Here at work, we often need to find a string from the list of strings that is the closest match to some other input string. Currently, we are using Needleman-Wunsch algorithm. The algorithm often returns a lot of false-positives (if we set the minimum-score too low), sometimes it doesn't find a match when it should (when the minimum-score is too high) and, most of the times, we need to check the results by hand. We thought we should try other alternatives.
Do you have any experiences with the algorithms?
Do you know how the algorithms compare to one another?
I'd really appreciate some advice.
PS: We're coding in C#, but you shouldn't care about it - I'm asking about the algorithms in general.
Oh, I'm sorry I forgot to mention that.
No, we're not using it to match duplicate data. We have a list of strings that we are looking for - we call it search-list. And then we need to process texts from various sources (like RSS feeds, web-sites, forums, etc.) - we extract parts of those texts (there are entire sets of rules for that, but that's irrelevant) and we need to match those against the search-list. If the string matches one of the strings in search-list - we need to do some further processing of the thing (which is also irrelevant).
We can not perform the normal comparison, because the strings extracted from the outside sources, most of the times, include some extra words etc.
Anyway, it's not for duplicate detection.
OK, Needleman-Wunsch(NW) is a classic end-to-end ("global") aligner from the bioinformatics literature. It was long ago available as "align" and "align0" in the FASTA package. The difference was that the "0" version wasn't as biased about avoiding end-gapping, which often allowed favoring high-quality internal matches easier. Smith-Waterman, I suspect you're aware, is a local aligner and is the original basis of BLAST. FASTA had it's own local aligner as well that was slightly different. All of these are essentially heuristic methods for estimating Levenshtein distance relevant to a scoring metric for individual character pairs (in bioinformatics, often given by Dayhoff/"PAM", Henikoff&Henikoff, or other matrices and usually replaced with something simpler and more reasonably reflective of replacements in linguistic word morphology when applied to natural language).
Let's not be precious about labels: Levenshtein distance, as referenced in practice at least, is basically edit distance and you have to estimate it because it's not feasible to compute it generally, and it's expensive to compute exactly even in interesting special cases: the water gets deep quick there, and thus we have heuristic methods of long and good repute.
Now as to your own problem: several years ago, I had to check the accuracy of short DNA reads against reference sequence known to be correct and I came up with something I called "anchored alignments".
The idea is to take your reference string set and "digest" it by finding all locations where a given N-character substring occurs. Choose N so that the table you build is not too big but also so that substrings of length N are not too common. For small alphabets like DNA bases, it's possible to come up with a perfect hash on strings of N characters and make a table and chain the matches in a linked list from each bin. The list entries must identify the sequence and start position of the substring that maps to the bin in whose list they occur. These are "anchors" in the list of strings to be searched at which an NW alignment is likely to be useful.
When processing a query string, you take the N characters starting at some offset K in the query string, hash them, look up their bin, and if the list for that bin is nonempty then you go through all the list records and perform alignments between the query string and the search string referenced in the record. When doing these alignments, you line up the query string and the search string at the anchor and extract a substring of the search string that is the same length as the query string and which contains that anchor at the same offset, K.
If you choose a long enough anchor length N, and a reasonable set of values of offset K (they can be spread across the query string or be restricted to low offsets) you should get a subset of possible alignments and often will get clearer winners. Typically you will want to use the less end-biased align0-like NW aligner.
This method tries to boost NW a bit by restricting it's input and this has a performance gain because you do less alignments and they are more often between similar sequences. Another good thing to do with your NW aligner is to allow it to give up after some amount or length of gapping occurs to cut costs, especially if you know you're not going to see or be interested in middling-quality matches.
Finally, this method was used on a system with small alphabets, with K restricted to the first 100 or so positions in the query string and with search strings much larger than the queries (the DNA reads were around 1000 bases and the search strings were on the order of 10000, so I was looking for approximate substring matches justified by an estimate of edit distance specifically). Adapting this methodology to natural language will require some careful thought: you lose on alphabet size but you gain if your query strings and search strings are of similar length.
Either way, allowing more than one anchor from different ends of the query string to be used simultaneously might be helpful in further filtering data fed to NW. If you do this, be prepared to possibly send overlapping strings each containing one of the two anchors to the aligner and then reconcile the alignments... or possibly further modify NW to emphasize keeping your anchors mostly intact during an alignment using penalty modification during the algorithm's execution.
Hope this is helpful or at least interesting.
Related to the Levenstein distance: you might wish to normalize it by dividing the result with the length of the longer string, so that you always get a number between 0 and 1 and so that you can compare the distance of pair of strings in a meaningful way (the expression L(A, B) > L(A, C) - for example - is meaningless unless you normalize the distance).
We are using the Levenshtein distance method to check for duplicate customers in our database. It works quite well.
Alternative algorithms to look at are agrep (Wikipedia entry on agrep),
FASTA and BLAST biological sequence matching algorithms. These are special cases of approximate string matching, also in the Stony Brook algorithm repositry. If you can specify the ways the strings differ from each other, you could probably focus on a tailored algorithm. For example, aspell uses some variant of "soundslike" (soundex-metaphone) distance in combination with a "keyboard" distance to accomodate bad spellers and bad typers alike.
Use FM Index with Backtracking, similar to the one in Bowtie fuzzy aligner
In order to minimize mismatches due to slight variations or errors in spelling, I've used the Metaphone algorithm, then Levenshtein distance (scaled to 0-100 as a percentage match) on the Metaphone encodings for a measure of closeness. That seems to have worked fairly well.
To expand on Cd-MaN's answer, it sounds like you're facing a normalization problem. It isn't obvious how to handle scores between alignments with varying lengths.
Given what you are interested in, you may want to obtain p-values for your alignment. If you are using Needleman-Wunsch, you can obtain these p-values using Karlin-Altschul statistics http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html
BLAST will can local alignment and evaluate them using these statistics. If you are concerned about speed, this would be a good tool to use.
Another option is to use HMMER. HMMER uses Profile Hidden Markov Models to align sequences. Personally, I think this is a more powerful approach since it also provides positional information. http://hmmer.janelia.org/
Related
I looking for a algorithm, function or technique that can take a string and convert it to a number. I would like the algorithm or function to have the following properties:
Identical string yields the same calculated value
Similar strings would yield similar values (similar can be defined as similar in meaning or similar in composition)
Capable of handling strings of variable length
I read an article several years ago that gives me hope that this can be achieved. Unfortunately, I have been unable to recall the source of the article.
Similar in composition is pretty easy, I'll let somebody else tackle that.
Similar in meaning is a lot harder, but fun :), I remember reading an article about how a neural network was trained to construct a 2D "semantic meaning graph" of a whole bunch of english words, where the distance between two words represented how "similar" they are in meaning, just by training it on wikipedia articles.
You could do the same thing, but make it one-dimensional, that will give you a single continuous number, where similar words will be close to each other.
Non-serious answer: Map everything to 0
Property 1: check. Property 2: check. Property 3: check.
But I figure you want dissimilar strings to get different values, too. The question then is, what is similar and what is not.
Essentially, you are looking for a hash function.
There are a lot of hash functions designed with different objectives. Crypographic hashes for examples are pretty expensive to compute, because you want to make it really hard to go backwards or even predict how a change to the input affects the output. So they try really hard to violate your condition 2. There are also simpler hash functions that mostly try to spread the data. They mostly try to ensure that close input values are not close to each other afterwards (but it is okay if it is predictable).
You may want to read up on Wikipedia:
https://en.wikipedia.org/wiki/Hash_function#Finding_similar_substrings
(Yes, it has a section on "Finding similar substrings" via Hashing)
Wikipedia also has a list of hash functions:
https://en.wikipedia.org/wiki/List_of_hash_functions
There is a couple of related stuff for you. For example minhash could be used. Here is a minhash-inspired approach for you: Define a few random lists of all letters in your alphabet. Say I have the letters "abcde" only for this example. I'll only use two lists for this example. Then my lists are:
p1 = "abcde"
p2 = "edcba"
Let f1(str) be the index in p1 of the first letter in my test word, f2(str) the first letter in p2. So the word "bababa" would map to 0,3. The word "ababab" also. The word "dada" would make to 0,1, while "ce" maps to 2,0. Note that this map is invariant to word permutations (because it treats them as sets) and for long texts it will converge to "0,0". Yet with some fine tuning it can give you a pretty fast chance of finding candidates for closer inspection.
Fuzzy hashing (context triggered piecewise hashing) may be what you are looking for.
Implemenation: ssdeep
Explanation of the algorithm: Identifying almost identical files using context triggered piecewise hashing
I think you're probably after a hash function, as numerous posters have said. However, similar in meaning is also possible, after a fashion: use something like Latent Dirichlet Allocation or Latent Semantic Analysis to map your word into multidimensional space, relative to a model trained on a large collection of text (these pre-trained models can be downloaded if you don't have access to a representative sample of the kind of text you're interested in). If you need a scalar value rather than multi-dimensional vector (it's hard to tell, you don't say what you want it for) you could try a number of things like the probability of the most probable topic, the mean across the dimensions, the index of the most probable topic, etc. etc.
num = 0
for (byte in getBytes(str))
num += UnsignedIntValue(byte)
This would meet all 3 properties(for #2, this works on the strings binary composition).
I'm using tesseract for OCR and have noticed, that sometimes segmentation errors occur and characters, that "obviously" belong together are split into separted strings.
Based on a list of characters and their bounding boxes found in one text line and the prilimanary OCR result suggesting, which of these characters belong to one word, which algorithms can I apply to correct segmentation errors or verify the result?
So this this the data available:
List<Word> words;
for(Word word : words){
for(Char c : word.getChars()){
char ch = c.getValue();
Rectangle rect = c.getRect();
}
}
For OCR post-correction that takes into account the characters and words, but admittedly not the bounding boxes, one common practice is
to use a dictionary of valid words, as comprehensive as possible
to check the words that results from the OCR algorithm against that dictionary
if a word cannot be found as an exact match in the dictionary, to try and find a similar one
To make this possible, you need to prepare the dictionary implementation so it enables a search for similar strings, also known as approximate string matching or fuzzy string matching.
The two main approaches for this that I am aware of are
Levenshtein atomata, as described by Schulz et al (DOI: 10.1007/s10032-002-0082-8)
Metric trees, such as the BK tree described by Baeza-Yates and Navarro (DOI: 10.1109/SPIRE.1998.712978)
These approaches, as well as general approximate string matching approaches (such as search tries, q-grams matching and n-gram matching) all inherently use some kind of edit distance measure, more or less similar to Levenshtein distance. After analysing the specific OCR errors you are dealing with, you might want to adjust the edit distance algorithm and the other resources you are using to your specific needs. This may involve things like:
Assume a lower substitution distance between characters that your OCR program confuses frequently, or characters that look particularly similar when rendered with the font or style you are dealing with
Take possible segmentation errors into account by putting frequently occurring pairs of words in the dictionary (in addition to single words)
Ensure that your dictionary contains as many named entities and other domain specific (or corpus specific) elements
Further more, you can try to use a grammar, and/or a statistical language model, such as a Hidden Markov Model or Conditional Random Field model -- similar to the models used by POS taggers -- to make word corrections in context.
Different software projects have different coding convention; even in the same project there may be different languages used and will have different convention. What is good for searching documentation (which appear outside the source files), with identifier tokens from the source code?
For example if the source has self._def_passwd, or this.defPasswrd, a query on the documentation tree should strive to match default password.
So far I've been trying to sort by Levenshtein distance, which works nicely for small edit distances, but there are too many false positives when I increase the threshold, which is problematic with white spaces in documentation.
8 0.666667 announcement getContent AnnouncementBean.java(Token.Name.Function )
8 0.666667 announcement getPercent DataObservation.java (Token.Name.Function)
8 0.666667 announcement GroupBean GroupBean.java (Token.Name.Class)
where the first value is the Levenshtein distance, second one the distance divided by the length of the word matched.
I'm thinking to
look into Jaccard, Tanimoto algorithms
intellisence/suggest kinda code
Somewhere in SO there were posts on some algorithms that bio guys use for matching sequences
Come up with regular expressions chain rules based on http://en.wikipedia.org/wiki/Naming_convention_%28programming%29
the last one being literally the last option. Which other algorithms do you think would could give better results for this kinda stuff?
Try using weighted edit distance, here you can encode knowledge of usual abbreviation, probable character mistakes by distance in keyboard. For example you can zero weight to vowels like [ao] and password will be equal to pswrd. Other option is to build word level edit distance and use synonyms here. I also have builded EditDistance which works simultaneousnesly with words and characters.
We have a list of about 150,000 words, and when the user enters a free text, the system should present a list of words from the dictionary, that are very close to words in the free text.
For instance, the user enters: "I would like to buy legoe toys in Walmart". If the dictionary contains "Lego", "Car" and "Walmart", the system should present "Lego" and "Walmart" in the list. "Walmart" is obvious because it is identical to a word in the sentence, but "Lego" is similar enough to "Legoe" to be mentioned, too. However, nothing is similar to "Car", so that word is not shown.
Showing the list should be realtime, meaning that when the user has entered the sentence, the list of words must be present on the screen. Does anybody know a good algorithm for this?
The dictionary actually contains concepts which may include a space. For instance, "Lego spaceship". The perfect solution recognizes these multi-word concepts, too.
Any suggestions are appreciated.
Take a look at http://norvig.com/spell-correct.html for a simple algorithm. The article uses Python, but there are links to implementations in other languages at the end.
You will be doing quite a few lookups of words against a fixed dictionary. Therefore you need to prepare your dictionary. Logically, you can quickly eliminate candidates that are "just too different".
For instance, the words car and dissimilar may share a suffix, but they're obviously not misspellings of each other. Now why is that so obvious to us humans? For starters, the length is entirely different. That's an immediate disqualification (but with one exception - below). So, your dictionary should be sorted by word length. Match your input word with words of similar length. For short words that means +/- 1 character; longer words should have a higher margin (exactly how well can your demographic spell?)
Once you've restricted yourself to candidate words of similar length, you'd want to strip out words that are entirely dissimilar. With this I mean that they use entirely different letters. This is easiest to compare if you sort the letters in a word alphabetically. E.g. car becomes "acr"; rack becomes "ackr". You'll do this in preprocessing for your dictionary, and for each input word. The reason is that it's cheap to determine the (size of an) difference of two sorted sets. (Add a comment if you need explanation). car and rack have an difference of size 1, car and hat have a difference of size 2. This narrows down your set of candidates even further. Note that for longer words, you can bail out early when you've found too many differences. E.g. dissimilar and biography have a total difference of 13, but considering the length (8/9) you can probably bail out once you've found 5 differences.
This leaves you with a set of candidate words that use almost the same letters, and also are almost the same length. At this point you can start using more refined algorithms; you don't need to run 150.000 comparisons per input word anymore.
Now, for the length exception mentioned before: The problem is in "words" like greencar. It doesn't really match a word of length 8, and yet for humans it's quite obvious what was meant. In this case, you can't really break the input word at any random boundary and run an additional N-1 inexact matches against both halves. However, it is feasible to check for just a missing space. Just do a lookup for all possible prefixes. This is efficient because you'll be using the same part of the dictionary over and over, e.g. g gr, gre, gree, etc. For every prefix that you've found, check if the remaining suffixis also in the dictionery, e.g. reencar, eencar. If both halves of the input word are in the dictionary, but the word itself isn't, you can assume a missing space.
You would likely want to use an algorithm which calculates the Levenshtein distance.
However, since your data set is quite large, and you'll be comparing lots of words against it, a direct implementation of typical algorithms that do this won't be practical.
In order to find words in a reasonable amount of time, you will have to index your set of words in some way that facilitates fuzzy string matching.
One of these indexing methods would be to use a suffix tree. Another approach would be to use n-grams.
I would lean towards using a suffix tree since I find it easier to wrap my head around it and I find it more suited to the problem.
It might be of interest to look at a some algorithms such as the Levenshtein distance, which can calculate the amount of difference between 2 strings.
I'm not sure what language you are thinking of using but PHP has a function called levenshtein that performs this calculation and returns the distance. There's also a function called similar_text that does a similar thing. There's a code example here for the levenshtein function that checks a word against a dictionary of possible words and returns the closest words.
I hope this gives you a bit of insight into how a solution could work!
I have a big collection of human generated content. I want to find the words or phrases that occur most often. What is an efficient way to do this?
Don't reinvent the wheel. Use a full text search engine such as Lucene.
The simple/naive way is to use a hashtable. Walk through the words and increment the count as you go.
At the end of the process sort the key/value pairs by count.
the basic idea is simple -- in executable pseudocode,
from collections import defaultdict
def process(words):
d = defaultdict(int)
for w in words: d[w] += 1
return d
Of course, the devil is in the details -- how do you turn the big collection into an iterator yielding words? Is it big enough that you can't process it on a single machine but rather need a mapreduce approach e.g. via hadoop? Etc, etc. NLTK can help with the linguistic aspects (isolating words in languages that don't separate them cleanly).
On a single-machine execution (net of mapreduce), one issue that can arise is that the simple idea gives you far too many singletons or thereabouts (words occurring once or just a few times), which fill memory. A probabilistic retort to that is to do two passes: one with random sampling (get only one word in ten, or one in a hundred) to make a set of words that are candidates for the top ranks, then a second pass skipping words that are not in the candidate set. Depending on how many words you're sampling and how many you want in the result, it's possible to compute an upper bound on the probability that you're going to miss an important word this way (and for reasonable numbers, and any natural language, I assure you that you'll be just fine).
Once you have your dictionary mapping words to numbers of occurrences you just need to pick the top N words by occurrences -- a heap-queue will help there, if the dictionary is just too large to sort by occurrences in its entirety (e.g. in my favorite executable pseudocode, heapq.nlargest will do it, for example).
Look into the Apriori algorithm. It can be used to find frequent items and/or frequent sets of items.
Like the wikipedia article states, there are more efficient algorithms that do the same thing, but this could be a good start to see if this will apply to your situation.
Maybe you can try using a PATRICIA trie or practical algorithm to retrieve information coded in alphanumeric trie?
Why not a simple map with key as the word and the Counter as the Value.
It will give the top used words, by taking the high value counter.
It is just a O(N) operation.