues are closed in 111 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of SurfinPy is 2.0.2

            kandi-Quality Quality

              SurfinPy has 0 bugs and 59 code smells.

            kandi-Security Security

              SurfinPy has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              SurfinPy code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              SurfinPy is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              SurfinPy releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.
              It has 1323 lines of code, 109 functions and 25 files.
              It has medium code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed SurfinPy and discovered the below as its top functions. This is intended to give you an instant insight into SurfinPy implemented functionality, and help decide if they suit your requirements.
            • Calculate phase bias
            • R Evaluate the phase energy for a given data
            • Normalise the phase energy of a phase
            • Calculate bulk energy
            • Calculate Vib calculations
            • Calculate the zpeptron ze
            • Calculate the zpe and entropy of a file
            • Calculate the entropy
            • Calculate the temperature correction range
            • Fit a cubic spline
            • Calculate the gibbs for a given time
            • Fit a function to a nist file
            Get all kandi verified functions for this library.

            SurfinPy Key Features

            No Key Features are available at this moment for SurfinPy.

            SurfinPy Examples and Code Snippets

            No Code Snippets are available at this moment for SurfinPy.

            Community Discussions

            QUESTION

            TensorFlow word embedding model + LDA Negative values in data passed to LatentDirichletAllocation.fit
            Asked 2022-Feb-24 at 09:31

            I am trying to use a pre-trained model from TensorFlow hub instead of frequency vectorization techniques for word embedding before passing the resultant feature vector to the LDA model.

            I followed the steps for the TensorFlow model, but I got this error upon passing the resultant feature vector to the LDA model:

            ...

            ANSWER

            Answered 2022-Feb-24 at 09:31

            As the fit function of LatentDirichletAllocation does not allow a negative array, I will recommend you to apply softplus on the embeddings.

            Here is the code snippet:

            Source https://stackoverflow.com/questions/71249109

            QUESTION

            Display document to topic mapping after LSI using Gensim
            Asked 2022-Feb-22 at 19:27

            I am new to using LSI with Python and Gensim + Scikit-learn tools. I was able to achieve topic modeling on a corpus using LSI from both the Scikit-learn and Gensim libraries, however, when using the Gensim approach I was not able to display a list of documents to topic mapping.

            Here is my work using Scikit-learn LSI where I successfully displayed document to topic mapping:

            ...

            ANSWER

            Answered 2022-Feb-22 at 19:27

            In order to get the representation of a document (represented as a bag-of-words) from a trained LsiModel as a vector of topics, you use Python dict-style bracket-accessing (model[bow]).

            For example, to get the topics for the 1st item in your training data, you can use:

            Source https://stackoverflow.com/questions/71218086

            QUESTION

            Normalizing Topic Vectors in Top2vec
            Asked 2022-Feb-16 at 16:13

            I am trying to understand how Top2Vec works. I have some questions about the code that I could not find an answer for in the paper. A summary of what the algorithm does is that it:

            • embeds words and vectors in the same semantic space and normalizes them. This usually has more than 300 dimensions.
            • projects them into 5-dimensional space using UMAP and cosine similarity.
            • creates topics as centroids of clusters using HDBSCAN with Euclidean metric on the projected data.

            what troubles me is that they normalize the topic vectors. However, the output from UMAP is not normalized, and normalizing the topic vectors will probably move them out of their clusters. This is inconsistent with what they described in their paper as the topic vectors are the arithmetic mean of all documents vectors that belong to the same topic.

            This leads to two questions:

            How are they going to calculate the nearest words to find the keywords of each topic given that they altered the topic vector by normalization?

            After creating the topics as clusters, they try to deduplicate the very similar topics. To do so, they use cosine similarity. This makes sense with the normalized topic vectors. In the same time, it is an extension of the inconsistency that normalizing topic vectors introduced. Am I missing something here?

            ...

            ANSWER

            Answered 2022-Feb-16 at 16:13

            I got the answer to my questions from the source code. I was going to delete the question but I will leave the answer any way.

            It is the part I missed and is wrong in my question. Topic vectors are the arithmetic mean of all documents vectors that belong to the same topic. Topic vectors belong to the same semantic space where words and documents vector live.

            That is why it makes sense to normalize them since all words and documents vectors are normalized, and to use the cosine metric when looking for duplicated topics in the higher original semantic space.

            Source https://stackoverflow.com/questions/71143240

            QUESTION

            Extract Topic Scores for Documents LDA Gensim Python
            Asked 2021-Dec-10 at 10:33

            I am trying to extract topic scores for documents in my dataset after using and LDA model. Specifically, I have followed most of the code from here: https://www.machinelearningplus.com/nlp/topic-modeling-gensim-python/

            I have completed the topic model and have the results I want, but the provided code only gives the most dominant topic for each document. Is there a simple way to modify the following code to give me the scores for say the 5 most dominant topics?

            ...

            ANSWER

            Answered 2021-Dec-10 at 10:33

            Right this is a crusty example because you haven't provided data to reproduce but using some gensim testing corpus, texts and dictionary we can do:

            Source https://stackoverflow.com/questions/70295773

            QUESTION

            How to get list of words for each topic for a specific relevance metric value (lambda) in pyLDAvis?
            Asked 2021-Nov-24 at 10:43

            I am using pyLDAvis along with gensim.models.LdaMulticore for topic modeling. I have totally 10 topics. When I visualize the results using pyLDAvis, there is a bar called lambda with this explanation: "Slide to adjust relevance metric". I am interested to extract the list of words for each topic separately for lambda = 0.1. I cannot find a way to adjust lambda in the document for extracting keywords.

            I am using these lines:

            ...

            ANSWER

            Answered 2021-Nov-24 at 10:43

            You may want to read this github page: https://nicharuc.github.io/topic_modeling/

            According to this example, your code could go like this:

            Source https://stackoverflow.com/questions/69492078

            QUESTION

            Wait. BoW and Contextual Embeddings have different sizes
            Asked 2021-Oct-11 at 15:19

            Working with the OCTIS package, I am running a CTM topic model on the BBC (default) dataset.

            ...

            ANSWER

            Answered 2021-Oct-11 at 15:19

            I'm one of the developers of OCTIS.

            Short answer: If I understood your problem, you can fix this issue by modifying the parameter "bert_path" of CTM and make it dataset-specific, e.g. CTM(bert_path="path/to/store/the/files/" + data)

            TL;DR: I think the problem is related to the fact that CTM generates and stores the document representations in some files with a default name. If these files already exist, it uses them without generating new representations, even if the dataset has changed in the meantime. Then CTM will raise that issue because it is using the BOW representation of a dataset, but the contextualized representations of another dataset, resulting in two representations with different dimensions. Changing the name of the files with respect to the name of the dataset will allow the model to retrieve the correct representations.

            If you have other issues, please open a GitHub issue in the repo. I've found out about this issue by chance.

            Source https://stackoverflow.com/questions/69521210

            QUESTION

            Can I input a pandas dataframe into "TfidfVectorizer"? If so, how do I find out how many documents are in my dataframe?
            Asked 2021-Sep-20 at 01:19

            Here's the raw data:

            Here's about the first half of the data after reading it into a pandas dataframe:

            I'm trying to run TfidfVectorizer but I keep getting the following error:

            ...

            ANSWER

            Answered 2021-Sep-20 at 01:19

            You should pass a column of data to the fit_transform function. Here is the example

            Source https://stackoverflow.com/questions/69248109

            QUESTION

            Should bi-gram and tri-gram be used in LDA topic modeling?
            Asked 2021-Sep-13 at 21:11

            I read several posts(here and here) online about LDA topic modeling. All of them only use uni-grams. I would like to know why bi-grams and tri-grams are not used for LDA topic modeling?

            ...

            ANSWER

            Answered 2021-Sep-13 at 08:30

            It's a matter of scale. If you have 1000 types (ie "dictionary words"), you might end up (in the worst case, which is not going to happen) with 1,000,000 bigrams, and 1,000,000,000 trigrams. These numbers are hard to manage, especially as you will have a lot more types in a realistic text.

            The gains in accuracy/performance don't outweigh the computational cost here.

            Source https://stackoverflow.com/questions/69157848

            QUESTION

            Determine the correct number of topics using latent semantic analysis
            Asked 2021-Sep-08 at 11:20

            Starting from the following example

            ...

            ANSWER

            Answered 2021-Sep-08 at 11:20

            You can compute the explained variance with a range of the possible number of components. The maximum number of components is the size of your vocabulary.

            Source https://stackoverflow.com/questions/69091520

            QUESTION

            Pandas: LDA Top n keywords and topics with weights
            Asked 2021-Jun-23 at 08:01

            I am doing a topic modelling task with LDA, and I am getting 10 components with 15 top words each:

            ...

            ANSWER

            Answered 2021-Jun-23 at 08:01

            If I understand correctly, you have a dataframe with all values and you want to keep the top 10 in each row, and have 0s on remaining values.

            Here we transform each row by:

            • getting the 10th highest values
            • reindexing to the original index of the row (thus the columns of the dataframe) and filling with 0s:

            Source https://stackoverflow.com/questions/68092351

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

            Vulnerabilities

            No vulnerabilities reported

            Install SurfinPy

            surfinpy is a Python 3 package and requires a typical scientific Python stack. Use of the tutorials requires Anaconda/Jupyter to be installed.

            Support

            To build the documentation from scratch.
            Find more information at:

            Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items

            Find more libraries
            Install
          • PyPI

            pip install surfinpy

          • CLONE
          • HTTPS

            https://github.com/symmy596/SurfinPy.git

          • CLI

            gh repo clone symmy596/SurfinPy

          • sshUrl

            git@github.com:symmy596/SurfinPy.git

          • Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link

            Consider Popular Topic Modeling Libraries

            gensim

            by RaRe-Technologies

            Familia

            by baidu

            BERTopic

            by MaartenGr

            Top2Vec

            by ddangelov

            lda

            by lda-project

            Try Top Libraries by symmy596

            PythonMaps-Scipy-2022

            by symmy596HTML

            Polypy

            by symmy596Python

            Advanced_Practical_Chemistry_Teaching

            by symmy596Jupyter Notebook

            towards-data-science-articles

            by symmy596Jupyter Notebook

            Bond-Length-Calculator

            by symmy596Jupyter Notebook