Status: mostly implemented (fuzzycat) Bibliographic Entity Fuzzy Match and Verification ==================================================== This document summarizes work so far on entity "fuzzy matching" and match verification, notes some specific upcoming use cases for such methods, and proposes new generic routines to be implemented. There are three main routines desired: **Match verification:** given two bibliographic metadata records (or two entire entities), confirm whether they refer to the exact same version of the entity. Optionally, also determine if they are not the exact same entity, but are variations of the same entity (eg, releases that should be grouped under a shared work entity). Performance is not as critical as correctness. Should be a pure, in-memory routine (not touch the network or external services). **Fuzzy matching:** of bibliographic metadata to entity in current/live Fatcat catalog. Eg, given complete or partial metadata about a paper or other entity, return a list of candidate matches. Emphasis on recall over precision; better to return false matches than missed records. This would likely hit the fatcat elasticsearch indexes (search.fatcat.wiki), which are continuously updated to be in sync with the catalog itself (API). Expected to scale to, eg, 5-10 lookups per second and operate over up to a couple million entities during cleanup or merging operations. Should operate per record, on-demand, always up-to-date (aka, not a batch process). **Bulk fuzzy match:** a tool capable of matching hundreds or billions of raw metadata records against the entire fatcat catalog, resulting in candidate fuzzy match pairs or groupings. The two main applications are de-duplicating or grouping releases over the entire catalog (aka, matching the catalog against itself), matching billions of citations (structured partial metadata) against release entities, and grouping citations which fail to match to existing entities against each other. Likely to include a batch mode, though may also include an efficient per-record lookup API as well. As a terminology note, the outputs of a fuzzy match are called "candidate matches", and the output of match verificatino would be "confirmed match" or "confident match". A "self-match" is when an exact complete entity is compared to a set it already exists in, and matches to itself (aka, fatcat entity identifier is exact match). "Identifier matches" are an easy case when external identifiers (like DOI, ISSN, ORCID) are used for matching; note that the Fatcat lookup API always returns the first such match, when there may actually be multiple entities with the same external identifier, so this may not always be sufficient. ## Container Matching Containers are a simpler case, so will discuss those first. Function signatures would look like: verify_container_match(left:container, right:container) -> status:str match_container_fuzzy(record:??) -> [candidate:container] Verify statuses could be: - `exact`: all metadata fields match byte-for-byte - `strong`: good confidence these are the same - `weak`: could be a match, perhaps missing enough metadata to be confident - `ambiguous`: not enough confidence that is or even isn't a match - `not-match`: confident that these are *not* the same container (TODO: better word?) Alternatively, could return a confidence floating point number, but that puts burdern of interpretation on external code. Fields of interest would be at least: - name - original name - aliases - publisher - abbrev Some test cases that match verification should probably handle (just making these up): - differences in title whitespace and capitalization - title of one record has ISSN appended ("PLOS One" matches "PLOS One 1932-6203") - title of one record has publisher appended ("PLOS One" matches "PLOS One (Public Library of Science)") - record with original (non-English) name in name field matches fatcat record where the non-Enlish title is in `original_title` field - difference of "The" doesn't matter ("Lancet" matches "The Lancet") - detect and reject bogus names Nice to haves: - records with only abbreviation or acroynm match (for "official" abbreviations and acronyms, which may need to be recorded as alias). - records of full name match when the "official" title is now an acroynum (eg, "British Medical Journal" matches "The BMJ") - optionally, detect and return `ambiguous` for a fixed list of known-ambiguous names (eg, two journals with very similar titles, name or acronym along can't distinguish) Can't remember if we already have aliases stored in container entity `extra` yet, but idea is to store "also known as" names to help with fuzzy matching. The main application of these routines would be adding container linkage to releases where we have a container name but no identifier (eg, an ISSN). We have millions of releases (many with DOIs) that have a container name but no linked container. We also want to import millions of papers based on GROBID metadata alone, where we will likely only extract a journal name, and will want to do lookups on that. For the particular case of containers, we'll probably want to memoize results (aka, cache lookups) for efficiency. Probably will also want a unified helper function like: match_container(name:str, **kwargs) -> (status:str, match:Option) which would handle caching (maybe this is a class/object not a function?), call `match_container_fuzzy()` to get candidates, call `verify_container_match()` on each candidate, and ensure there is only one `exact` or `strong` match. Eg, if there are multiple `weak` matches, should return `ambiguous` for the group overall. Another speculative application of these routines could be as part of chocula, to try and find "true" ISSNs for records where we know the ISSN is not registered or invalid (eg, ISSN checksum digit fails). Another would be to look for duplicate container/ISSNs, where there are multiple ISSNs for the same journal but only one has any papers actually published; in that case we would maybe want to mark the other container entity as a "stub". Test datasets: - in kibana/ES, filter for "`container_id` does not exist" and "`container_name` exists" - in sandcrawler, dump `grobid` table and look in the metadata snippet, which includes extracted journal info ## Release Matching (verification and fuzzy, not bulk fuzzy) For release entities, the signature probably looks something like: verify_release_match(left:release, right:release) -> status:str how confident, based on metadata, that these are same release, or should be grouped under same work? exact_release_match(left:release, right:release) -> bool exact_work_match(left:release, right:release) -> bool Instead of full release entities, we could use partial metadata in the form of a python dataclass or named tuple. If we use a struct, will need a routine to convert full entities to the partial struct; if we use full entities, will probably want a helper to construct entities from partial metadata. Don't know which fields would be needed, but guessing at least the following, in priority order: - if full entity: `ident` (and `work_id` for case of releases) - `title` - `authors` (at least list of surnames, possibly also raw and given names) - `ext_ids` - `release_year` (and full `release_date` if available) - volume, issue, pages - `subtitle` - `original_title` - container name (and `container_id` if available) - `release_type` and `release_stage` (particularly for work/release grouping vs. match) For releases, the "status" output could be: - `strong` (good confidence) - `weak` (seems good, but maybe not enough metadata to be sure) - `work-strong` (good confidence that same work, but not same release) - `work-weak` - `ambiguous` - `not-match` (name?) Cases we should handle: - ability to filter out self-matches from fuzzy matcher. Eg, if we want to find a duplicate of an existing release, should be able to filter out self-match (as a kwarg?) - ability to filter out entire categories of matches. eg, match only to published works (`release_stage`), only to papers (`release_type`), only not match to longtail OA papers (`is_longtail_oa` ES flag) - have an in-memory stoplist for ambiguous titles (eg, "abstract", "index") - differences in punctuation, capitalization - single-character typos - subtitle/title matching (eg: {title: "Important Research", subtitle: "A History"} should match {title: "Important Research: A History", subtitle: None}) - record with only one author, surname only should be able to match against full author list. maybe a flag to indicate this case? eg, for matching some citation styles where only one author is listed - years are +/- 1. certainly for pre-prints ("work matches"), but also different databases sometimes have different semantics about whether "publication date" or "submission date" or "indexed date" are used as the `release_date` (which we consider the "publication date"). Maybe "weak" match in this case - (probably a lot more i'm not thinking of) Nice to have (but harder?): - journal/container matching where one side has an abbreviation, acronym, or alias of the other. does this require a network fetch? maybe cached or pre-loaded? may not be important, do testing first. Note that entire container entity is transcluded when doing full release entity API lookups. This may be important for citation matching/verification Will probably want a helper function to check that a metadata record (or entity) has enough metadata and seems in-scope for matching. For example, a record with title of just "Abstract" should probably be blocked from any match attempt, because there are so many records with that metadata. On the other hand, if there is an external identifier (eg, DOI), could still attempt a direct match. Maybe something like: can_verify_match(release:release) -> boolean Test datasets: - PDFs crawled as part of longtail OA crawls (see context below). We have both fatcat release already imported, and new GROBID-extracted works. Can use glutton fuzzy matching for comparison, or verify those glutton matches - many, many unmatched reference strings. will do separate Optionally, we could implement a glutton-compatible API with equivalent or better performance for doing GROBID "header consolidation". If performance is great, could even use it for reference conslidation at crawl/ingest time. ## Bulk Fuzzy Current concept for this is to implement Semantic Scholar's algorithm (described below) in any of python, golang, or rust, to function for all these use-cases: - grouping releases in fatcat which are variants of the same work (or, eg, publisher registered multiple DOIs for same paper by accident) into the same work - reference matching from structured partial metadata to fatcat releases - grouping of unmatched references (from reference matching) as structured partial metadata, with the goal of finding, eg, the "100,000 most cited papers which do not have a fatcat entity", and creating fatcat entities for them Optionally, we could also architect/design this tool to replace biblio-glutton for ingest-time "reference consolidation", by exposing a biblio-glutton compatible API. If this isn't possible or hard it could become a later tool instead. Eg, shouldn't sacrifice batch performance for this. In particular, for ingest-time reference matching we'd want the backing corpus to be updated continuously, which might be tricky or in conflict with batch-mode design. ## Existing Fatcat Work ### Hadoop matching pipeline In Summer 2018, the fatcat project had a wonderful volunteer, Ellen Spertus. Ellen implemented a batch fuzzy matching pipeline in Scala (using the Scalding map/reduce framework) that ran on our Hadoop cluster. We used it to "join" GROBID metadata from PDF files against a Crossref metadata dump. The Scala job worked by converting input metadata records into simple "bibjson" metadata subsets (plus keeping the original record identifiers, eg Crossref DOI or PDF file hash, for later import). It created a key for each record by normalizing the title (removing all whitespace and non-alphanumeric characters, lower-casing, etc; we called this a "slug"), and filtering out keys from a blocklist. We used the map/reduce framework to then join the two tables on these keys, and then filtered the output pairs with a small bit of addiitonal title similarity comparison logic, then dumped the list of pairs as a table to Hadoop, sorted by join key (slug). I can't remember if we had any other heuristics in the Scala code. This was followed by a second processing stage in python, which iterated over the full list. It grouped pairs by key, and discarded any groups that had too many pairs (on the assumption that the titles were too generic). It then ran additional quality checks (much easier/faster to implement in python) on year, author names (eg, checking that the number of authors matched). The output of this filtering was then fed into a fatcat importer which matched the PDFs to releases based on DOI. We got several million matches using this technique. In the end we really only ran this pipeline once. Hadoop (and HBase in particular) ended up being frustrating to work with, as jobs took hours or days to run, and many bugs would only appear when run against the full dataset. A particular problem that came up with the join approach was N^2 explosions for generic titles, where the number of join rows would get very large (millions of rows) for generic titles, even after we filtered out the top couple hundred most popular join keys. TODO: should update this section with specific algorithms and parameters used by reading the Scala and Python source ## Longtail OA Import Filtering Not directly related to matching, but filtering mixed-quality metadata. As part of Longtail OA preservation work, we ran a crawl of small OA journal websites, and then ran GROBID over the resulting PDFs to extract metadata. We then filtered the output metadata using quality heuristics, then inserted both new releases (with no external identifiers, just the extracted metadata) and the associated file. The metadata filtering pipeline is interesting because of all the bad metadata it detected. Eg, long titles, used the normalization and blocklist from the Hadoop matching work, poor author metadata, etc. A big problem that was only noticed after this import was that actually many of the papers imported were duplicates of existing fatcat papers with DOIs or other identifiers. This was because the crawl ended up spidering some general purpose repositories, which contained copies of large-publisher OA papers (eg, PLOS papers). The solution to this will use fuzzy matching in two ways. First, for future imports of this type, we will fuzzy matches against the catalog to check that there isn't already a metadata record; possibly link the file to matched existing entities (based on confidence), but certainly don't create new records unless sure that there isn't an existing one (`no-match`). Also need to ensure there are not duplicates *within* each import batch, but either running the import slowly in a single thread (so elasticsearch and the matching system has time to synchronize), or doing a batch fuzzy match first. Or possibly some other pre-filtering idea. Secondly, we can go back over these longtail OA works (which are tagged as such in the fatcat catalog) and attempt to match them against non-longtail fatcat releases (eg, those with existing PMID or DOI), and merge the releases together (note: redirecting the longtail release to the full one, resulting in a single release, not just doing work grouping of releases). A separate problem from this import is that none of the papers have container linkage (though many or all have container names successfully extracted). After doing release-level merging, we should use container fuzzy matching to update container linkage for these entities. We could potentially do this as a two stage project where we dump all the container name strings, prioritize them by release count, and iterate on container matching until we are happy with the results, then run the actual release updates. ### biblio-glutton [biblio-glutton][biblio-glutton] is a companion tool for GROBID to do record matching and metadata enrichment of both "header" metadata (aka, extracted metadata about the fulltext paper in the PDF itself) and references (extracted from the reference/bibliography section of the fulltext paper). GROBID calls this "consolidation". biblio-glutton supports a couple different metadata index sources, including Crossref dumps. IA has patched both GROBID and biblio-glutton to work with fatcat metadata directly, and to embed fatcat release identifiers in output TEI-XML when there is a match. We have found performance to be fine for header consolidation, but too slow for reference consolidation. This is because there is only one glutton lookup per PDF for header mode, vs 20-50 lookups per PDF for reference consolidation, which takes longer than the overall PDF extraction. In our default configuration, we only do header consolidation. biblio-glutton runs as a REST API server, which can be queried separately from the GROBID integration. It uses the JVM (can't remember if Java or Scala), and works by doing an elasticsearch query to find candidates, then selects the best candidate (if any) and looks up full metadata records from one or more LMDB key/value databases. It requires it's own elasticsearch index with a custom schema, and large LMDB files on disk (should be SSD for speed). The process of updating the LMDB files and elasticsearch index are currently manual (with some scripts), generated using bulk metadata fatcat dumps. This means the glutton results get out of sync from the fatcat catalog. The current update process involves stopping glutton (which means stopping all GROBID processing) for a couple hours. Compare this to the fatcat search index (search.fatcat.wiki), which is continuously updated from the changelog feed, and even during index schema changes has zero (or near zero) downtime. [biblio-glutton]: https://github.com/kermitt2/biblio-glutton ## Existing External Work and Reading "The Lens MetaRecord and LensID: An open identifier system for aggregated metadata and versioning of knowledge artefacts" ### Semantic Scholar Semantic Scholar described their technique for doing bulk reference matching and entity merging, summarized here: Fast candidate lookups are done using only a subset of the title. Title strings are turned in to an array of normalized tokens (words), with stopwords (like "a", "the") removed. Two separate indices are created: one with key as the the first three tokens, and the other with the key as the last three tokens. For each key, there will be a bucket of many papers (or just paper global identifiers). A per-paper lookup by title will fetch candidates from both indices. It is also possible to iterate over both indices by bucket and doing further processing between all the papers, then combined the matches/groups from both iterations. The reason for using two indices is to be robust against mangled metadata where there is added junk or missing words at either the beginning or end of the title. To verify candidate pairs, the Jaccard similarity is calculated between the full original title strings. This flexibly allows for character typos (human or OCR), punctuation differences, and for longer titles missing or added words. Roughly, the amount of difference is proportional to the total length of the strings, so short titles must be a near-exact match, while long titles can have entire whole words different. In addition to the title similarity check, only the first author surnames and year of publication are further checked as heuristics to confirm matches. If I recall correctly, not even the journal name is is compared. They have done both performance and correctness evaluation of this process and are happy with the results, particularly for reference matching. My (Bryan) commentary on this is that it is probably a good thing to try implementing for bulk fuzzy candidate generation. I have noticed metadata issues on Semantic Scholar with similarly titles papers getting grouped, or fulltext PDF copies getting matched to the wrong paper. I think for fatcat we should be more conservative, which we can do in our match verification function. ### Crossref Crossref has done a fair amount of work on the reference matching problem and detecting duplicate records. In particular, Dominika Tkaczyk has published a number of papers and blog posts: https://fatcat.wiki/release/search?q=author%3A%22Dominika+Tkaczyk%22 https://www.crossref.org/authors/dominika-tkaczyk/ Some specific posts: "Double trouble with DOIs" "Reference matching: for real this time" Java implementation and testing/evaluation framework for their reference matcher: - -