I have stored a lot of news articles from RSS feeds from different sources in an elasticsearch index. At the moment when I do a search query, it will return me a lot of similar news articles for one query, because the same news topics gets covered by many RSS sources.
Instead what I would like to do is return only one news article out of a group of articles to the same topic. So I somehow need to recognize, which articles are about the same topic, cluster these documents and return only the "best" article out of such a cluster.
What would be the most convenient way to approach that problem?
Can I somehow make use of the elasticsearch more-like-this API? Or is the https://github.com/carrot2/elasticsearch-carrot2 plugin the way to go? Or is there simply no convenient way and I have to implement somehow my own version of http://en.wikipedia.org/wiki/K-means_clustering or http://en.wikipedia.org/wiki/Non-negative_matrix_factorization to cluster my documents?
I don't think you'll be able to do the clustering adequately from within Elasticsearch. But you can definitely use the clustering results in your ES query.
If I were going to do it, I would use the data you have as input for a clustering algorithm, probably implemented in Apache Spark. I've written a few blog posts about using ES and Spark together (here's one: http://blog.qbox.io/deploy-elasticsearch-and-apache-spark-to-the-cloud). Exactly how to do that is probably outside the scope of a StackOverflow answer, but there are lots of ways to go about it. You certainly don't have to use Spark, of course (I just like it). Pick your favorite programming paradigm to implement clustering, or even use a third-party library. There are plenty out there.
Once I was happy with my clustering results, I would save the cluster meta-data back to ES as a "parent" dataset. So every article would have a parent document representing the cluster to which the article belonged. This relationship could then be used (maybe with a top child query, or has parent or something) to return the results you are wanting.
ES is not particularly useful for clustering. Most clustering algorithms require pairwise distance computations, which is easiest if you can fit all your data into a huge matrix (and then factor it)
So it may well be easier (and faster) to work outside ES!
None of the approaches work half as good as advertised. See e.g. “reading tea leaves”. Everybody who constructs such an algorithm is happy to get anything out, and will tune and fiddle parameters and rerun until the result looks nice. The technical term is cherry picking. Evaluation is incredibly sloppy, and if you look at the results closely, they aren't any better than choosing a random key word (say, car) and doing a text search on that. Much more meaningful than those “topics” discovered by topic models that nobody can decipher in practise. So good luck...
Chang, J., Gerrish, S., Wang, C., Boyd-graber, J. L., & Blei, D. M. (2009). Reading tea leaves: How humans interpret topic models. In Advances in neural information processing systems (pp. 288-296)
Carrot (as mentioned in the question) is very good for clustering the results of a query - it only scales up to 100's or 1000's of documents but that may be enough. If you need larger scales, then methods like locality sensitive hashing avoids the need to calculate all the pairwise distances. Using ES's "more-like-this" could work as a quick-and-dirty alternative to hashing, but would probably need some post-processing.
TL;DR
I need help understanding some parts of a specific algorithm for structured data classification. I'm also open to suggestions for different algorithms for this purpose.
Hi all!
I'm currently working on a system involving classification of structured data (I'd prefer not to reveal anything more about it) for which I'm using a simple backpropagation through structure (BPTS) algorithm. I'm planning on modifying the code to make use of a GPU for an additional speed boost later, but at the moment I'm looking for better algorithms than BPTS that I could use.
I recently stumbled on this paper -> [1] and I was amazed by the results. I decided to give it a try, but I have some trouble understanding some parts of the algorithm, as its description is not very clear. I've already emailed some of the authors requesting clarification, but haven't heard from them yet, so, I'd really appreciate any insight you guys may have to offer.
The high-level description of the algorithm can be found in page 787. There, in Step 1, the authors randomize the network weights and also "Propagate the input attributes of each node through the data structure from frontier nodes to root forwardly and, hence, obtain the output of root node". My understanding is that Step 1 is never repeated, since it's the initialization step. The part I quote indicates that a one-time activation also takes place here. But, what item in the training dataset is used for this activation of the network? And is this activation really supposed to happen only once? For example, in the BPTS algorithm I'm using, for each item in the training dataset, a new neural network - whose topology depends on the current item (data structure) - is created on the fly and activated. Then, the error backpropagates, the weights are updated and saved, and the temporary neural network is destroyed.
Another thing that troubles me is Step 3b. There, the authors mention that they update the parameters {A, B, C, D} NT times, using equations (17), (30) and (34). My understanding is that NT denotes the number of items in the training dataset. But equations (17), (30) and (34) already involve ALL items in the training dataset, so, what's the point of solving them (specifically) NT times?
Yet another thing I failed to get is how exactly their algorithm takes into account the (possibly) different structure of each item in the training dataset. I know how this works in BPTS (I described it above), but it's very unclear to me how it works with their algorithm.
Okay, that's all for now. If anyone has any idea of what might be going on with this algorithm, I'd be very interested in hearing it (or rather, reading it). Also, if you are aware of other promising algorithms and / or network architectures (could long short term memory (LSTM) be of use here?) for structured data classification, please don't hesitate to post them.
Thanks in advance for any useful input!
[1] http://www.eie.polyu.edu.hk/~wcsiu/paper_store/Journal/2003/2003_J4-IEEETrans-ChoChiSiu&Tsoi.pdf
I have a database, consisting of a whole bunch of records (around 600,000) where some of the records have certain fields missing. My goal is to find a way to predict what the missing data values should be (so I can fill them in) based on the existing data.
One option I am looking at is clustering - i.e. representing the records that are all complete as points in some space, looking for clusters of points, and then when given a record with missing data values try to find out if there are any clusters that could belong in that are consistent with the existing data values. However this may not be possible because some of the data fields are on a nominal scale (e.g. color) and thus can't be put in order.
Another idea I had is to create some sort of probabilistic model that would predict the data, train it on the existing data, and then use it to extrapolate.
What algorithms are available for doing the above, and is there any freely available software that implements those algorithms (This software is going to be in c# by the way).
This is less of an algorithmic and more of a philosophical and methodological question. There are a few different techniques available to tackle this kind of question. Acock (2005) gives a good introduction to some of the methods. Although it may seem that there is a lot of math/statistics involved (and may seem like a lot of effort), it's worth thinking what would happen if you messed up.
Andrew Gelman's blog is also a good resource, although the search functionality on his blog leaves something to be desired...
Hope this helps.
Acock (2005)
http://oregonstate.edu/~acock/growth-curves/working%20with%20missing%20values.pdf
Andrew Gelman's blog
http://www.stat.columbia.edu/~cook/movabletype/mlm/
Dealing with missing values is a methodical question that has to do with the actual meaning of the data.
Several methods you can use (detailed post on my blog):
Ignore the data row. This is usually done when the class label is missing (assuming you data mining goal is classification), or many attributes are missing from the row (not just one). However you'll obviously get poor performance if the percentage of such rows is high
Use a global constant to fill in for missing values. Like "unknown", "N/A" or minus infinity. This is used because sometimes is just doesnt make sense to try and predict the missing value. For example if you have a DB if, say, college candidates and state of residence is missing for some, filling it in doesn't make much sense...
Use attribute mean. For example if the average income of a US family is X you can use that value to replace missing income values.
Use attribute mean for all samples belonging to the same class. Lets say you have a cars pricing DB that, among other things, classifies cars to "Luxury" and "Low budget" and you're dealing with missing values in the cost field. Replacing missing cost of a luxury car with the average cost of all luxury cars is probably more accurate then the value you'd get if you factor in the low budget cars
Use data mining algorithm to predict the value. The value can be determined using regression, inference based tools using Baysian formalism , decision trees, clustering algorithms used to generate input for step method #4 (K-Mean\Median etc.)
I'd suggest looking into regression and decision trees first (ID3 tree generation) as they're relatively easy and there are plenty of examples on the net.
As for packages, if you can afford it and you're in the Microsoft world look at SQL Server Analysis Services (SSAS for short) that implement most of the mentioned above.
Here are some links to free data minning software packages:
WEKA - http://www.cs.waikato.ac.nz/ml/weka/index.html
ORANGE - http://www.ailab.si/orange
TANAGRA - http://eric.univ-lyon2.fr/~ricco/tanagra/en/tanagra.html
Although not C# he's a pretty good intro to decision trees and baysian learning (using Ruby):
http://www.igvita.com/2007/04/16/decision-tree-learning-in-ruby/
http://www.igvita.com/2007/05/23/bayes-classification-in-ruby/
There's also this Ruby library that I find very useful (also for learning purposes):
http://ai4r.rubyforge.org/machineLearning.html
There should be plenty of samples for these algorithms online in any language so I'm sure you'll easily find C# stuff too...
Edited:
Forgot this in my original post. This is a definately MUST HAVE if you're playing with data mining...
Download Microsoft SQL Server 2008 Data Mining Add-ins for Microsoft Office 2007 (It requires SQL Server Analysis Services - SSAS - which isn't free but you can download a trial).
This will allow you to easily play and try out the different techniques in Excel before you go and implement this stuff yourself. Then again, since you're in the Microsoft ecosystem, you might even decide to go for an SSAS based solution and count on the SQL Server guys to do it for ya :)
Predicting missing values is generally considered to be part of data cleansing phase which needs to be done before the data is mined or analyzed further. This is quite prominent in real world data.
Please have a look at this algorithm http://arxiv.org/abs/math/0701152
Currently Microsoft SQL Server Analysis Services 2008 also comes with algorithms like these http://technet.microsoft.com/en-us/library/ms175312.aspx which help in predictive modelling of attributes.
cheers
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After reading Stevey Yegge's Get That Job At Google article, I found this little quote interesting:
Whenever someone gives you a problem, think graphs. They are the most fundamental and flexible way of representing any kind of a relationship, so it's about a 50–50 shot that any interesting design problem has a graph involved in it. Make absolutely sure you can't think of a way to solve it using graphs before moving on to other solution types. This tip is important!
What are some examples of problems that are best represented and/or solved by graph data structures/algorithms?
One example I can think of: navigation units (ala Garmin, TomTom), that supply road directions from your current location to another, utilize graphs and advanced pathing algorithms.
What are some others?
Computer Networks: Graphs model intuitively model computer networks and the Internet. Often nodes will represent end-systems or routers, while edges represent connections between these systems.
Data Structures: Any data structure that makes use of pointers to link data together is making use of a graph of some kind. This includes tree structures and linked lists which are used all the time.
Pathing and Maps: Trying to find shortest or longest paths from some location to a destination makes use of graphs. This can include pathing like you see in an application like Google maps, or calculating paths for AI characters to take in a video game, and many other similar problems.
Constraint Satisfaction: A common problem in AI is to find some goal that satisfies a list of constraints. For example, for a University to set it's course schedules, it needs to make sure that certain courses don't conflict, that a professor isn't teaching two courses at the same time, that the lectures occur during certain timeslots, and so on. Constraint satisfaction problems like this are often modeled and solved using graphs.
Molecules: Graphs can be used to model atoms and molecules for studying their interaction and structure among other things.
I am very very interested in graph theory and ive used it solved so many different kinds of problem. You can solve a lot of Path related problem, matching problem, structure problems using graph.
Path problems have a lot of applications.
This was in a career cup's interview question.
Say you want to find the longest sum of a sub array. For example, [1, 2, 3, -1] has the longest sum of 6. Model it as a Directed Acyclic Graph (DAG), add a dummy source, dummy destination. Connect each node with an edge which has a weight corresponding to the number. Now use the Longest Path algorithm in the DAG to solve this problem.
Similarly, Arbitrage problems in financial world or even geometry problems of finding the longest overlapping structure is a similar path problem.
Some obvious ones would be the network problems (where your network could have computers people, organisation charts, etc).
You can glean a lot of structural information like
which point breaks the graph into two pieces
what is the best way to connect them
what is the best way to reach one place to another
is there a way to reach one place from another, etc.
I've solved a lot of project management related problems using graphs. A sequence of events can be pictured as a directed graph (if you don't have cycles then thats even better). So, now you can
sort the events according to their priority
you can find the event that is the most crucial (that is would free a lot of other projects)
you can find the duration needed to solve the total project (path problem), etc.
A lot of matching problems can be solved by graph. For example, if you need to match processors to the work load or match workers to their jobs. In my final exam, I had to match people to tables in restaurants. It follows the same principle (bipartite matching -> network flow algorithms). Its simple yet powerful.
A special graph, a tree, has numerous applications in the computer science world. For example, in the syntax of a programming language, or in a database indexing structure.
Most recently, I also used graphs in compiler optimization problems. I am using Morgan's Book, which is teaching me fascinating techniques.
The list really goes on and on and on. Graphs are a beautiful math abstraction for relation. You really can do wonders, if you can model it correctly. And since the graph theory has found so many applications, there are many active researches in the field. And because of numerous researches, we are seeing even more applications which is fuelling back researches.
If you want to get started on graph theory, get a good beginner discrete math book (Rosen comes to my mind), and you can buy books from authors like Fould or Even. CLRS also has good graph algorithms.
Your source code is tree structured, and a tree is a type of graph. Whenever you hear people talking about an AST (Abstract Syntax Tree), they're talking about a kind of graph.
Pointers form graph structures. Anything that walks pointers is doing some kind of graph manipulation.
The web is a huge directed graph. Google's key insight, that led them to dominate in search, is that the graph structure of the web is of comparable or greater importance than the textual content of the pages.
State machines are graphs. State machines are used in network protocols, regular expressions, games, and all kinds of other fields.
It's rather hard to think of anything you do that does not involve some sort of graph structure.
An example most people are familiar: build systems. Make is the typical example, but almost any good build system relies on a Directed Acyclic Graph. The basic idea is that the direction models the dependency between a source and a target, and you should "walk" the graph in a certain order to build things correctly -> this is an example of topological sort.
Another example is source control system: again based on a DAG. It is used for merging, for example, to find common parent.
Well, many program optimization algorithms that compilers use are based on graphs (e.g., figure out call graph, flow control, lots of static analysis).
Many optimization problems are based on graph. Since many problems are reducable to graph colouring and similar problems, then many other problems are also graph based.
I'm not sure I agree that graphs are the best way to represent every relation and I certainly try to avoid these "got a nail, let's find a hammer" approaches. Graphs often have poor memory representations and many algorithms are actually more efficient (in practice) when implemented with matrices, bitsets, and other things.
OCR. Picture a page of text scanned at an angle, with some noise in the image, where you must find the space between lines of text. One way is to make a graph of pixels, and find the shortest path from one side of the page to the other, where the difference in brightness is the distance between pixels.
This example is from the Algorithm Design Manual, which has lots of other real world examples of graph problems.
One popular example is garbage collection.
The collector starts with a set of references, then traverses all the objects they reference, then all the objects referenced there and so on. Everything it finds is added into a graph of reachable objects. All other objects are unreachable and collected.
To find out if two molecules can fit together. When developing drugs one is often interested in seeing if the drug molecules can fit into larger molecules in the body. The problem with determining whether this is possible is that molecules are not static. Different parts of the molecule can rotate around their chemical bindings so that a molecule can change into quite a lot of different shapes.
Each shape can be said to represent a point in a space consisting of shapes. Solving this problem involves finding a path through this space. You can do that by creating a roadmap through space, which is essentially a graph consisting of legal shapes and saying which shape a shape can turn into. By using a A* graph search algorithm through this roadmap you can find a solution.
Okay that was a lot of babble that perhaps wasn't very understandable or clear. But my point was that graphs pop up in all kinds of problems.
Graphs are not data structures. They are mathematical representation of relations. Yes, you can think and theoretize about problems using graphs, and there is a large body of theory about it. But when you need to implement an algorithm, you are choosing data structures to best represent the problem, not graphs. There are many data structures that represent general graphs, and even more for special kinds of graphs.
In your question, you mix these two things. The same theoretical solution may be in terms of graph, but practical solutions may use different data structures to represent the graph.
The following are based on graph theory:
Binary trees and other trees such as Red-black trees, splay trees, etc.
Linked lists
Anything that's modelled as a state machine (GUIs, network stacks, CPUs, etc)
Decision trees (used in AI and other applications)
Complex class inheritance
IMHO most of the domain models we use in normal applications are in some respect graphs. Already if you look at the UML diagrams you would notice that with a directed, labeled graph you could easily translate them directly into a persistence model. There are some examples of that over at Neo4j
Cheers
/peter
Social connections between people make an interesting graph example. I've tried to model these connections at the database level using a traditional RDMS but found it way too hard. I ended up choosing a graph database and it was a great choice because it makes it easy to follow connections (edges) between people (nodes).
Graphs are great for managing dependencies.
I recently started to use the Castle Windsor Container, after inspecting the Kernel I found a GraphNodes property. Castle Windsor uses a graph to represent the dependencies between objects so that injection will work correctly. Check out this article.
I have also used simple graph theory to develop a plugin framework, each graph node represent a plugin, once the dependencies have been defined I can traverse the graph to create a plugin load order.
I am planning on changing the algorithm to implement Dijkstra's algorithm so that each plugin is weighted with a specific version, thus a simple change will only load the latest version of the plugin.
I with I had discovered this sooner. I like that quote "Whenever someone gives you a problem, think graphs." I definitely think that's true.
Profiling and/or Benchmarking algorithms and implementations in code.
Anything that can be modelled as a foreign key in a relational database is essentially an edge and nodes in a graph.
Maybe that will help you think of examples, since most things are readily modelled in a RDBMS.
You could take a look at some of the examples in the Neo4j wiki,
http://wiki.neo4j.org/content/Domain_Modeling_Gallery
and the projects that Neo4j is used in (the known ones)
http://wiki.neo4j.org/content/Neo4j_In_The_Wild .
Otherwise, Recommender Algorithms are a good use for Graphs, see for instance PageRank, and other stuff at
https://github.com/tinkerpop/gremlin/wiki/pagerank
Analysing transaction serialisability in database theory.
You can utilise graphs anywhere you can define the problem domain objects into nodes and the solution as the flow of control and/or data amongst the nodes.
Considering the fact that trees are indeed connected-acyclic graphs, there are even more areas you can use the graph theory.
Basically nearlly all common data structures like trees, lists, queues, etc, can be thought as type of graph, some with different type of constraint.
To my experiences, I have used graph intensively in network flow problems, which is used in lots of areas like telecommunication network routing and optimisation, workload assignment, matching, supply chain optimisation and public transport planning.
Another interesting area is social network modelling as previous answer mentioned.
There are far more, like integrated circuit optimisation, etc.
I am a graph/network enthusiast and this just for my curiosity :)
I am trying to model the StackOverflow community as a graph/network. Assume that the people in the SO community are nodes and that the answers given to any of the question establishes a relationship between these nodes. The relationship can be assumed to be directed(link from answer -> question) or undirected. The graph could be weighted and that the weights of the nodes could represented number of vote-ups/downs (normalized on the scale of 0 to 1).
What kind of graph/network does one end up with at any given snapshot of time? Is it scale-free? Is it a small-world? The graph is continuously evolving over a period of time and i would like to understand its structure and dynamics.
Is there a way where can i retrieve this relationship data from - may be SO APIs or some one from SO can help me out with (sample) data?
Clarification edit:
Scale-free network: A network whose degree distribution asymptotically follows a power law Small-world: A network that has sub-networks characterized by presence of connections between almost any two nodes within them and most pairs of nodes are connected by at least one short path.
To the second part of your question:
Is there a way where can i retrieve
this relationship data from - may be
SO APIs or some one from SO can help
me out with (sample) data?
Try these questions instead. There are a lot of plans to implement an API to access SO data. Some things are in change, but there are possibilities to screen-scrape the data or access them via JSON (afaik).
Is there a guide to accessing StackOverflow data programmatically?
What would you want to see in a StackOverflow API?
Are there plans for a StackOverflow API?
Try it out. Good luck!
What kind of graph/network does one end up with at any given snapshot of time? Is it scale-free? Is it a small-world? The graph is continuously evolving over a period of time and i would like to understand its structure and dynamics.
It takes only a few links between remote clusters to turn a random network into a small world one, so it's quite likely to be small world.
As to whether it's scale free, that would require there to be a few posters with lots of answers and many with only one or two. I seem to recall Jeff saying that there were lots with only one question in one of the pod-casts; you might be better off asking the question there rather than here, as he will have the data.