Related
I am doing a project for my degree and I have an actual client from another college. They want me to do all this stuff with topic modeling to an sql file of paper abstracts he's given me. I have zero experience with topic modeling but I've been using Gensim and Nlkt in a Jupyter notebook for this.
What he want's right now is for me to generate 10 or more topics, record the top 10 most overall common words from the LDA's results, and then if they are very frequent in each topic, remove them from the resulting word cloud and if they are more variant, remove the words from just the topics where they are infrequent and keep them in the more relevant topics.
He also wants me to compare the frequency of each topic from the sql files of other years. And, he wants these topics to have a name generated smartly from the computer.
I have topic models per year and overall, but of course they do not appear exactly the same way in each year. My biggest concern is the first thing he wants with the removal process. Is any of this possible? I need help figuring out where to look as google is giving me not what I want as I am probably searching it wrong.
Thank you!
Show some of the code you use so we can give you more useful tips. Also use nlp tag, the tags you used are kind of specific and not followed by many people so your question might be hard to find for the relevant users.
By the whole word-removal thing do you mean stop words too? Or did you already remove those? Stop words are very common words ("the", "it", "me" etc.) which often appear high in most frequent word lists but do not really have any meaning for finding topics.
First you remove the stop words to make the most common words list more useful.
Then, as he requested, you look which (more common) words are common in ALL the topics (I can imagine in case of abstracts this is stuff like hypothesis, research, paper, results etc., so stuff that is abstract-specific but not useful for determining topics within different abstracts and remove those. I can imagine for this kind of analysis as well as the initial LDA it makes sense to use all the data from all years to have a large amount of data for the model to recognize patterns. But you should try around the variations and see if the per year or overall versions get you nicer results.
After you have your global word lists per topic you go back to the original data (split up by year) to count the frequencies of how often the combined words from a topic occur per year. If you view this over the years you probably can see trends like some topics that are popular in the last few years/now but if you go back far enough they werent relevant.
The last thing you mentioned (automatically assigning labels to topics) is actually something quite tricky, depending on how you go about it.
The "easy" way would be e.g. just use the most frequent word in each topic as label but the results will probably be underwhelming.
A more advanced approach is Topic Labeling. Or you can try an approach like modified text summarization using more powerful models.
Top k problem - searching BEST k (3 or 1000) elements in DB
There is fundamental problem with relational DB, that to find top k elems, there is a need to process ALL rows in table. Which make it useless on big data.
I'm making application (for university research, not really my invention, I'm implementing and trying to improve original idea) that allows you to effectively find top k elements by visiting only 3-5% of stored data. Which make it really fast.
There are even user preferences, so on some domain, you can specify function that specify best value for user and aggregation function that specify most significant attributes.
For example DB of cars: attributes:(price, mileage, age of car, ccm, fuel/mile, type of car...) and user values for example 10*price + 5*fuel/mile + 4*mileage + age of car, (s)he doesn't care about type of car and other. - this is aggregation specification
Then for each attribute (price, mileage, ...), there can be totally different "value-function" that specifies best value for user. So for example (price: lower, the better, then value go down, up to $50k, where value is 0 (user don't want car more expensive than 50k). Mileage: other function based on his/hers criteria, ans so on...
You can see that there is quite freedom to specify your preferences and acording to it, best k elements in DB will be found quickly.
I've spent many sleepless night thinking about real-life usability. Who can benefit from that query db? But I failed to whomp up anything and sticking to only academic write-only stance. :-( I hope there can be some real usage for that, but I don't see any....
.... do YOU have any idea how to use that in real-life, real problem, etc...
I'd love to hear from You.
Have a database of people's CVs and establish hiring criteria for different jobs, allowing for a dynamic display of the top k candidates.
Also, considering the fast nature of your solution, you can think of exploiting it in rendering near real-time graphs of highly dynamic data, like stock market quotes or even applications in molecular or DNA-related studies.
New idea: perhaps your research might have applications in clustering, where you would use it to implement a fast k - Nearest Neighbor clustering by complex criteria without having to scan the whole data set each time. This would lead to faster clustering of larger data sets in respect with more complex criteria in picking the K-NN for each data node.
There are unlimited possible real-use scenarios. Getting the top-n values is used all the time.
But I highly doubt that it's possible to get top-n objects without having an index. An index can only be built if the properties that will be searched are known ahead of searching. And if that's the case, a simple index in a relational database is able to provide the same functionality.
It's used in financial organizations all the time, you need to see the most profitable assets / least profitable, etc.
I have the following requirement: -
I have many (say 1 million) values (names).
The user will type a search string.
I don't expect the user to spell the names correctly.
So, I want to make kind of Google "Did you mean". This will list all the possible values from my datastore. There is a similar but not same question here. This did not answer my question.
My question: -
1) I think it is not advisable to store those data in RDBMS. Because then I won't have filter on the SQL queries. And I have to do full table scan. So, in this situation how the data should be stored?
2) The second question is the same as this. But, just for the completeness of my question: how do I search through the large data set?
Suppose, there is a name Franky in the dataset.
If a user types as Phranky, how do I match the Franky? Do I have to loop through all the names?
I came across Levenshtein Distance, which will be a good technique to find the possible strings. But again, my question is do I have to operate on all 1 million values from my data store?
3) I know, Google does it by watching users behavior. But I want to do it without watching user behavior, i.e. by using, I don't know yet, say distance algorithms. Because the former method will require large volume of searches to start with!
4) As Kirk Broadhurst pointed out in an answer below, there are two possible scenarios: -
Users mistyping a word (an edit
distance algorithm)
Users not knowing a word and guessing
(a phonetic match algorithm)
I am interested in both of these. They are really two separate things; e.g. Sean and Shawn sound the same but have an edit distance of 3 - too high to be considered a typo.
The Soundex algorithm may help you out with this.
http://en.wikipedia.org/wiki/Soundex
You could pre-generate the soundex values for each name and store it in the database, then index that to avoid having to scan the table.
the Bitap Algorithm is designed to find an approximate match in a body of text. Maybe you could use that to calculate probable matches. (it's based on the Levenshtein Distance)
(Update: after having read Ben S answer (use an existing solution, possibly aspell) is the way to go)
As others said, Google does auto correction by watching users correct themselves. If I search for "someting" (sic) and then immediately for "something" it is very likely that the first query was incorrect. A possible heuristic to detect this would be:
If a user has done two searches in a short time window, and
the first query did not yield any results (or the user did not click on anything)
the second query did yield useful results
the two queries are similar (have a small Levenshtein distance)
then the second query is a possible refinement of the first query which you can store and present to other users.
Note that you probably need a lot of queries to gather enough data for these suggestions to be useful.
I would consider using a pre-existing solution for this.
Aspell with a custom dictionary of the names might be well suited for this. Generating the dictionary file will pre-compute all the information required to quickly give suggestions.
This is an old problem, DWIM (Do What I Mean), famously implemented on the Xerox Alto by Warren Teitelman. If your problem is based on pronunciation, here is a survey paper that might help:
J. Zobel and P. Dart, "Phonetic String Matching: Lessons from Information Retieval," Proc. 19th Annual Inter. ACM SIGIR Conf. on Research and Development in Information Retrieval (SIGIR'96), Aug. 1996, pp. 166-172.
I'm told by my friends who work in information retrieval that Soundex as described by Knuth is now considered very outdated.
Just use Solr or a similar search server, and then you won't have to be an expert in the subject. With the list of spelling suggestions, run a search with each suggested result, and if there are more results than the current search query, add that as a "did you mean" result. (This prevents bogus spelling suggestions that don't actually return more relevant hits.) This way, you don't require a lot of data to be collected to make an initial "did you mean" offering, though Solr has mechanisms by which you can hand-tune the results of certain queries.
Generally, you wouldn't be using an RDBMS for this type of searching, instead depending on read-only, slightly stale databases intended for this purpose. (Solr adds a friendly programming interface and configuration to an underlying Lucene engine and database.) On the Web site for the company that I work for, a nightly service selects altered records from the RDBMS and pushes them as a documents into Solr. With very little effort, we have a system where the search box can search products, customer reviews, Web site pages, and blog entries very efficiently and offer spelling suggestions in the search results, as well as faceted browsing such as you see at NewEgg, Netflix, or Home Depot, with very little added strain on the server (particularly the RDBMS). (I believe both Zappo's [the new site] and Netflix use Solr internally, but don't quote me on that.)
In your scenario, you'd be populating the Solr index with the list of names, and select an appropriate matching algorithm in the configuration file.
Just as in one of the answers to the question you reference, Peter Norvig's great solution would work for this, complete with Python code. Google probably does query suggestion a number of ways, but the thing they have going for them is lots of data. Sure they can go model user behavior with huge query logs, but they can also just use text data to find the most likely correct spelling for a word by looking at which correction is more common. The word someting does not appear in a dictionary and even though it is a common misspelling, the correct spelling is far more common. When you find similar words you want the word that is both the closest to the misspelling and the most probable in the given context.
Norvig's solution is to take a corpus of several books from Project Gutenberg and count the words that occur. From those words he creates a dictionary where you can also estimate the probability of a word (COUNT(word) / COUNT(all words)). If you store this all as a straight hash, access is fast, but storage might become a problem, so you can also use things like suffix tries. The access time is still the same (if you implement it based on a hash), but storage requirements can be much less.
Next, he generates simple edits for the misspelt word (by deleting, adding, or substituting a letter) and then constrains the list of possibilities using the dictionary from the corpus. This is based on the idea of edit distance (such as Levenshtein distance), with the simple heuristic that most spelling errors take place with an edit distance of 2 or less. You can widen this as your needs and computational power dictate.
Once he has the possible words, he finds the most probable word from the corpus and that is your suggestion. There are many things you can add to improve the model. For example, you can also adjust the probability by considering the keyboard distance of the letters in the misspelling. Of course, that assumes the user is using a QWERTY keyboard in English. For example, transposing an e and a q is more likely than transposing an e and an l.
For people who are recommending Soundex, it is very out of date. Metaphone (simpler) or Double Metaphone (complex) are much better. If it really is name data, it should work fine, if the names are European-ish in origin, or at least phonetic.
As for the search, if you care to roll your own, rather than use Aspell or some other smart data structure... pre-calculating possible matches is O(n^2), in the naive case, but we know in order to be matching at all, they have to have a "phoneme" overlap, or may even two. This pre-indexing step (which has a low false positive rate) can take down the complexity a lot (to in the practical case, something like O(30^2 * k^2), where k is << n).
You have two possible issues that you need to address (or not address if you so choose)
Users mistyping a word (an edit distance algorithm)
Users not knowing a word and guessing (a phonetic match algorithm)
Are you interested in both of these, or just one or the other? They are really two separate things; e.g. Sean and Shawn sound the same but have an edit distance of 3 - too high to be considered a typo.
You should pre-index the count of words to ensure you are only suggesting relevant answers (similar to ealdent's suggestion). For example, if I entered sith I might expect to be asked if I meant smith, however if I typed smith it would not make sense to suggest sith. Determine an algorithm which measures the relative likelihood a word and only suggest words that are more likely.
My experience in loose matching reinforced a simple but important learning - perform as many indexing/sieve layers as you need and don't be scared of including more than 2 or 3. Cull out anything that doesn't start with the correct letter, for instance, then cull everything that doesn't end in the correct letter, and so on. You really only want to perform edit distance calculation on the smallest possible dataset as it is a very intensive operation.
So if you have an O(n), an O(nlogn), and an O(n^2) algorithm - perform all three, in that order, to ensure you are only putting your 'good prospects' through to your heavy algorithm.
I'm thinking the answer is no, but I'd love it it anybody had any insight into how to crawl a tree structure to any depth in SQL (MySQL), but with a single query
More specifically, given a tree structured table (id, data, data, parent_id), and one row in the table, is it possible to get all descendants (child/grandchild/etc), or for that matter all ancestors (parent/grandparent/etc) without knowing how far down or up it will go, using a single query?
Or is using some kind of recursion require, where I keep querying deeper until there are no new results?
Specifically, I'm using Ruby and Rails, but I'm guessing that's not very relevant.
Yes, this is possible, it's a called a Modified Preorder Tree Traversal, as best described here
Joe Celko's Trees and Hierarchies in SQL for Smarties
A working example (in PHP) is provided here
http://www.sitepoint.com/article/hierarchical-data-database/2/
Here are several resources:
http://forums.mysql.com/read.php?10,32818,32818#msg-32818
Managing Hierarchical Data in MySQL
http://lists.mysql.com/mysql/201896
Basically, you'll need to do some sort of cursor in a stored procedure or query or build an adjacency table. I'd avoid recursion outside of the db: depending on how deep your tree is, that could get really slow/sketchy.
Daniel Beardsley's answer is not that bad a solution at all when the main questions you are asking are 'what are all my children' and 'what are all my parents'.
In response to Alex Weinstein, this method actually results in less updates to nodes on a parent movement than in the Celko technique. In Celko's technique, if a level 2 node on the far left moves to under a level 1 node on the far right, then pretty much every node in the tree needs updating, rather than just the node's children.
What I would say however is that Daniel possibly stores the path back to root the wrong way around.
I would store them so that the query would be
SELECT FROM table WHERE ancestors LIKE "1,2,6%"
This means that mysql can make use of an index on the 'ancestors' column, which it would not be able to do with a leading %.
I came across this problem before and had one wacky idea. You could store a field in each record that is concatenated string of it's direct ancestors' ids all the way back to the root.
Imagine you had records like this (indentation implies heirarchy and the numbers are id, ancestors.
1, "1"
2, "2,1"
5, "5,2,1"
6, "6,2,1"
7, "7,6,2,1"
11, "11,6,2,1"
3, "3,1"
8, "8,3,1"
9, "9,3,1"
10, "10,3,1"
Then to select the descendents of id:6, just do this
SELECT FROM table WHERE ancestors LIKE "%6,2,1"
Keeping the ancestors column up to date might be more trouble than it's worth to you, but it's feasible solution in any DB.
Celko's technique (nested sets) is pretty good. I also have used an adjacency table with fields "ancestor" and "descendant" and "distance" (e.g. direct children/parents have a distance of 1, grandchildren/grandparents have a distance of 2, etc).
This needs to be maintained, but is fairly easy to do for inserts: you use a transaction, then put the direct link (parent, child, distance=1) into the table, then INSERT IGNORE a SELECTion of existing parent&children by adding distances (I can pull up the SQL when I have a chance), which wants an index on each of the 3 fields for performance. Where this approach gets ugly is for deletions... you basically have to mark all the items that have been affected and then rebuild them. But an advantage of this is that it can handle arbitrary acyclic graphs, whereas the nested set model can only do straight hierarchies (e.g. each item except the root has one and only one parent).
SQL isn't a Turing Complete language, which means you're not going to be able to perform this sort of looping. You can do some very clever things with SQL and tree structures, but I can't think of a way to describe a row which has a certain id "in its hierarchy" for a hierarchy of arbitrary depth.
Your best bet is something along the lines of what #Dan suggested, which is to just work your way through the tree in some other, more capable language. You can actually generate a query string in a general-purpose language using a loop, where the query is just some convoluted series of joins (or sub-queries) which reflects the depth of the hierarchy you are looking for. That would be more efficient than looping and multiple queries.
This can definitely be done and it isn't that complicated for SQL. I've answered this question and provided a working example using mysql procedural code here:
MySQL: How to find leaves in specific node
Booth: If you are satisfied, you should mark one of the answers as accepted.
I used the "With Emulator" routine described in https://stackoverflow.com/questions/27013093/recursive-query-emulation-in-mysql (provided by https://stackoverflow.com/users/1726419/yossico). So far, I've gotten very good results (performance wise), but I don't have an abundance of data or a large number of descendents to search through/for.
You're almost definitely going to want to employ some recursion for that. And if you're doing that, then it would be trivial (in fact easier) to get the entire tree rather than bits of it to a fixed depth.
In really rough pseudo-code you'll want something along these lines:
getChildren(parent){
children = query(SELECT * FROM table WHERE parent_id = parent.id)
return children
}
printTree(root){
print root
children = getChildren(root)
for child in children {
printTree(child)
}
}
Although in practice you'd rarely want to do something like this. It will be rather inefficient since it's making one request for every row in the table, so it'll only be sensible for either small tables, or trees that aren't nested too deeply. To be honest, in either case you probably want to limit the depth.
However, given the popularity of these kinds of data structure, there may very well be some MySQL stuff to help you with this, specifically to cut down on the numbers of queries you need to make.
Edit: Having thought about it, it makes very little sense to make all these queries. If you're reading the entire table anyway, then you can just slurp the whole thing into RAM - assuming it's small enough!
For a school project, I need to create a way to create personnalized queries based on end-user choices.
Since the user can choose basically any fields from any combination of tables, I need to find a way to map the tables in order to make a join and not have extraneous data (This may lead to incoherent reports, but we're willing to live with that).
For up to two tables, I already managed to design an algorithm that works fine. However, when I add another table, I can't find a way to path through my database. All tables available for the personnalized reports can be linked together so it really all falls down to finding which path to use.
You might be able to try some form of an A* algorithm. Basically this looks at each of the possible next options to choose and applies a heuristic to it, a function that determines roughly how far it is between this node and your goal. It then chooses the one that is closer and repeats. The hardest part of implementing A* is designing a good heuristic.
Without more information on how the tables fit together, or what you mean by a 'path' through the tables, it's hard to recommend something though.
Looks like it didn't like my link, probably the * in it, try:
http://en.wikipedia.org/wiki/A*_search_algorithm
Edit:
If that is the whole database, I'd go with a depth-first exhaustive search.
I thought about using A* or a similar algorithm, but as you said, the hardest part is about designing the heuristic.
My tables are centered around somewhat of a backbone with quite a few branches each leading to at most a single leaf node. Here is the actual map (table names removed because I'm paranoid). Assuming I want to view data from tha A, B and C tables, I need an algorithm to find the blue path.