I am trying to identify observations that match between two datasets, using text string vectors $contractor and $employer, and create a TRUE/FALSE indicator on whether the contractor is in the employer list.
library(caTools)
list<-data.frame(ID=c(1:6),
employer=c("a.c. construction","abc concrete company","xyz pool construction inc","frank studebager llc","annoying contractors llc","beaumont ditch digging co inc"))
jobs<-data.frame(contractor=c("a-c construction","hank hill construction","xyz pool const incorporated","frank studebaer co","hank hill const"),
value=c(400000,284590,410280,310980))
jobs$match<-pmatch(jobs$contractor,list$employer,duplicates.ok=TRUE)
The pmatch command says there are 0 matches, but this is because the company names are sloppily entered and not spelled consistently; there are obviously matches. I have also used the fuzzy matching command agrepl, but in my actual data the number and quality of matching varies incredibly with small changes to the accepted Levenshtein distance.
There are also some answers here and here but my lack of advanced programming experience has kept me from applying the concepts there. Any thoughts are appreciated!
Related
I'm trying to merge two large datasets. The common variable, first and last name, vary in spelling between the datasets and there are many duplicates, even between similarly spelled names. I've included download links for the files and some R code below. I'll walk through what I've tried and what went wrong.
There are a few R tutorials that have tried to tackle (the common) problem of record linking, but none of dealt with large datasets. I'm hoping the SO community can help me solve this problem.
The first dataset is a large file (several hundred thousand
rows) of Federal Elections Commission political contributions.
The second is a custom dataset of the name and companies of
every Internet company founder (~5,000 rows)
https://www.dropbox.com/s/lfbr9lmurv791il/010614%20CB%20Founders%20%20-%20CB%20Founders.csv?dl=0
--Attempted code matching with regular expressions--
My first attempt, thanks to the help of previous SO suggestions, was to use agrep and regular string matching. This narrowed down the names, but resulted in too many duplicates
#Load files#
expends12 <- fread("file path for FEC", sep="|", header=FALSE)
crunchbase.raw <- fread("file path for internet founders")
exp <- expends12
cr <- crunchbase.raw
#user regular string matching#
exp$xsub= gsub("^([^,]+)\\, (.{7})(.+)", "\\2 \\1", tolower(expends12$V8))
cr$ysub= gsub("^(.{7})([^ ]+) (.+)", "\\1 \\3", tolower(cr$name))
#merge files#
fec.merge <- merge(exp,cr, by.x="xsub", by.y="ysub")
The result is 6,900 rows, so there are (a lot) of duplicates. Many rows are people with similar names as Internet founders, such as Alexander Black, but are from different states and have different job titles. So, now its a question of finding the real Internet founder.
One option to narrow the results would be filter the results by states. So, I might only take the Alexander Black from California or New York, because that is where most startups are founded. I might also only take certain job titles, such as CEO or founder. But, many founders had jobs before and after their companies, so i wouldn't want to narrow by job title too much.
Alternatively, there is an r package, RecordLinkage, but as I far as I can tell, there needs to be similar rows and columns between the datasets, which is a nonstarter for this task
I'm familiar with R, but have somewhat limited statistical knowledge and programming ability. Any step-by-step help is very much appreciated. Thank you and please let me know if there's any trouble downloading the data.
Why don't you select the columns you need from both datasets, rename them similarly and in the result object, you get the row indices for matches returned. As long as you don't reorder things, you can use the results to match both datasets.
I'm attempting to clean up a database that, over the years, had acquired many duplicate records, with slightly different names. For example, in the companies table, there are names like "Some Company Limited" and "SOME COMPANY LTD!".
My plan was to export the offending tables into R, convert names to lower case, replace common synonyms (like "limited" -> "ltd"), strip out non-alphabetic characters and then use agrep to see what looks similar.
My first problem is that agrep only accepts a single pattern to match, and looping over every company name to match against the others is slow. (Some tables to be cleaned will have tens, possibly hundreds of thousands of names to check.)
I've very briefly looked at the tm package (JSS article), and it seems very powerful but geared towards analysing big chunks of text, rather than just names.
I have a few related questions:
Is the tm package appropriate for this sort of task?
Is there a faster alternative to agrep? (Said function uses the
Levenshtein edit distance which is anecdotally slow.)
Are there other suitable tools in R, apart from agrep and tm?
Should I even be doing this in R, or should this sort of thing be
done directly in the database? (It's an Access database, so I'd
rather avoid touching it if possible.)
If you're just doing small batches that are relatively well-formed, then the compare.linkage() or compare.dedup() functions in the RecordLinkage package should be a great starting point. But if you have big batches, then you might have to do some more tinkering.
I use the functions jarowinkler(), levenshteinSim(), and soundex() in RecordLinkage to write my own function that use my own weighting scheme (also, as it is, you can't use soundex() for big data sets with RecordLinkage).
If I have two lists of names that I want to match ("record link"), then I typically convert both to lower case and remove all punctuation. To take care of "Limited" versus "LTD" I typically create another vector of the first word from each list, which allows extra weighting on the first word. If I think that one list may contain acronyms (maybe ATT or IBM) then I'll acronym-ize the other list. For each list I end up with a data frame of strings that I would like to compare that I write as separate tables in a MySQL database.
So that I don't end up with too many candidates, I LEFT OUTER JOIN these two tables on something that has to match between the two lists (maybe that's the first three letters in each list or the first three letters and the first three letters in the acronym). Then I calculate match scores using the above functions.
You still have to do a lot of manual inspection, but you can sort on the score to quickly rule out non-matches.
Maybe google refine could help. It looks maybe more fitted if you have lots of exceptions and you don't know them all yet.
What you're doing is called record linkage, and it's been a huge field of research over many decades already. Luckily for you, there's a whole bunch of tools out there that are ready-made for this sort of thing. Basically, you can point them at your database, set up some cleaning and comparators (like Levenshtein or Jaro-Winkler or ...), and they'll go off and do the job for you.
These tools generally have features in place to solve the performance issues, so that even though Levenshtein is slow they can run fast because most record pairs never get compared at all.
The Wikipedia link above has links to a number of record linkage tools you can use. I've personally written one called Duke in Java, which I've used successfully for exactly this. If you want something big and expensive you can buy a Master Data Management tool.
In your case probably something like edit-distance calculation would work, but if you need to find near duplicates in larger text based documents, you can try
http://www.softcorporation.com/products/neardup/
I have a dataset with individuals names, addresses, phone numbers, etc. Some individuals appear multiple times, with slightly varying names/ and/or addressees and/or phone numbers. A snippet of the fake data is shown below:
first last address phone
Jimmy Bamboo P.O. Box 1190 xxx-xx-xx00
Jimmy W. Bamboo P.O. Box 1190 xxx-xx-xx22
James West Bamboo P.O. Box 219 xxx-66-xxxx
... and so on. Some times E. is spelled out as east, St. as Street, at other times they are not.
What I need to do is run through almost 120,000 rows of data to identify each unique individual based on their names, addresses, and phone numbers. Anyone have a clue as to how this might be done without manually running through each record, one at a time? The more I stare at it the more I think its impossible without making some judgment calls and saying if at least two or three fields are the same treat this as a single individual.
thanks!!
Ani
As I mentioned in the comments, this is not trivial. You have to decide the trade-off of programmer time/solution complexity with results. You will not achieve 100% results. You can only approach it, and the time and complexity cost will increase the closer to 100% you get. Start with an easy solution (exact matches), and see what issue most commonly causes the missed matches. Implement a fuzzy solution to address that. Rinse and repeat.
There are several tools you can use (we use them all).
1) distance matching, like Damerau Levenshtein . you can use this for names, addresses and other things. It handles error like transpositions, minor spelling, omitted characters, etc.
2) phonetic word matching - soundex is not good. There are other more advanced ones. We ended up writing our own to handle the mix of ethnicities we commonly encounter.
3) nickname lookups - many nicknames will not get caught by either phonetic or distance matching - names like Fanny for Frances. There are many nicknames like that. You can build a lookup of nicknames to regular name. Consider though the variations like Jennifer -> Jen, Jenny, Jennie, Jenee, etc.
Names can be tough. Creative spelling of names seems to be a current fad. For instance, our database has over 30 spelling variations of the name Kaitlynn, and they are all spellings of actual names. This makes nickname matching tough when you're trying to match Katy to any of those.
Here are some other answers on similar topics I've made here on stackoverflow:
Processing of mongolian names
How to solve Dilemma of storing human names in MySQL and keep both discriminability and a search for similar names?
MySQL Mixing Damerau–Levenshtein Fuzzy with Like Wildcard
You can calculate the pairwise matrix of Levenshtein distances.
See this recent post for more info: http://www.markvanderloo.eu/yaRb/2013/02/26/the-stringdist-package/
I'm attempting to clean up a database that, over the years, had acquired many duplicate records, with slightly different names. For example, in the companies table, there are names like "Some Company Limited" and "SOME COMPANY LTD!".
My plan was to export the offending tables into R, convert names to lower case, replace common synonyms (like "limited" -> "ltd"), strip out non-alphabetic characters and then use agrep to see what looks similar.
My first problem is that agrep only accepts a single pattern to match, and looping over every company name to match against the others is slow. (Some tables to be cleaned will have tens, possibly hundreds of thousands of names to check.)
I've very briefly looked at the tm package (JSS article), and it seems very powerful but geared towards analysing big chunks of text, rather than just names.
I have a few related questions:
Is the tm package appropriate for this sort of task?
Is there a faster alternative to agrep? (Said function uses the
Levenshtein edit distance which is anecdotally slow.)
Are there other suitable tools in R, apart from agrep and tm?
Should I even be doing this in R, or should this sort of thing be
done directly in the database? (It's an Access database, so I'd
rather avoid touching it if possible.)
If you're just doing small batches that are relatively well-formed, then the compare.linkage() or compare.dedup() functions in the RecordLinkage package should be a great starting point. But if you have big batches, then you might have to do some more tinkering.
I use the functions jarowinkler(), levenshteinSim(), and soundex() in RecordLinkage to write my own function that use my own weighting scheme (also, as it is, you can't use soundex() for big data sets with RecordLinkage).
If I have two lists of names that I want to match ("record link"), then I typically convert both to lower case and remove all punctuation. To take care of "Limited" versus "LTD" I typically create another vector of the first word from each list, which allows extra weighting on the first word. If I think that one list may contain acronyms (maybe ATT or IBM) then I'll acronym-ize the other list. For each list I end up with a data frame of strings that I would like to compare that I write as separate tables in a MySQL database.
So that I don't end up with too many candidates, I LEFT OUTER JOIN these two tables on something that has to match between the two lists (maybe that's the first three letters in each list or the first three letters and the first three letters in the acronym). Then I calculate match scores using the above functions.
You still have to do a lot of manual inspection, but you can sort on the score to quickly rule out non-matches.
Maybe google refine could help. It looks maybe more fitted if you have lots of exceptions and you don't know them all yet.
What you're doing is called record linkage, and it's been a huge field of research over many decades already. Luckily for you, there's a whole bunch of tools out there that are ready-made for this sort of thing. Basically, you can point them at your database, set up some cleaning and comparators (like Levenshtein or Jaro-Winkler or ...), and they'll go off and do the job for you.
These tools generally have features in place to solve the performance issues, so that even though Levenshtein is slow they can run fast because most record pairs never get compared at all.
The Wikipedia link above has links to a number of record linkage tools you can use. I've personally written one called Duke in Java, which I've used successfully for exactly this. If you want something big and expensive you can buy a Master Data Management tool.
In your case probably something like edit-distance calculation would work, but if you need to find near duplicates in larger text based documents, you can try
http://www.softcorporation.com/products/neardup/
I need to automatically match product names (cameras, laptops, tv-s etc) that come from different sources to a canonical name in the database.
For example "Canon PowerShot a20IS", "NEW powershot A20 IS from Canon" and "Digital Camera Canon PS A20IS"
should all match "Canon PowerShot A20 IS". I've worked with levenshtein distance with some added heuristics (removing obvious common words, assigning higher cost to number changes etc), which works to some extent, but not well enough unfortunately.
The main problem is that even single-letter changes in relevant keywords can make a huge difference, but it's not easy to detect which are the relevant keywords. Consider for example three product names:
Lenovo T400
Lenovo R400
New Lenovo T-400, Core 2 Duo
The first two are ridiculously similar strings by any standard (ok, soundex might help to disinguish the T and R in this case, but the names might as well be 400T and 400R), the first and the third are quite far from each other as strings, but are the same product.
Obviously, the matching algorithm cannot be a 100% precise, my goal is to automatically match around 80% of the names with a high confidence.
Any ideas or references is much appreciated
I think this will boil down to distinguishing key words such as Lenovo from chaff such as New.
I would run some analysis over the database of names to identify key words. You could use code similar to that used to generate a word cloud.
Then I would hand-edit the list to remove anything obviously chaff, like maybe New is actually common but not key.
Then you will have a list of key words that can be used to help identify similarities. You would associate the "raw" name with its keywords, and use those keywords when comparing two or more raw names for similarities (literally, percentage of shared keywords).
Not a perfect solution by any stretch, but I don't think you are expecting one?
The key understanding here is that you do have a proper distance metric. That is in fact not your problem at all. Your problem is in classification.
Let me give you an example. Say you have 20 entries for the Foo X1 and 20 for the Foo Y1. You can safely assume they are two groups. On the other hand, if you have 39 entries for the Bar X1 and 1 for the Bar Y1, you should treat them as a single group.
Now, the distance X1 <-> Y1 is the same in both examples, so why is there a difference in the classification? That is because Bar Y1 is an outlier, whereas Foo Y1 isn't.
The funny part is that you do not actually need to do a whole lot of work to determine these groups up front. You simply do an recursive classification. You start out with node per group, and then add the a supernode for the two closest nodes. In the supernode, store the best assumption, the size of its subtree and the variation in it. As many of your strings will be identical, you'll soon get large subtrees with identical entries. Recursion ends with the supernode containing at the root of the tree.
Now map the canonical names against this tree. You'll quickly see that each will match an entire subtree. Now, use the distances between these trees to pick the distance cutoff for that entry. If you have both Foo X1 and Foo Y1 products in the database, the cut-off distance will need to be lower to reflect that.
edg's answer is in the right direction, I think - you need to distinguish key words from fluff.
Context matters. To take your example, Core 2 Duo is fluff when looking at two instances of a T400, but not when looking at a a CPU OEM package.
If you can mark in your database which parts of the canonical form of a product name are more important and must appear in one form or another to identify a product, you should do that. Maybe through the use of some sort of semantic markup? Can you afford to have a human mark up the database?
You can try to define equivalency classes for things like "T-400", "T400", "T 400" etc. Maybe a set of rules that say "numbers bind more strongly than letters attached to those numbers."
Breaking down into cases based on manufacturer, model number, etc. might be a good approach. I would recommend that you look at techniques for term spotting to try and accomplish that: http://www.worldcat.org/isbn/9780262100854
Designing everything in a flexible framework that's mostly rule driven, where the rules can be modified based on your needs and emerging bad patterns (read: things that break your algorithm) would be a good idea, as well. This way you'd be able to improve the system's performance based on real world data.
You might be able to make use of a trigram search for this. I must admit I've never seen the algorithm to implement an index, but have seen it working in pharmaceutical applications, where it copes very well indeed with badly misspelt drug names. You might be able to apply the same kind of logic to this problem.
This is a problem of record linkage. The dedupe python library provides a complete implementation, but even if you don't use python, the documentation has a good overview of how to approach this problem.
Briefly, within the standard paradigm, this task is broken into three stages
Compare the fields, in this case just the name. You can use one or more comparator for this, for example an edit distance like the Levenshtein distance or something like the cosine distance that compares the number of common words.
Turn an array fo distance scores into a probability that a pair of records are truly about the same thing
Cluster those pairwise probability scores into groups of records that likely all refer to the same thing.
You might want to create logic that ignores the letter/number combination of model numbers (since they're nigh always extremely similar).
Not having any experience with this type of problem, but I think a very naive implementation would be to tokenize the search term, and search for matches that happen to contain any of the tokens.
"Canon PowerShot A20 IS", for example, tokenizes into:
Canon
Powershot
A20
IS
which would match each of the other items you want to show up in the results. Of course, this strategy will likely produce a whole lot of false matches as well.
Another strategy would be to store "keywords" with each item, such as "camera", "canon", "digital camera", and searching based on items that have matching keywords. In addition, if you stored other attributes such as Maker, Brand, etc., you could search on each of these.
Spell checking algorithms come to mind.
Although I could not find a good sample implementation, I believe you can modify a basic spell checking algorithm to comes up with satisfactory results. i.e. working with words as a unit instead of a character.
The bits and pieces left in my memory:
Strip out all common words (a, an, the, new). What is "common" depends on context.
Take the first letter of each word and its length and make that an word key.
When a suspect word comes up, looks for words with the same or similar word key.
It might not solve your problems directly... but you say you were looking for ideas, right?
:-)
That is exactly the problem I'm working on in my spare time. What I came up with is:
based on keywords narrow down the scope of search:
in this case you could have some hierarchy:
type --> company --> model
so that you'd match
"Digital Camera" for a type
"Canon" for company and there you'd be left with much narrower scope to search.
You could work this down even further by introducing product lines etc.
But the main point is, this probably has to be done iteratively.
We can use the Datadecision service for matching products.
It will allow you to automatically match your product data using statistical algorithms. This operation is done after defining a threshold score of confidence.
All data that cannot be automatically matched will have to be manually reviewed through a dedicated user interface.
The online service uses lookup tables to store synonyms as well as your manual matching history. This allows you to improve the data matching automation next time you import new data.
I worked on the exact same thing in the past. What I have done is using an NLP method; TF-IDF Vectorizer to assign weights to each word. For example in your case:
Canon PowerShot a20IS
Canon --> weight = 0.05 (not a very distinguishing word)
PowerShot --> weight = 0.37 (can be distinguishing)
a20IS --> weight = 0.96 (very distinguishing)
This will tell your model which words to care and which words to not. I had quite good matches thanks to TF-IDF.
But note this: a20IS cannot be recognized as a20 IS, you may consider to use some kind of regex to filter such cases.
After that, you can use a numeric calculation like cosine similarity.