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ArXivExplore 1.0.2.wl
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(* ::Package:: *)
(* ::Section:: *)
(*0. Package Header*)
(* ::Subsection:: *)
(*Begin Package*)
BeginPackage["DanieleGregori`ArXivExplore`"];
(*BeginPackage["My`ArXivExplore`"];*)
(* ::Subsection::Closed:: *)
(*Main database*)
ArXivDataset::usage = "ArXivDataset[All] returns the whole ArXiv dataset cleaned and ordered by date of first version;
ArXivDataset[cat] returns only the dataset for a specified primary category 'cat';
ArXivDataset[[cat,All}] returns the dataset of all articles sharing (as primary or as cross-list) the cateory 'cat'.";
(*Notice: in the present version all datasets are updated up to June 2024.*)
ArXivDatasetLookup::usage =
"ArXivDatasetLookup[key] returns all the specified values for the key 'key' of the whole ArXiv dataset;
ArXivDatasetLookup[key,subdataset_List] returns all the specified keys of a certain subdataset;
ArXivDatasetLookup[key,cat_String] returns all the specified keys of a the specified primary category 'cat';
ArXivDatasetLookup[key,{cat_String,All}] returns all the specified keys of a the specified primary or cross-list category 'cat'";
ArXivDatasetAggregate::usage =
"ArXivDatasetAggregate[prefix_String] aggregates all primary categories with a given prefix;
ArXivDatasetAggregate[{prefix_String,All}] aggregates all primary or cross-list categories with a given prefix.";
ArXivDatasetSubset::usage =
"ArXivDatasetSubset[idL_List] allow to create a custom dataset with the given article id list 'idL'.";
arXivDatasetKeys::usage = "arXivDatasetKeys returns all possible database keys";
(* ::Subsection::Closed:: *)
(*Categories*)
ArXivCategories::usage =
"ArXivCategories[id] returns all the categories of a given id, searching in the whole ArXiv dataset;
ArXivCategories[id,cat] returns all the categories of a given id, from the ArXiv subdataset of the given category;
ArXivCategories[All,cat] returns all categories of a given category 'cat', associated with their id.";
ArXivCategoriesPrimary::usage =
"ArXivCategoriesPrimary[id] returns all primary categories of a given id, searching in the whole ArXiv dataset;
ArXivCategoriesPrimary[id,cat] returns all primary categories of a given id, from the ArXiv subdataset of the given category;
ArXivCategoriesPrimary[All,cat] returns all primary categories of a given category 'cat', associated with their id.";
ArXivTopCategories::usage =
"ArXivTopCategories[All] returns the ranking of all primary categories, in terms of their corresponding total articles;
ArXivTopCategories[cut] returns only the first 'cut' most frequent primary categories, with the number of corresponding articles.";
ArXivCategoriesLegend::usage = "ArXivCategoriesLegend[cat_String] associates each primary category name with its fulldescription.";
arXivCategoriesUnion::usage = "arXivCategoriesUnion returns all possible categories";
(*arXivCategoriesAssoc;*)
(* ::Subsection::Closed:: *)
(*T EX scraping*)
ArXivTeXDocument::usage = "ArXivTeXDocument[id] scrapes the TeX source of a given article id.";
ArXivTeXSections::usage = "ArXivTeXSections[id] scrapes from the TeX source the sections of a given article id.";
ArXivTeXIntroduction::usage = "ArXivTeXIntroduction[id] scrapes from the TeX source the introduction section of a given article id.";
(*arXivTeXBeginEnd;*)
(*arXivTeXPartVisualize;*)
ArXivTeXFormulae::usage =
"ArXivTeXFormulae[tex] scrapes from source TeX 'tex' all formulae and returns an association with each type;
ArXivTeXFormulae[tex,wordeq] scrapes from source TeX 'tex' the formulae only of a given type 'wordeq'.";
(* ::Subsection::Closed:: *)
(*Citations*)
ArXivCitationsTotal::usage =
"ArXivCitationsTotal[id_String] returns the total citations of a given article id;
ArXivCitationsTotal[idL_List] returns the total citations of a each article of the id list 'idL'.";
ArXivCitations::usage =
"ArXivCitations[id_String] returns all ids of articles citing a given article id;
ArXivCitations[idL_List] returns all ids of articles citing each article of the id list 'idL'.";
ArXivCitationsAuthor::usage =
"ArXivCitationsAuthor[author] returns all pairs of ids of which the first is an article of a given author - on all ArXiv - and the last is another paper that cites it;
ArXivCitationsAuthor[author,cat] returns all pairs of ids of which the first is an article of a given author - in category 'cat' - and the last is another paper that cites it;
ArXivCitationsAuthor[authorL_List,cat] returns all pairs of ids of which the first is an article of a given list of authors 'authorL' - in category 'cat' - and the last is another paper that cites it;
ArXivCitationsAuthor[authorL_List,catL_List] returns all pairs of ids of which the first is an article of a given the two lists 'doubleL' - the first made of author names and the second of corresponding categories - and the last is another paper that cites it.";
ArXivGraphAuthor::usage =
"ArXivGraphAuthor[author_String,cat_] returns a citation graph of a given author in a given category 'cat';
ArXivGraphAuthor[authorL_List,cat_] returns a citation graph of a given author list 'authorL' in a given category 'cat';
ArXivGraphAuthor[authorL_List,catL_List] returns a citation graph of a given the two lists 'doubleL' - the first made of author names and the second of corresponding categories.";
ArXivGraph::usage =
"ArXivGraph[id_String] returns a citation graph of the given article id;
ArXivGraph[idL_List] returns a citation graph of the given article id list 'idL'.";
(*
ArXivGraph[idL_List,n_Integer] returns a citation graph of the given article id list 'idL', iterated 'n' times.*)
(* ::Subsection:: *)
(*Main data*)
(* ::Subsubsection::Closed:: *)
(*Articles*)
ArXivArticles::usage = "ArXivArticles[id] returns all article dataset items of a given article id or list of ids.";
(* ::Subsubsection::Closed:: *)
(*IDs*)
ArXivIDs::usage =
"ArXivIDs[All] returns all article ids on ArXiv;
ArXivIDs[cat_String] returns all article ids of a given primary category 'cat' on ArXiv;
ArXivIDs[{cat_String,All}] returns all article ids of a given primary or cross-list category 'cat' on ArXiv.";
(* ::Subsubsection::Closed:: *)
(*Titles*)
ArXivTitles::usage =
"ArXivTitles[id] returns all the titles of a given article id;
ArXivTitles[All,cat] returns all titles of a given category 'cat', associated with their id.";
(* ::Subsubsection::Closed:: *)
(*Abstracts*)
ArXivAbstracts::usage =
"ArXivAbstracts[id] returns all the abstracts of a given article id;
ArXivAbstracts[All,cat] returns all abstracts of a given category 'cat', associated with their id.";
(* ::Subsubsection::Closed:: *)
(*Versions*)
ArXivVersions::usage =
"ArXivVersions[id] returns all the versions of a given article id, searching in the whole ArXiv dataset;
ArXivVersions[All] returns all versions on all ArXiv, associated with their id;
ArXivVersions[id,cat] returns all the versions of a given article id, from the ArXiv subdataset of the given category;
ArXivVersions[All,cat] returns all versions of a given category 'cat', associated with their id.";
(*arXivVersionsID::usage=
"arXivVersionsID[All] returns all versions on all ArXiv, associated with their id;
arXivVersionsID[cat] returns all versions of a given category 'cat', associated with their id.";*)
arXivVersionsFirstID::usage =
"arXivVersionsFirstID[All] returns all first versions dates on all ArXiv, associated with their id;
arXivVersionsFirstID[cat] returns all first versions dates of a given category 'cat', associated with their id.";
ArXivDates::usage =
"ArXivDates[All] returns all first versions dates on all ArXiv, associated with their id;
ArXivDates[cat] returns all first versions dates on all ArXiv, associated with their id;
ArXivDates[All,cat,int] returns an association between all article ids of a given category 'cat' and their dates in time resolution 'int'.";
(*ArXivVersions::usage = "ArXivVersions[category] returns all article versions of a given primary category.";*)
(*ArXivVersionFirstDate::usage = "ArXivVersionFirstDate[idmcategory] returns the first article versions of a given id in a given primary category.";*)
(* ::Subsubsection::Closed:: *)
(*Authors*)
(*double author list to fix*)
ArXivAuthors::usage =
"ArXivAuthors[id] returns the authors (appropriately cleaned) of a given article id, searching on all ArXiv;
ArXivAuthors[id,cat] returns the authors (appropriately cleaned) of a given article id, searching only in the category 'cat';
ArXivAuthors[All,cat] returns all authors (appropriately cleaned) of a given category.";
ArXivTopAuthors::usage =
"ArXivTopAuthors[All,n] returns all most prolific authors on all ArXiv, with more than 'n' papers;
ArXivTopAuthors[cat,n] returns all most prolific authors in a given category 'cat', with more than 'n' papers.";
ArXivArticlesAuthor::usage =
"ArXivArticlesAuthor[author_String] returns all articles of a given author, searching on all ArXiv;
ArXivArticlesAuthor[author_String,cat] returns all articles of a given author, searching only in a given category 'cat';
ArXivArticlesAuthor[authorL_List,cat] returns all articles of a given author, with possible names given as a list 'authorL', searching only in a given category 'cat';
ArXivArticlesAuthor[author_String,cat] returns all articles of a given author searching in all categories of the list 'catL';
ArXivArticlesAuthor[authorL_List,catL_List] returns all articles of a given author, with possible names given as a list 'authorL', searching in each category of the list 'catL'.";
(* ::Subsection:: *)
(*Word statistics*)
(* ::Subsubsection::Closed:: *)
(*Total*)
(*to improve*)
ArXivArticlesTrend::usage =
"ArXivArticlesTrend[cat,int] returns an association with the total new articles submissions in the category 'cat' for each time period of resolution 'int'.";
(*ArXivArticlesCount::usage =
"ArXivArticlesCount[All,int] returns a TimeSeries of a given resolution 'int', counting all new articles submissions on all ArXiv;
ArXivArticlesCount[cat,int] returns a TimeSeries of a given resolution 'int', counting all new articles submissions in the category 'cat'.";*)
(* ::Subsubsection::Closed:: *)
(*Cleaned titles/abstracts*)
arXivTitlesCleanID::usage =
"arXivTitlesCleanID[cat] returns an association between all cleaned titles in a given category 'cat' associated and their respective ids.";
arXivTitlesCleanDated::usage =
"arXivTitlesCleanDated[cat,int] returns an association between all cleaned titles in a given category 'cat' associated and their respective dates.";
arXivAbstractsCleanID::usage =
"arXivAbstractsCleanID[cat] returns an association between all cleaned abstracts in a given category 'cat' associated and their respective ids.";
arXivAbstractsCleanDated::usage =
"arXivAbstractsCleanDated[cat,int] returns an association between all cleaned abstracts in a given category 'cat' associated and their respective dates.";
(* ::Subsubsection::Closed:: *)
(*Single words*)
arXivTitlesWordID::usage =
"arXivTitlesWordID[cat_,word_String] returns all cleaned titles in which a 'word' appears, associated with their article ids";
arXivAbstractsWordID::usage =
"arXivAbstractsWordID[cat_,word_String] returns all cleaned abstracts in which a 'word' appears, associated with their article ids";
arXivTitlesWordDated::usage =
"arXivTitlesWordDated[cat_,word_String] returns all cleaned titles in which a 'word' appears, associated with their dates";
arXivAbstractsWordDated::usage =
"arXivAbstractsWordDated[cat_,word_String] returns all cleaned abstracts in which a 'word' appears, associated with their dates";
arXivTitlesWordTrend::usage=
"arXivTitlesWordTrend[cat,word_String,int_:\"Month\"] returns all total title words 'word', associated with their dates of time resolutions 'int'.";
arXivAbstractsWordTrend::usage=
"arXivAbstractsWordTrend[cat,word_String,int_:\"Month\"] returns all total abstract words 'word', associated with their dates of time resolutions 'int'.";
(* ::Subsubsection::Closed:: *)
(*Neighbour words*)
arXivTitlesWordNeighboursID::usage =
"arXivTitlesWordNeighboursID[cat,n_Integer:2] returns all 'n'-neighbour words in cleaned titles of a given category 'cat', as an association with their ids;
arXivTitlesWordNeighboursID[cat,wordNeigh_String] returns all cleaned titles where the word neighbour combination 'wordNeigh' appears, in a given category 'cat', as an association with their ids.";
arXivTitlesWordNeighboursDated::usage=
"arXivTitlesWordNeighboursDated[cat,n_Integer,int_:\"Month\"] returns all 'n'-neighbour words in cleaned titles of a given category 'cat', as an association with its date strings of resolution 'int'.";
ArXivTitlesWordNeighboursTop::usage=
"ArXivTitlesWordNeighboursTop[cat,n_Integer:2,cut_Integer] returns all most frequent ever 'n'-neighbour words in cleaned titles of a given category 'cat', up to a cut-off 'cut'.";
arXivAbstractsWordNeighboursID::usage =
"arXivAbstractsWordNeighboursID[cat,n_Integer:2] returns all 'n'-neighbour words in cleaned abstracts of a given category 'cat', as an association with their ids.";
arXivAbstractsWordNeighboursDated::usage=
"arXivAbstractsWordNeighboursDated[cat,n_Integer,int_:\"Month\"] returns all 'n'-neighbour words in cleaned abstracts of a given category 'cat', as an association with its dates of resolution 'int'.";
ArXivAbstractsWordNeighboursTop::usage=
"ArXivAbstractsWordNeighboursTop[cat,n_Integer:2,cut_Integer:100] returns all most frequent ever 'n'-neighbour words in cleaned abstracts of a given category 'cat', up to a cut-off 'cut'.";
arXivTitlesWordNeighboursTrend::usage =
"arXivTitlesWordNeighboursTrend[cat,n_Integer:2,cut_Integer:10000,int_:\"Month\"] returns all most frequent 'n'-neighbour words in cleaned titles of a given category 'cat', as an association with its dates of resolution 'int', up to a cut-off 'cut';
arXivTitlesWordNeighboursTrend[cat,wordNeigh_String,cut_Integer:10000,int:\"Month\"] returns all total occurences of neighbour words 'wordNeigh' in titles of a given category 'cat', as an association with its dates of resolution 'int', using a cut-off 'cut'.";
arXivAbstractsWordNeighboursTrend::usage =
"arXivAbstractsWordNeighboursTrend[cat,n_Integer:2,cut_Integer:100,int_:\"Month\"] returns all most frequent 'n'-neighbour words in cleaned abstracts of a given category 'cat', as an association with its dates of resolution 'int', up to a cut-off 'cut';
arXivAbstractsWordNeighboursTrend[cat,wordNeigh_String,cut_Integer:100,int_:\"Month\"] all total occurences of neighbour words 'wordNeigh' in abstracts of a given category 'cat', as an association with its dates of resolution 'int', using a cut-off 'cut'.";
(* ::Subsubsection::Closed:: *)
(*Combinations words*)
arXivTitlesWordCombinationID::usage =
"arXivTitlesWordCombinationID[cat,wordComb_And,int_:\"Month\"] returns all cleaned titles where the combination of words 'wordComb' appears, associated with their article ids.";
arXivAbstractsWordCombinationID::usage =
"arXivAbstractsWordCombinationID[cat,wordComb_And,int_:\"Month\"] returns all cleaned abstracts where the combination of words 'wordComb' appears, associated with their article ids.";
arXivTitlesWordCombinationDated::usage =
"arXivTitlesWordCombinationDated[cat,wordComb_And,int_:\"Month\"] returns all cleaned titles where the combination of words 'wordComb' appears, associated with their dates of time resolutions 'int'.";
arXivAbstractsWordCombinationDated::usage =
"arXivAbstractsWordCombinationDated[cat,wordComb_And,int_:\"Month\"] returns all cleaned abstracts where the combination of words 'wordComb' appears, associated with their dates of time resolutions 'int'.";
arXivTitlesWordCombinationTrend::usage =
"arXivTitlesWordCombinationTrend[cat,wordComb_And,int_:\"Month\"] returns all total combinations of title words 'wordComb', associated with their dates of time resolutions 'int'.";
arXivAbstractsWordCombinationTrend::usage =
"arXivAbstractsWordCombinationTrend[cat,wordComb_And,int_:\"Month\"] returns all total combinations of abstract words 'wordComb', associated with their dates of time resolutions 'int'.";
(* ::Subsubsection::Closed:: *)
(*Top and search*)
ArXivTopTitles::usage =
"ArXivTopTitles[cat,cutoff] returns all 'cutoff' most frequent title words, with their number of occurrences, in a given category 'cat';
ArXivTopTitles[cat,cutoff,n] returns all 'cutoff' most frequent title 'n'-words neighbours, with their number of occurrences, in a given category 'cat'.";
ArXivTopAbstracts::usage =
"ArXivTopAbstracts[cat,cutoff] returns all 'cutoff' most frequent abstract words, with their number of occurrences, in a given category 'cat';
ArXivTopAbstracts[cat,cutoff,n] returns all 'cutoff' most frequent abstract 'n'-words neighbours, with their number of occurrences, in a given category 'cat'.";
(*combinations to add*)
arXivTitlesWordSearch::usage =
"arXivTitlesWordSearch[word,cat] returns the ranking of the word among all most popular title words in a given category 'cat', with also its number of occurences.";
arXivAbstractsWordSearch::usage =
"arXivAbstractsWordSearch[word,cat] returns the ranking of the word among all most popular abstract words in a given category 'cat', with also its number of occurences.";
arXivTitlesWordNeighboursSearch::usage =
"arXivTitlesWordNeighboursSearch[wordNeigh,cat] returns the ranking of the word neighbours 'wordNeigh' among all most popular title words in a given category 'cat', with also its number of occurences.";
arXivAbstractsWordNeighboursSearch::usage =
"arXivAbstractsWordNeighboursSearch[word,cat] returns the ranking of the word neighbours 'wordNeigh' among all most popular abstract words in a given category 'cat', with also its number of occurences.";
(* ::Subsubsection::Closed:: *)
(*Word citations*)
(*ArXivTitlesWordCitationTrend::usage =
"ArXivTitlesWordCitationTrend[cat_,word_,int_:\"Month\"] returns a list of rules with the total citations every time period 'int' (with date as string) of every article in category 'cat' having in the (cleaned) title a given word.";*)
(*arXivTitlesWordCitationID::usage=
"arXivTitlesWordCitationID[cat,word] returns all total citations of all articles containing a certain 'word', in category 'cat', associated with their ids.";*)
(*arXivTitlesWordNeighboursCitationID::usage=
"arXivTitlesWordNeighboursCitationID[cat,wordNeigh] returns all total citations of all articles containing a certain word neighbour 'wordNeigh', in category 'cat', associated with their ids.";*)
ArXivCitationsTitles::usage=
"ArXivCitationsTitles[cat,word] returns all total citations of all articles containing a certain word or word neighbour 'word', in category 'cat', associated with their ids.";
(* ::Subsubsection::Closed:: *)
(*WordCloud video (to update)*)
(*below to update*)
(*ArXivTitlesWordCloudVideo::usage =
"ArXivTitlesWordCloudVideo[cat,int_:\"Month\"] creates a video of wordclouds of title words in a given category 'cat', over all time with resolution 'int'.";*)
(* ::Subsection::Closed:: *)
(*ArXivLogos*)
ArXivLogosTitles::usage =
"ArXivLogosTitles[word_String,cat] returns all titles in category 'cat' containing the word 'word', associated with their article id or date;
ArXivLogosTitles[wordAnd_And,cat] returns all titles in category 'cat' containing the word conjuction (And) 'wordAnd', associated with their article id or date;
ArXivLogosTitles[wordOr_Or,cat] returns all titles in category 'cat' containing the word inclusive disjunction (Or) 'wordOr', associated with their article id or date;
ArXivLogosTitles[wordXor_Xor,cat] returns all titles in category 'cat' containing the word exclusive disjunction (Xor) 'wordXor', associated with their article id or date.";
ArXivLogosAbstracts::usage =
"ArXivLogosAbstracts[word_String,cat] returns all abstracts in category 'cat' containing the word 'word', associated with their article id or date;
ArXivLogosAbstracts[wordAnd_And,cat] returns all abstracts in category 'cat' containing the word conjuction (And) 'wordAnd', associated with their article id or date;
ArXivLogosAbstracts[wordOr_Or,cat] returns all abstracts in category 'cat' containing the word inclusive disjunction (Or) 'wordOr', associated with their article id or date;
ArXivLogosAbstracts[wordXor_Xor,cat] returns all abstracts in category 'cat' containing the word exclusive disjunction (Xor) 'wordXor', associated with their article id or date.";
(* ::Subsection::Closed:: *)
(*ArXiv Plot*)
ArXivPlot::usage=
"ArXivPlot[All,cat] draws a DateListPlot of all total article submissions in category 'cat';
ArXivPlot[word_String,cat] draws a DateListPlot of the share of popularity of a title word 'word' in category 'cat';
ArXivPlot[wordL_List,cat] draws a DateListPlot of the share of popularity of the title words list 'wordL' in category 'cat';
ArXivPlot[wordC_And,cat] draws a DateListPlot of the share of popularity of the title words combination 'wordC' in category 'cat';
ArXivPlot[All,logos,cat] draws a DateListPlot of all total articles with the title words construct 'logos' in category 'cat'.";
ArXivPlotTitles::usage=
"ArXivPlotTitles[word_String,cat] draws a DateListPlot of the share of popularity of a title word 'word' in category 'cat';
ArXivPlotTitles[wordL_List,cat] draws a DateListPlot of the share of popularity of the title words list 'wordL' in category 'cat';
ArXivPlotTitles[wordC_And,cat] draws a DateListPlot of the share of popularity of the title words combination 'wordC' in category 'cat';
ArXivPlotTitles[All,logos,cat] draws a DateListPlot of all total articles with the title words construct 'logos' in category 'cat'.";
ArXivPlotAbstracts::usage=
"ArXivPlotAbstracts[word_String,cat] draws a DateListPlot of the share of popularity of an abstract word 'word' in category 'cat';
ArXivPlotAbstracts[wordL_List,cat] draws a DateListPlot of the share of popularity of the abstract words list 'wordL' in category 'cat';
ArXivPlotAbstracts[wordC_And,cat] draws a DateListPlot of the share of popularity of the abstract words combination 'wordC' in category 'cat';
ArXivPlotAbstracts[All,logos,cat] draws a DateListPlot of all total articles with the abstract words construct 'logos' in category 'cat'.";
(* ::Subsection:: *)
(*Neural networks*)
(* ::Subsubsection::Closed:: *)
(*Vocabularies*)
ArXivTitlesVocabulary::usage =
"ArXivTitlesVocabulary[cut_Integer] gives the word vocabulary of all (cleaned) titles of the 'cut' most frequent categories;
ArXivTitlesVocabulary[catL_List] gives the word vocabulary of all (cleaned) titles of the list of categories 'catL'.";
ArXivAbstractsVocabulary::usage =
"ArXivAbstractsVocabulary[cut_Integer] gives the word vocabulary of all (cleaned) abstracts of the 'cut' most frequent categories;
ArXivAbstractsVocabulary[catL_List] gives the word vocabulary of all (cleaned) abstracts of the list of categories 'catL'.";
(* ::Subsubsection::Closed:: *)
(*Category Classifier*)
ArXivClassifyCategoryNet::usage =
"ArXivClassifyCategoryNet[cut_Integer,dim_Integer,drop] gives a net classifying the 'cut' most frequent categories, embedding titles and abstracts in dimension 'dim', with dropout ratio 'drop';
ArXivClassifyCategoryNet[catL_List,dim_Integer,drop] gives a net classifying the 'catL' list of categories, embedding titles and abstracts in dimension 'dim', with dropout ratio 'drop';
ArXivClassifyCategoryNet[catL_List,dim_List,drop] gives a net classifying the 'catL' list of categories, embedding titles in dimension dim[[1]], abstracts in dimension dim[[2]], catenate them and later pass them into a linear layer with dimension dim[[3]], with dropout ratio 'drop'.";
ArXivClassifyCategoryTrainTest::usage =
"ArXivClassifyCategoryTrainTest[cut_Integer,nids_Integer] gives a training and test sets for the net ArXivClassifyCategoryNet[cut,dim,drop] classifying the 'cut' most frequent categories, using up to 'nids' random articles in each category;
ArXivClassifyCategoryTrainTest[catL_List,nids_Integer] gives a training and test sets for the net ArXivClassifyCategoryNet[catL,dim,drop] classifying the 'catL' list of categories, using up to 'nids' random articles in each category.";
(* ::Subsubsection::Closed:: *)
(*Author Classifier*)
ArXivClassifyAuthorNet::usage =
"ArXivClassifyAuthorNet[authorL_List,cat,dim_Integer,drop] gives a net classifying the 'authorL' list of authors in the same category 'cat', embedding titles and abstracts in dimension 'dim', with dropout ratio 'drop';
ArXivClassifyAuthorNet[authorL_List,cat,dim_List,drop] gives a net classifying the 'authorL' list of authors in the same category 'cat', embedding titles in dimension dim[[1]], abstracts in dimension dim[[2]], catenate them and later passing them into a linear layer with dimension dim[[3]], with dropout ratio 'drop';
ArXivClassifyAuthorNet[authorL_List,catL_List,dim_List,drop] gives a net classifying the 'authorL' list of authors in categories given by 'catL' list, embedding titles in dimension dim[[1]], abstracts in dimension dim[[2]], catenate them and later passing them into a linear layer with dimension dim[[3]], with dropout ratio 'drop'.";
ArXivClassifyAuthorTrainTest::usage =
"ArXivClassifyAuthorTrainTest[authorL_List,cat,nids_Integer] gives a training and test sets for the net ArXivClassifyCategoryNet[authorL,dim,drop] classifying the 'authorL' list of authors in the same category 'cat', using up to 'nids' random articles each;
ArXivClassifyAuthorTrainTest[authorL_List,catL_List,nids_Integer] gives a training and test sets for the net ArXivClassifyCategoryNet[authorL,dim,drop] classifying the 'authorL' list of authors, in the categories given by the list 'catL', using up to 'nids' random articles each.";
(* ::Subsection::Closed:: *)
(*LLM*)
(*ArXivLLMConceptDefine;ArXivDefineConcept;*)
(*ArXivLLMAuthorReport;ArXivReportAuthor;*)
(*we want to use aso FindTextualAnswer*)
(*use just simgle word and add criterion "MostRecent" or "MostCitations"*)
ArXivExplainConcept::usage =
"ArXivExplainConcept[concept_String,id_String] explains 'concept' given an article id;
ArXivExplainConcept[concept_String,idL_List] explains 'concept' given an articles list 'idL'.";
ArXivExplainAuthor::usage =
"ArXivExplainAuthor[author_String] explains the work of an 'author';
ArXivExplainAuthor[author_String,cat_] explains the work of an 'author' in category 'cat';
ArXivExplainAuthor[authorL_List] explains the work of an author whose possible names are the list 'authorL'.;
ArXivExplainAuthor[authorL_List,catL_List] the two lists 'doubleL' - the first made of author names and the second of corresponding categories.";
(* ::Subsection:: *)
(*End public Header*)
Begin["DanieleGregori`Private`"];
(*Begin["My`Private`"];*)
(* ::Section:: *)
(*1. ArXiv main database*)
(* ::Subsection:: *)
(*Dataset from Kaggle (optional)*)
(* ::Subsubsection::Closed:: *)
(*Dataset Kaggle download*)
(*only when new download from Kaggle is made:*)
(*you need a Kaggle account*)
(*dirDatabase=FileNameJoin[{StringDelete[NotebookDirectory[],"Kernel"~~_~~EndOfString],"Assets"}];*)
(*datasetFull=Block[{rawDbText,rawDb},
rawDbText=Import[FileNameJoin[{dirDatabase,"arxiv-metadata-oai-snapshot.json"}],"Text"]//EchoTiming;
rawDb=StringJoin["{\"id\":",#]&/@StringSplit[rawDbText,"{\"id\":"]//EchoTiming;
ParallelMap[Interpreter["JSON"],rawDb]//EchoTiming];
Export[FileNameJoin[{dirDatabase,"arxiv-database.json"}],datasetFull]//EchoTiming;*)
(* ::Subsubsection::Closed:: *)
(*Kaggle delete duplicate articles*)
(*datasetDuplicateFree=Block[{ds,idFull,idsDuplicate,positionsDuplicates},
ds=datasetFull;
idFull=Map[Lookup[#,"id"]&,ds]//EchoFunction[Length]//EchoFunction[DuplicateFreeQ]//EchoTiming;
idsDuplicate=Cases[Normal@ReverseSort@Counts[idFull],HoldPattern[_String->n_Integer/;n>=2]]//EchoTiming//Echo;
positionsDuplicates=Position[ds,{"id"->#,__}]&/@Keys[idsDuplicate];
Join[
DeleteCases[ds,Apply[Alternatives,{"id"->#,__}&/@Keys[idsDuplicate]]],
Part[ds,Flatten[Last/@positionsDuplicates]
]
]]//QuietEcho//EchoTiming;*)
(* ::Subsubsection::Closed:: *)
(*Kaggle dataset date ordered*)
(*dateObjects=Block[{assMonths},
assMonths=<|"Jan"->1,"Feb"->2,"Mar"->3,"Apr"->4,"May"->5,"Jun"->6,"Jul"->7,"Aug"->8,"Sep"->9,"Oct"->10,"Nov"->11,"Dec"->12|>;
Map[DateObject@Reverse@
ToExpression@MapAt[
assMonths[#]&,
StringSplit[StringDrop[StringDrop[
Lookup[First@Lookup[#,"versions"],"created"]
,5],-12]],
{2}]&,
datasetDuplicateFree]]//EchoTiming;*)
(*datasetDateOrdered=Flatten[
Values@KeySort@
Merge[Rule@@@
Transpose[{dateObjects,datasetDuplicateFree}],
Identity],
1];//EchoTiming*)
(*ArXivDataset[All]=datasetDateOrdered;*)
(*Export[FileNameJoin[{dirDatabase,"arxiv-database.json"}],ArXivDataset[All]]//EchoTiming;*)
(*datasetDateObjects[All]=KeySort@Merge[Rule@@@Transpose[{dateObjects,datasetDuplicateFree}],Identity];
arXivDatasetDated[All]["Day"]=datasetDateObjects[All];
arXivDatasetDated[All]["Month"]=Map[Flatten[#,1]&,Merge[KeyValueMap[DateObject@Drop[First[#1],-1]->#2&,datasetDateObjects[All]],Identity]];
arXivDatasetDated[All]["Year"]=Map[Flatten[#,1]&,Merge[KeyValueMap[DateObject@Drop[First[#1],-2]->#2&,datasetDateObjects[All]],Identity]];*)
(* ::Subsection:: *)
(*Dataset cleaned import*)
(* ::Subsubsection::Closed:: *)
(*Dataset local import*)
dirDatabase=FileNameJoin[{StringDelete[NotebookDirectory[],"Kernel"~~_~~EndOfString],"Assets"}];
datasetLocal=Import[First@Flatten@StringCases[FileNames["*",dirDatabase],__~~"arxiv-database.json"],"JSON"](*//EchoTiming*);
(*with format json it takes just a bit more than 1 minute*)
(* ::Subsubsection::Closed:: *)
(*Dataset WolframCloud import*)
(*it can take me up to 1 hour to upload*)
(*CloudPut[ArXivDataset[All],"arxiv-database",Permissions->"Public"]//EchoTiming;*)
(*it can take me around 15 minutes do download*)
(* ::Input:: *)
(*(*databaseGet=CloudGet["https://www.wolframcloud.com/obj/dangregori/arxiv-database"]//EchoTiming;*)*)
(* ::Subsubsection::Closed:: *)
(*Dataset setting*)
If[
(datasetLocal=!=$Failed&&ValueQ[datasetLocal])(*//EchoFunction["local imp: ",#&]*),
ArXivDataset[All]=datasetLocal,
ArXivDataset[All]=CloudGet["https://www.wolframcloud.com/obj/dangregori/arxiv-database"]//EchoFunction["cloud imp: ", (#=!=$Failed&&ValueQ[#])&](*;
Export[FileNameJoin[{dirDatabase,"arxiv-database.json"}],ArXivDataset[All],"JSON"]*)];
(* ::Subsubsection::Closed:: *)
(*Dataset dates*)
(*the following dateObjects takes long, about 1 minute*)
(*it would be more clever to compute just the needed dateobjects and then distribute them*)
(*dateObjects=Block[{assMonths},
assMonths=<|"Jan"->1,"Feb"->2,"Mar"->3,"Apr"->4,"May"->5,"Jun"->6,"Jul"->7,"Aug"->8,"Sep"->9,"Oct"->10,"Nov"->11,"Dec"->12|>;
Map[DateObject@Reverse@
ToExpression@MapAt[
assMonths[#]&,
StringSplit[StringDrop[StringDrop[
Lookup[First@Lookup[#,"versions"],"created"]
,5],-12]],
{2}]&,
ArXivDataset[All]]](*//EchoTiming*);*)
(*dateObjects takes half the time*)
(*it can be redundant with arXivVersionsFirstDate later*)
dateStrings=Block[{assMonths},
assMonths=<|"Jan"->1,"Feb"->2,"Mar"->3,"Apr"->4,"May"->5,"Jun"->6,"Jul"->7,"Aug"->8,"Sep"->9,"Oct"->10,"Nov"->11,"Dec"->12|>;
Map[Reverse@
ToExpression@MapAt[
assMonths[#]&,
StringSplit[StringDrop[StringDrop[
Lookup[First@Lookup[#,"versions"],"created"]
,5],-12]],
{2}]&,
ArXivDataset[All]]];
dateObjects=Map[DateObject,dateStrings];
(*(possibly redundant)*)
datasetDateObjects[All]=KeySort@Merge[Rule@@@Transpose[{dateObjects,ArXivDataset[All]}],Identity];
arXivDatasetDated[All]["Day"]=datasetDateObjects[All];
arXivDatasetDated[All]["Month"]=Map[Flatten[#,1]&,Merge[KeyValueMap[DateObject@Drop[First[#1],-1]->#2&,datasetDateObjects[All]],Identity]];
arXivDatasetDated[All]["Year"]=Map[Flatten[#,1]&,Merge[KeyValueMap[DateObject@Drop[First[#1],-2]->#2&,datasetDateObjects[All]],Identity]];
(* ::Section:: *)
(*2. Scraping extra data*)
(* ::Subsection:: *)
(*T EX source files *)
(* ::Subsubsection::Closed:: *)
(*T EX import*)
linksTeXFunc[id_]:="https://arxiv.org/e-print/"<>id
importTeX[id_]:=Import[linksTeXFunc[id],"Text"]
importTeXDoc[id_]:=StringCases[importTeX[id],"\\begin{document}"~~__~~"\\end{document}"][[1]]
(* ::Subsubsection::Closed:: *)
(*T EX partition*)
sectionsTeX[id_]:=(*to improve, it does not always work*)StringSplit[importTeX[id],"\\section"]
ArXivTeXDocument[id_]:=importTeXDoc[id]
ArXivTeXSections[id_]:=(*to improve, it does not always work*)StringSplit[importTeXDoc[id],"\\section"]
sectionsTeXDoc[id_]:=ArXivExtractSections[id]
sectionsNone[id_]:=Block[{tex,texDoc},
texDoc=Enclose@ConfirmQuiet[importTeXDoc[id],Part::partw];
tex=If[!FailureQ[texDoc],texDoc,importTeX[id]];
StringSplit[tex,{"\\end{abstract}","\\begin{thebibliography}"}]]
(* ::Input:: *)
(**)
(*for debugging:*)
(*splitTeX20[id_]:=StringPartition[#,Floor[StringLength[#]/20]]&@importTeX[id]
splitTeX50[id_]:=StringPartition[#,Floor[StringLength[#]/50]]&@importTeX[id]
splitTeX[id_,length_]:=StringPartition[#,length]&@importTeX[id]*)
(* ::Subsection::Closed:: *)
(*Introduction extraction*)
(*about 10% success, can improve*)
(* ::Input::Initialization:: *)
ArXivTeXIntroduction[id_]:=(*to improve, it does not always work*)
Block[{
tex,texDoc,
sections,sectionsAlternative,sectionNone,
casesIntro,casesIntroAlter(*obsolete*),
ifSplitF,
tryCases,trySecond},
texDoc=Enclose@ConfirmQuiet[importTeXDoc[id],Part::partw];
tex=If[!FailureQ[texDoc],texDoc,importTeX[id]];
(*
texUncomm=importTeXDocUncomm[id];*)
(*
EchoFunction["string length tex doc: ",StringLength[texDoc]];*)
sections=StringSplit[tex,"\\section"];
(*having a tex structured in section is not always the case*)
(*other separators: *)
sectionsAlternative=StringSplit[tex,{(*"\\emph",*)"\\sxn",(*"\\textbf",*)"\\newsec"}];
(*no separators, only bibliography: *)
sectionNone=StringSplit[tex,{"\\end{abstract}","\\begin{thebibliography}"}];
casesIntro=
{"{Introduction}"~~__,"{Introduction.}"~~__,"{\\bf Introduction}"~~__,"{\\bf Introduction.}"~~__,"{\\label{"~~__~~"}"<>"Introduction}"~~__,"{\\label{"~~__~~"}"~~Whitespace..~~"Introduction}"~~__,
"{Introduction"~~__~~"\\label{"~~__~~"}}"~~__,
"{Summary}"~~__};
casesIntroAlter=casesIntro;
tryCases=
Flatten@
DeleteCases[
If[Echo[Length[sections],"length sections"]>1,
StringCases[sections,casesIntro],
If[Echo[Length[sectionsAlternative],"length sections alternative"]>1,
StringCases[sectionsAlternative,casesIntroAlter],{sectionNone[[2]]}]
]
,{}];
trySecond=
If[Length[sections]>1,
sections[[2]],
If[Length[sectionsAlternative]>1,
sectionsAlternative[[2]],tex]
];
If[Echo[Length[tryCases],"length cases"]>=1,tryCases[[1]],trySecond]
]//QuietEcho
(* ::Subsection::Closed:: *)
(*Formulae extraction*)
(*can improve*)
arXivTeXBeginEnd[tex_String]:=Module[{listbeg,listend,indexes1},
listbeg=EchoFunction[Length]@StringPosition[tex,"\\begin"];
listend=EchoFunction[Length]@StringPosition[tex,"\\end"];
indexes1=Echo@Union[First/@listbeg,First/@listend];
Join[Table[
First@StringCases[
StringTake[StringDrop[tex,indexes1[[i]]],UpTo[Min[indexes1[[i]]+14,indexes1[[i+1]]]]],
Shortest["begin{"~~__~~"}"]|Shortest["end{"~~__~~"}"]],{i,Range[Length[indexes1]-1]}],{"end{document}"}]]
arXivTeXPartVisualize[texlist_List,keyword_String]:=
Association@DeleteCases[
MapIndexed[First[#2]->TabView@StringCases[#,Shortest["\\begin{"<>keyword<>"}"~~__~~"\\end{"<>keyword<>"}"]]&,texlist],
HoldPattern[_Integer->TabView[{}]]]
ArXivTeXFormulae[id_String,eqword_String]:=
StringCases[ArXivTeXDocument[id],Shortest["\\begin{"<>eqword<>"}"~~__~~"\\end{"<>eqword<>"}"]]
ArXivTeXFormulae[id_String]:=
Association@DeleteCases[Join[
{"$"->StringCases[ArXivTeXDocument[id],Shortest["$"~~__~~"$"]]},
Table[
word->StringCases[ArXivTeXDocument[id],Shortest["\\begin{"<>word<>"}"~~__~~"\\end{"<>word<>"}"]],
{word,{"equation","align","aligned","gather","equation*","align*","aligned*","gather*"}}](*,
{"\\be"->StringCases[ArXivTeXDocument[id],Shortest["\\be"~~__~~"\\ee"]],
"\\bea"->StringCases[ArXivTeXDocument[id],Shortest["\\bea"~~__~~"\\eea"]],
"\\ba"->StringCases[ArXivTeXDocument[id],Shortest["\\ba"~~__~~"\\ea"]]}*)],
HoldPattern[_String->{}]]
(* ::Subsection::Closed:: *)
(*Citations*)
apiCitationsFull[articles_List,field_:"citationCount"]:=Block[{response,posnull,responseclean},(*AssociationThread[articles,*)
response=URLExecute[
HTTPRequest[
"https://api.semanticscholar.org/graph/v1/paper/batch",
<|
"Method"->"POST",
"Headers"->{"Content-Type"->"application/json"},
"Query"->{"fields"->field(*"referenceCount,citationCount,title"*)},
"Body"->ExportString[<|"ids"->Map[StringJoin["ARXIV:",#]&,articles]|>,"JSON"]
|>],
"RawJSON"
];
responseclean=DeleteCases[Sow@response,Null];
posnull=Complement[Table[{i},{i,Length[articles]}],Position[response,<|"paperId"->_String,"citationCount"->_Integer|>]];
If[field=="citationCount",AssociationThread[Delete[articles,posnull],responseclean],response]](*]*)
apiCitationsIDs[articles_List]:=Block[{response},
response=URLExecute[
HTTPRequest[
"https://api.semanticscholar.org/graph/v1/paper/batch",
<|
"Method"->"POST",
"Headers"->{"Content-Type"->"application/json"},
"Query"->{"fields"->"externalIds"},
"Body"->ExportString[<|"ids"->articles|>,"JSON"]
|>],
"RawJSON"
];
Map[Lookup[Lookup[#,"externalIds"],"ArXiv"]&,response]]
ArXivCitationsTotal[articles_List,field_:"citationCount"]:=
KeyValueMap[{#1,Lookup[#2,field]}&,
Association@(*EchoFunction["missing data for id: ",Keys@Complement[Normal@apiCitationsFullGlob[articles],#]&]@*)
DeleteCases[Normal@apiCitationsFull[articles,field],
HoldPattern[_String->_Symbol]]]
ArXivCitationsTotal[id_String,field_:"citationCount"]:=
ArXivCitationsTotal[{id},field]
ArXivCitations[id_String]:=
DeleteMissing@apiCitationsIDs[Flatten@Map[Lookup[#,"paperId"]&,Lookup[apiCitationsFull[{id},"citations"],"citations"]]]
ArXivCitations[idL_List]:=Association@Map[#->ArXivCitations[#]&,idL]
(*ArXivCitations[id_String,n_Integer]:=*)
ArXivCitationsAuthor[author_String,cat___]:=ArXivCitationsAuthor[author,cat]=Block[{part,list1,listc},
part=Partition[Flatten@Values@ArXivArticlesAuthor[author,cat],UpTo[8]];
list1=Quiet@
Flatten[Sow@MapIndexed[Monitor[Table[(Pause[3];(i->ArXivCitations[i])),{i,#}],ProgressIndicator[First[#2]/(Length[part])]]&,part],1];
listc=ReplaceAll[List@@@
DeleteCases[list1,HoldPattern[_String->_DeleteMissing]],
{s_String,l_List?(MemberQ[#,_Lookup]&)}:>{s,DeleteCases[l,_Lookup]}];
Flatten[Map[Thread[Table[#[[1]],Length[#[[2]]]]->#[[2]]]&,listc]]]
ArXivCitationsAuthor[authorL_List,cat___]:=Flatten@Map[ArXivCitationsAuthor[#,cat]&,authorL]
ArXivCitationsAuthor[authorL_List,catL_List]:=Flatten@MapThread[ArXivCitationsAuthor[#1,#2]&,{authorL,catL}]
ArXivGraphAuthor[author_String,cat___,options:OptionsPattern[Graph]]:=
Graph[EchoFunction["total citations",Length]@ArXivCitationsAuthor[author,cat],options(*VertexLabels->Placed[Automatic,Tooltip]*)]
ArXivGraphAuthor[authorL_List,cat___,options:OptionsPattern[Graph]]:=
Graph[EchoFunction["total citations",Length]@Flatten@Map[ArXivCitationsAuthor[#,cat]&,authorL],options]
ArXivGraphAuthor[authorL_List,catL_List,options:OptionsPattern[Graph]]:=
Graph[EchoFunction["total citations",Length]@Flatten@MapThread[ArXivCitationsAuthor[#1,#2]&,{authorL,catL}],options]
ArXivGraph[id_String,options:OptionsPattern[Graph]]:=
Graph[Thread[id->EchoFunction["total citations",Length]@ArXivCitations[id]],options(*VertexLabels->Placed[Automatic,Tooltip]*)]
ArXivGraph[idL_List,options:OptionsPattern[Graph]]:=
Graph[EchoFunction["total citations",Length]@Nest[Cases[DeleteCases[Flatten@Map[Pause[3];Thread[#->Quiet@ArXivCitations[#]]&,#],_?(!FreeQ[#,Failure]&),\[Infinity]],HoldPattern[_String->_String]]&,idL,1],options]
(*ArXivGraph[id_String,options:OptionsPattern[Graph]]:=
Graph[]*)
(*EchoFunction[Length]@Nest[Cases[DeleteCases[Flatten@Map[Thread[#->Quiet@ArXivCitations[#]]&,#],_?(!FreeQ[#,Failure]&),\[Infinity]],HoldPattern[_String->_String]]&,ArXivCitations["1908.08030"],1]*)
(*Graph@%*)
(* ::Subsection::Closed:: *)
(*API new articles (for next release)*)
(*to do*)
(*ArXivNewArticles[]*)
(* ::Section:: *)
(*3. Main data functionality*)
(* ::Subsection:: *)
(*Dataset lookup utilities*)
(* ::Subsubsection::Closed:: *)
(*Dataset lookup (I)*)
datasetKeys=Flatten@Union[Keys/@ArXivDataset[All]];
arXivDatasetKeys=datasetKeys;
(*Clear[ArXivDatasetLookup]*)
ArXivDatasetLookup[key_String]/;MemberQ[datasetKeys,key]:=ArXivDatasetLookup[key]=Cases[ArXivDataset[All],(key->term_):>term,{2}]
ArXivDatasetLookup[key_String,subds_List]/;MemberQ[datasetKeys,key]:=ArXivDatasetLookup[key,subds]=Cases[subds,(key->term_):>term,{2}]
(* ::Subsubsection::Closed:: *)
(*IDs*)
(*maybe ArXivDatasetItem better set as function*)
arXivIDsAssoc[All]:=arXivIDsAssoc[All]=arXivIDsAssoc[]=ArXivDatasetLookup["id"];
arXivDatasetItem=AssociationThread[arXivIDsAssoc[All],ArXivDataset[All]];