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I'm having problems with the insertion using gremlin to Neptune.
I am trying to insert many nodes and edges, potentially hundred thousands of nodes and edges, with checking for existence.
Currently, we are using inject to insert the nodes, and the problem is that it is slow.
After running the explain command, we figured out that the problem was the coalesce and the where steps - it takes more than 99.9% of the run duration.
I want to insert each node and edge only if it doesn’t exist, and that’s why I am using the coalesce and where steps.
For example, the query we use to insert nodes with inject:
properties_list = [{‘uid’:’1642’},{‘uid’:’1322’}…]
g.inject(properties_list).unfold().as_('node')
.sideEffect(__.V().where(P.eq('node')).by(‘uid).fold()
.coalesce(__.unfold(), __.addV(label).property(Cardinality.single,'uid','1')))
With 1000 nodes in the graph and properties_list with 100 elements, running the query above takes around 30 seconds, and it gets slower as the number of nodes in the graph increases.
Running a naive injection with the same environment as the query above, without coalesce and where, takes less than 1 second.
I’d like to hear your suggestions and to know what are the best practices for inserting many nodes and edges (with checking for existence).
Thank you very much.
If you have a set of IDs that you want to check for existence, you can speed up the query significantly by also providing just a list of IDs to the query and calculating the intersection of the ones that exist upfront. Then, having calculated the set that need updates you can just apply them in one go. This will make a big difference. The reason you are running into problems is that the mid traversal V has a lot of work to do. In general it would be better to use actual IDs rather than properties (UID in your case). If that is not an option the same technique will work for property based IDs. The steps are:
Using inject or sideEffect insert the IDs to be found as one list and the corresponding map containing the changes to conditionally be applied in a separate map.
Find the intersection of the ones that exist and those that do not.
Using that set of non existing ones, apply the updates using the values in the set to index into your map.
Here is a concrete example. I used the graph-notebook for this but you can do the same thing in code:
Given:
ids = "['1','2','9998','9999']"
and
data = "[['id':'1','value':'XYZ'],['id':'9998','value':'ABC'],['id':'9999','value':'DEF']]"
we can do something like this:
g.V().hasId(${ids}).id().fold().as('exist').
constant(${data}).
unfold().as('d').
where(without('exist')).by('id').by()
which correctly finds the ones that do not already exist:
{'id': 9998, 'value': 'ABC'}
{'id': 9999, 'value': 'DEF'}
You can use this pattern to construct your conditional inserts a lot more efficiently (I hope :-) ). So to add the new vertices you might do:
g.V().hasId(${ids}).id().fold().as('exist').
constant(${data}).
unfold().as('d').
where(without('exist')).by('id').by().
addV('test').
property(id,select('d').select('id')).
property('value',select('d').select('value'))
v[9998]
v[9999]
As a side note, we are adding two new steps to Gremlin - mergeV and mergeE that will allow this to be done much more easily and in a more declarative style. Those new steps should be part of the TinkerPop 3.6 release.
I am new in storm framework(https://storm.incubator.apache.org/about/integrates.html),
I test locally with my code and I think If I remove stop words, it will perform well, but i search on line and I can't see any example that removing stopwords in storm.
If the size of the stop words list is small enough to fit in memory, the most straighforward approach would be to simply filter the tuples with an implementation of storm Filter that knows that list. This Filter could possibly poll the DB every so often to get the latest list of stop words if this list evolves over time.
If the size of the stop words list is bigger, then you can use a QueryFunction, called from your topology with the stateQuery function, which would:
receive a batch of tuples to check (say 10000 at a time)
build a single query from their content and look up corresponding stop words in persistence
attach a boolean to each tuple specifying what to with each one
+ add a Filter right after that to filter based on that boolean.
And if you feel adventurous:
Another and faster approach would be to use a bloom filter approximation. I heard that Algebird is meant to provide this kind of functionality and targets both Scalding and Storm (how cool is that?), but I don't know how stable it is nor do I have any experience in practically plugging it into Storm (maybe Sunday if it's rainy...).
Also, Cascading (which is not directly related to Storm but has a very similar set of primitive abstractions on top of map reduce) suggests in this tutorial a method based on left joins. Such joins exist in Storm and the right branch could possibly be fed with a FixedBatchSpout emitting all stop words every time, or even a custom spout that reads the latest version of the list of stop words from persistence every time, so maybe that would work too? Maybe? This also assumes the size of the stop words list is relatively small though.
I'm working on an iOS music app (written in C++) and my model looks more or less like this:
--Song
----Track
----Track
------Pattern
------Pattern
--------Note
--------Note
--------Note
So basically a Song has multiple Tracks, a Track can have multiple Patterns and a Pattern has multiple Notes. Each one of those things is represented by a class and except for the Song object, they're all stored inside vectors.
Each Note has a "frame" parameter so that I can calculate when a note should be played. For example, if I have 44100 samples / second and the frame for a particular note is 132300 I know that I need that Note at the start of the third second.
My question is how I should represent those notes for best performance? Right now I'm thinking of storing the notes in a vector datamember of each pattern and than loop all the Tracks of the Song, than look the Patterns and than loop the Notes to see which one has a frame datamember that is greater than 132300 and smaller than 176400 (start of 4th second).
As you can tell, that's a lot of loops and a song could be as long as 10 minutes. So I'm wondering if this will be fast enough to calculate all the frames and send them to the buffer on time.
One thing you should remember is that to improve performance, normally memory consumption would have to increase. It is also relevant (and justified) in this case, because I believe you want to store the same data twice, in different ways.
First of all, you should have this basic structure for a song:
map<Track, vector<Pattern>> tracks;
It maps each Track to a vector of Patterns. Map is fine, because you don't care about the order of tracks.
Traversing through Tracks and Patterns should be fast, as their amounts will not be high (I assume). The main performance concern is to loop through thousands of notes. Here's how I suggest to solve it:
First of all, for each Pattern object you should have a vector<Note> as your main data storage. You will write all the changes on the Pattern's contents to this vector<Note> first.
vector<Note> notes;
And for performance considerations, you can have a second way of storing notes:
map<int, vector<Notes>> measures;
This one will map each measure (by its number) in a Pattern to the vector of Notes contained in this measure. Every time data changes in the main notes storage, you will apply the same changes to data in measures. You could also do it only once every time before the playback, or even while playback, in a separate thread.
Of course, you could only store notes in measures, without having to sync two sources of data. But it may be not so convenient to work with when you have to apply mass operations on bunches of notes.
During the playback, before the next measure starts, the following algorithm would happen (roughly):
In every track, find all patterns, for which pattern->startTime <= [current playback second] <= pattern->endTime.
For each pattern, calculate current measure number and get vector<Notes> for the corresponding measure from the measures map.
Now, until the next measure (second?) starts, you only have to loop through current measure's notes.
Just keep those vectors sorted.
During playback, you can just keep a pointer (index) into each vector for the last note player. To search for new notes, you check have to check the following note in each vector, no looping through notes required.
Keep your vectors sorted, and try things out - that is more important and any answer you can receive here.
For all of your questions you should seek to answer then with tests and prototypes, then you will know if you even have a problem. And also while trying it out you will see things that you wouldn't normally see with just the theory alone.
and my model looks more or less like this:
Several critically important concepts are missing from your model:
Tempo.
Dynamics.
Pedal
Instrument
Time signature.
(Optional) Tonality.
Effect (Reverberation/chorus, pitch wheel).
Stereo positioning.
Lyrics.
Chord maps.
Composer information/Title.
Each Note has a "frame" parameter so that I can calculate when a note should be played.
Several critically important concepts are missing from your model:
Articulation.
Aftertouch.
Note duration.
I'd advise to take a look at lilypond. It is typesetting software, but it is also one of the most precise way to represent music in human-readable text format.
My question is how I should represent those notes for best performance?
Put them all into std::map<Timestamp, Note> and find segment you want to playing using lower_bound/upper_bound. Alternatively you could binary search them in flat std::vector as long as data is sorted.
Unless you want to make a "beeper", making music application is much more difficult than you think. I'd strongly recommend to try another project.
I'm working on a tool to visualize RNA secondary structure, for this purpose I have implemented Nussinov's algorithm which generates the RNA secondary structure as list with the corresponding indices, the code can be found here [0]
[0] http://dpaste.com/596262/
But I really stuck with understanding how I should visualize it (as a planar graph), the code above gives me a sequential list of the secondary structure, so can someone please suggest me as to how I can visualize the structure.An example of such tool can be found here [1]
[1] http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
and I know there are better algorithms but for now I would just want to visualize with this and once I understand visualization, I will go for a better algorithm.
Visualizing the secondary structure of RNA (or any graph, for that matter) algorithmically is a difficult problem. You need to take care that there are as few overlaps as possible while maintaining consistent link lengths. As the other answers have pointed out, there are a number of existing implementations that you can already use. I'll just throw in another one that's quite easy to use and requires no downloads:
forna - nibiru.tbi.univie.ac.at/forna
Here you just need to enter a dotbracket string:
>molecule_name
CGCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGUG
((((((((((..((((((.........))))))......).((((((.......))))))..)))))))))
This will give you a visualization that looks something like this:
This is computed using a combination of the ViennaRNA RNAplot program and d3's force-directed graph algorithm.
You could do this with jmol . Jmol allows you to add arbitrary bonds / atoms to a coordinate space using its java or I believe its javascript api also.
In general, of course, PDB file formats would be used for such data.
RNAviz is old but still commonly used. JalView apparently was supposed to get RNA secondary structure rendering thru a GSoC project last year, but I'm not sure what the status in the program is.
I need to create a search index for a collection of HTML pages.
I have no experience in implementing a search index at all, so any general information how to build one, what information to store, how to implement advanced searches such as "entire phrase", ranking of results etc.
I'm not afraid to build it myself, though I'd be happy to reuse an existing component (or use one to get started with a prototype). I am looking for a solution accessible from C++, preferrably without requiring additional installations at runtime. The content is static (so it makes sense to aggregate search information), but a search might have to accumulate results from multiple such repositories.
I can make a few educated guesses, though: create a map word ==> pages for all (relevant) words, a rank can be assigned to the mapping by promincence (h1 > h2 > ... > <p>) and proximity to top. Advanced searches could be built on top of that: searching for phrase "homo sapiens" could list all pages that contain "homo" and "sapiens", then scan all pages returned for locations where they occur together. However, there are a lot of problematic scenarios and unanswered questions, so I am looking for references to what should be a huge amount of existing work that somehow escapes my google-fu.
[edit for bounty]
The best resource I found until now is this and the links from there.
I do have an imlementation roadmap for an experimental system, however, I am still looking for:
Reference material regarding index creation and individual steps
available implementations of individual steps
reusable implementations (with above environment restrictions)
This process is generally known as information retrieval. You'll probably find this online book helpful.
Existing libraries
Here are two existing solutions that can be fully integrated into an application without requiring a separate process (I believe both will compile with VC++).
Xapian is mature and may do much of what you need, from indexing to ranked retrieval. Separate HTML parsing would be required because, AFAIK, it does not parse html (it has a companion program Omega, which is a front end for indexing web sites).
Lucene is a index/searching Apache library in Java, with an official pre-release C version lucy, and an unofficial C++ version CLucene.
Implementing information retrieval
If the above options are not viable for some reason, here's some info on the individual steps of building and using an index. Custom solutions can go from simple to very sophisticated, depending what you need for your application. I've broken the process into 5 steps
HTML processing
Text processing
Indexing
Retrieval
Ranking
HTML Processing
There are two approaches here
Stripping The page you referred to discusses a technique generally known as stripping, which involves removing all the html elements that won't be displayed and translating others to their display form. Personally, I'd preprocess using perl and index the resulting text files. But for an integrated solution, particularly one where you want to record significance tags (e.g. <h1>, <h2>), you probably want to role your own. Here is a partial implementation of a C++ stripping routine (appears in Thinking in C++ , final version of book here), that you could build from.
Parsing A level up in complexity from stripping is html parsing, which would help in your case for recording significance tags. However, a good C++ HTML parser is hard to find. Some options might be htmlcxx (never used it, but active and looks promising) or hubbub (C library, part of NetSurf, but claims to be portable).
If you are dealing with XHTML or are willing to use an HTML-to-XML converter, you can use one of the many available XML parsers. But again, HTML-to-XML converters are hard to find, the only one I know of is HTML Tidy. In addition to conversion to XHTML, its primary purpose is to fix missing/broken tags, and it has an API that could possibly be used to integrate it into an application. Given XHTML documents, there are many good XML parsers, e.g. Xerces-C++ and tinyXML.
Text Processing
For English at least, processing text to words is pretty straight forward. There are a couple of complications when search is involved though.
Stop words are words known a priori not to provide a useful distinction between documents in the set, such as articles and propositions. Often these words are not indexed and filtered from query streams. There are many stop word lists available on the web, such as this one.
Stemming involves preprocessing documents and queries to identify the root of each word to better generalize a search. E.g. searching for "foobarred" should yield "foobarred", "foobarring", and "foobar". The index can be built and searched on roots alone. The two general approaches to stemming are dictionary based (lookups from word ==> root) and algorithm based. The Porter algorithm is very common and several implementations are available, e.g. C++ here or C here. Stemming in the Snowball C library supports several languages.
Soundex encoding One method to make search more robust to spelling errors is to encode words with a phonetic encoding. Then when queries have phonetic errors, they will still map directly to indexed words. There are a lot of implementations around, here's one.
Indexing
The map word ==> page data structure is known as an inverted index. Its inverted because its often generated from a forward index of page ==> words. Inverted indexes generally come in two flavors: inverted file index, which map words to each document they occur in, and full inverted index, which map words to each position in each document they occur in.
The important decision is what backend to use for the index, some possibilities are, in order of ease of implementation:
SQLite or Berkly DB - both of these are database engines with C++ APIs that integrated into a project without requiring a separate server process. Persistent databases are essentially files, so multiple index sets can be search by just changing the associated file. Using a DBMS as a backend simplifies index creation, updating and searching.
In memory data structure - if your using a inverted file index that is not prohibitively large (memory consumption and time to load), this could be implemented as a std::map<std::string,word_data_class>, using boost::serialization for persistence.
On disk data structure - I've heard of blazingly fast results using memory mapped files for this sort of thing, YMMV. Having an inverted file index would involve having two index files, one representing words with something like struct {char word[n]; unsigned int offset; unsigned int count; };, and the second representing (word, document) tuples with just unsigned ints (words implicit in the file offset). The offset is the file offset for the first document id for the word in the second file, count is the number of document ids associate with that word (number of ids to read from the second file). Searching would then reduce to a binary search through the first file with a pointer into a memory mapped file. The down side is the need to pad/truncate words to get a constant record size.
The procedure for indexing depends on which backend you use. The classic algorithm for generating a inverted file index (detailed here) begins with reading through each document and extending a list of (page id, word) tuples, ignoring duplicate words in each document. After all documents are processed, sort the list by word, then collapsed into (word, (page id1, page id2, ...)).
The mifluz gnu library implements inverted indexes w/ storage, but without document or query parsing. GPL, so may not be a viable option, but will give you an idea of the complexities involved for an inverted index that supports a large number of documents.
Retrieval
A very common method is boolean retrieval, which is simply the union/intersection of documents indexed for each of the query words that are joined with or/and, respectively. These operations are efficient if the document ids are stored in sorted order for each term, so that algorithms like std::set_union or std::set_intersection can be applied directly.
There are variations on retrieval, wikipedia has an overview, but standard boolean is good for many/most application.
Ranking
There are many methods for ranking the documents returned by boolean retrieval. Common methods are based on the bag of words model, which just means that the relative position of words is ignored. The general approach is to score each retrieved document relative to the query, and rank documents based on their calculated score. There are many scoring methods, but a good starting place is the term frequency-inverse document frequency formula.
The idea behind this formula is that if a query word occurs frequently in a document, that document should score higher, but a word that occurs in many documents is less informative so this word should be down weighted. The formula is, over query terms i=1..N and document j
score[j] = sum_over_i(word_freq[i,j] * inv_doc_freq[i])
where the word_freq[i,j] is the number of occurrences of word i in document j, and
inv_doc_freq[i] = log(M/doc_freq[i])
where M is the number of documents and doc_freq[i] is the number of documents containing word i. Notice that words that occur in all documents will not contribute to the score. A more complex scoring model that is widely used is BM25, which is included in both Lucene and Xapian.
Often, effective ranking for a particular domain is obtained by adjusting by trial and error. A starting place for adjusting rankings by heading/paragraph context could be inflating word_freq for a word based on heading/paragraph context, e.g. 1 for a paragraph, 10 for a top level heading. For some other ideas, you might find this paper interesting, where the authors adjusted BM25 ranking for positional scoring (the idea being that words closer to the beginning of the document are more relevant than words toward the end).
Objective quantification of ranking performance is obtained by precision-recall curves or mean average precision, detailed here. Evaluation requires an ideal set of queries paired with all the relevant documents in the set.
Depending on the size and number of the static pages, you might want to look at an already existent search solution.
"How do you implement full-text search for that 10+ million row table, keep up with the load, and stay relevant? Sphinx is good at those kinds of riddles."
I would choose the Sphinx engine for full text searching. The licence is GPL but the also have a commercial version available. It is meant to be run stand-alone [2], but it can also be embedded into applications by extracting the needed functionality (be it indexing[1], searching [3], stemming, etc).
The data should be obtained by parsing the input HTML files and transforming them to plain-text by using a parser like libxml2's HTMLparser (I haven't used it, but they say it can parse even malformed HTML). If you aren't bound to C/C++ you could take a look at Beautiful Soup.
After obtaining the plain-texts, you could store them in a database like MySQL or PostgreSQL. If you want to keep everything embedded you should go with sqlite.
Note that Sphinx doesn't work out-of-the-box with sqlite, but there is an attempt to add support (sphinx-sqlite3).
I would attack this with a little sqlite database. You could have tables for 'page', 'term' and 'page term'. 'Page' would have columns like id, text, title and url. 'Term' would have a column containing a word, as well as the primary ID. 'Page term' would have foreign keys to a page ID and a term ID, and could also store the weight, calculated from the distance from the top and the number of occurrences (or whatever you want).
Perhaps a more efficient way would be to only have two tables - 'page' as before, and 'page term' which would have the page ID, the weight, and a hash of the term word.
An example query - you want to search for "foo". You hash "foo", then query all page term rows that have that term hash. Sort by descending weight and show the top ten results.
I think this should query reasonably quickly, though it obviously depends on the number and size of the pages in question. Sqlite isn't difficult to bundle and shouldn't need an additional installation.
Ranking pages is the really tricky bit here. With a large sample of pages you can use links quite a lot in working out ranks. Other wise you need to check how words seem to be placed, and also making sure your engine doesn't get fooled by 'dictionary' pages.
Good luck!