Source code for gensim.similarities.docsim

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2013 Radim Rehurek <>
# Licensed under the GNU LGPL v2.1 -

This module contains functions and classes for computing similarities across
a collection of documents in the Vector Space Model.

The main class is `Similarity`, which builds an index for a given set of documents.
Once the index is built, you can perform efficient queries like "Tell me how similar
is this query document to each document in the index?". The result is a vector
of numbers as large as the size of the initial set of documents, that is, one float
for each index document. Alternatively, you can also request only the top-N most
similar index documents to the query.

You can later add new documents to the index via `Similarity.add_documents()`.

How It Works

The `Similarity` class splits the index into several smaller sub-indexes ("shards"),
which are disk-based. If your entire index fits in memory (~hundreds of thousands
documents for 1GB of RAM), you can also use the `MatrixSimilarity` or `SparseMatrixSimilarity`
classes directly. These are more simple but do not scale as well (they keep the
entire index in RAM, no sharding).

Once the index has been initialized, you can query for document similarity simply by:

>>> index = Similarity('/tmp/tst', corpus, num_features=12) # build the index
>>> similarities = index[query] # get similarities between the query and all index documents

If you have more query documents, you can submit them all at once, in a batch:

>>> for similarities in index[batch_of_documents]: # the batch is simply an iterable of documents (=gensim corpus)
>>>     ...

The benefit of this batch (aka "chunked") querying is much better performance.
To see the speed-up on your machine, run ``python -m gensim.test.simspeed``
(compare to my results `here <>`_).

There is also a special syntax for when you need similarity of documents in the index
to the index itself (i.e. queries=indexed documents themselves). This special syntax
uses the faster, batch queries internally and **is ideal for all-vs-all pairwise similarities**:

>>> for similarities in index: # yield similarities of the 1st indexed document, then 2nd...
>>>     ...


import logging
import itertools
import os
import heapq

import numpy
import scipy.sparse

from gensim import interfaces, utils, matutils
from six.moves import map as imap, xrange, zip as izip

logger = logging.getLogger(__name__)

    import multiprocessing
    # by default, don't parallelize queries. uncomment the following line if you want that.
#    PARALLEL_SHARDS = multiprocessing.cpu_count() # use #parallel processes = #CPus
except ImportError:

class Shard(utils.SaveLoad):
    A proxy class that represents a single shard instance within a Similarity

    Basically just wraps (Sparse)MatrixSimilarity so that it mmaps from disk on
    request (query).

    def __init__(self, fname, index):
        self.dirname, self.fname = os.path.split(fname)
        self.length = len(index)
        self.cls = index.__class__"saving index shard to %s", self.fullname())
        self.index = self.get_index()

    def fullname(self):
        return os.path.join(self.dirname, self.fname)

    def __len__(self):
        return self.length

    def __getstate__(self):
        result = self.__dict__.copy()
        # (S)MS objects must be loaded via load() because of mmap (simple pickle.load won't do)
        if 'index' in result:
            del result['index']
        return result

    def __str__(self):
        return ("%s Shard(%i documents in %s)" % (self.cls.__name__, len(self), self.fullname()))

    def get_index(self):
        if not hasattr(self, 'index'):
            logger.debug("mmaping index from %s", self.fullname())
            self.index = self.cls.load(self.fullname(), mmap='r')
        return self.index

    def get_document_id(self, pos):
        """Return index vector at position `pos`.

        The vector is of the same type as the underlying index (ie., dense for
        MatrixSimilarity and scipy.sparse for SparseMatrixSimilarity.
        assert 0 <= pos < len(self), "requested position out of range"
        return self.get_index().index[pos]

    def __getitem__(self, query):
        index = self.get_index()
            index.num_best = self.num_best
            index.normalize = self.normalize
            raise ValueError("num_best and normalize have to be set before querying a proxy Shard object")
        return index[query]

def query_shard(args):
    query, shard = args  # simulate starmap (not part of multiprocessing in older Pythons)
    logger.debug("querying shard %s num_best=%s in process %s", shard, shard.num_best, os.getpid())
    result = shard[query]
    logger.debug("finished querying shard %s in process %s", shard, os.getpid())
    return result

[docs]class Similarity(interfaces.SimilarityABC): """ Compute cosine similarity of a dynamic query against a static corpus of documents ("the index"). Scalability is achieved by sharding the index into smaller pieces, each of which fits into core memory (see the `(Sparse)MatrixSimilarity` classes in this module). The shards themselves are simply stored as files to disk and mmap'ed back as needed. """
[docs] def __init__(self, output_prefix, corpus, num_features, num_best=None, chunksize=256, shardsize=32768, norm='l2'): """ Construct the index from `corpus`. The index can be later extended by calling the `add_documents` method. **Note**: documents are split (internally, transparently) into shards of `shardsize` documents each, converted to a matrix, for faster BLAS calls. Each shard is stored to disk under `output_prefix.shard_number` (=you need write access to that location). If you don't specify an output prefix, a random filename in temp will be used. `shardsize` should be chosen so that a `shardsize x chunksize` matrix of floats fits comfortably into main memory. `num_features` is the number of features in the `corpus` (e.g. size of the dictionary, or the number of latent topics for latent semantic models). `norm` is the user-chosen normalization to use. Accepted values are: 'l1' and 'l2'. If `num_best` is left unspecified, similarity queries will return a full vector with one float for every document in the index: >>> index = Similarity('/path/to/index', corpus, num_features=400) # if corpus has 7 documents... >>> index[query] # ... then result will have 7 floats [0.0, 0.0, 0.2, 0.13, 0.8, 0.0, 0.1] If `num_best` is set, queries return only the `num_best` most similar documents, always leaving out documents for which the similarity is 0. If the input vector itself only has features with zero values (=the sparse representation is empty), the returned list will always be empty. >>> index.num_best = 3 >>> index[query] # return at most "num_best" of `(index_of_document, similarity)` tuples [(4, 0.8), (2, 0.13), (3, 0.13)] You can also override `num_best` dynamically, simply by setting e.g. `self.num_best = 10` before doing a query. """ if output_prefix is None: # undocumented feature: set output_prefix=None to create the server in temp self.output_prefix = utils.randfname(prefix='simserver') else: self.output_prefix = output_prefix"starting similarity index under %s", self.output_prefix) self.num_features = num_features self.num_best = num_best self.norm = norm self.chunksize = int(chunksize) self.shardsize = shardsize self.shards = [] self.fresh_docs, self.fresh_nnz = [], 0 if corpus is not None: self.add_documents(corpus)
def __len__(self): return len(self.fresh_docs) + sum([len(shard) for shard in self.shards]) def __str__(self): return ("Similarity index with %i documents in %i shards (stored under %s)" % (len(self), len(self.shards), self.output_prefix))
[docs] def add_documents(self, corpus): """ Extend the index with new documents. Internally, documents are buffered and then spilled to disk when there's `self.shardsize` of them (or when a query is issued). """ min_ratio = 1.0 # 0.5 to only reopen shards that are <50% complete if self.shards and len(self.shards[-1]) < min_ratio * self.shardsize: # The last shard was incomplete (<; load it back and add the documents there, don't start a new shard self.reopen_shard() for doc in corpus: if isinstance(doc, numpy.ndarray): doclen = len(doc) elif scipy.sparse.issparse(doc): doclen = doc.nnz else: doclen = len(doc) if doclen < 0.3 * self.num_features: doc = matutils.unitvec(matutils.corpus2csc([doc], self.num_features).T, self.norm) else: doc = matutils.unitvec(matutils.sparse2full(doc, self.num_features), self.norm) self.fresh_docs.append(doc) self.fresh_nnz += doclen if len(self.fresh_docs) >= self.shardsize: self.close_shard() if len(self.fresh_docs) % 10000 == 0:"PROGRESS: fresh_shard size=%i", len(self.fresh_docs))
[docs] def shardid2filename(self, shardid): if self.output_prefix.endswith('.'): return "%s%s" % (self.output_prefix, shardid) else: return "%s.%s" % (self.output_prefix, shardid)
[docs] def close_shard(self): """ Force the latest shard to close (be converted to a matrix and stored to disk). Do nothing if no new documents added since last call. **NOTE**: the shard is closed even if it is not full yet (its size is smaller than `self.shardsize`). If documents are added later via `add_documents()`, this incomplete shard will be loaded again and completed. """ if not self.fresh_docs: return shardid = len(self.shards) # consider the shard sparse if its density is < 30% issparse = 0.3 > 1.0 * self.fresh_nnz / (len(self.fresh_docs) * self.num_features) if issparse: index = SparseMatrixSimilarity(self.fresh_docs, num_terms=self.num_features, num_docs=len(self.fresh_docs), num_nnz=self.fresh_nnz) else: index = MatrixSimilarity(self.fresh_docs, num_features=self.num_features)"creating %s shard #%s", 'sparse' if issparse else 'dense', shardid) shard = Shard(self.shardid2filename(shardid), index) shard.num_best = self.num_best shard.num_nnz = self.fresh_nnz self.shards.append(shard) self.fresh_docs, self.fresh_nnz = [], 0
[docs] def reopen_shard(self): assert self.shards if self.fresh_docs: raise ValueError("cannot reopen a shard with fresh documents in index") last_shard = self.shards[-1] last_index = last_shard.get_index()"reopening an incomplete shard of %i documents", len(last_shard)) self.fresh_docs = list(last_index.index) self.fresh_nnz = last_shard.num_nnz del self.shards[-1] # remove the shard from index, *but its file on disk is not deleted* logger.debug("reopen complete")
[docs] def query_shards(self, query): """ Return the result of applying shard[query] for each shard in self.shards, as a sequence. If PARALLEL_SHARDS is set, the shards are queried in parallel, using the multiprocessing module. """ args = zip([query] * len(self.shards), self.shards) if PARALLEL_SHARDS and PARALLEL_SHARDS > 1: logger.debug("spawning %i query processes", PARALLEL_SHARDS) pool = multiprocessing.Pool(PARALLEL_SHARDS) result = pool.imap(query_shard, args, chunksize=1 + len(args) / PARALLEL_SHARDS) else: # serial processing, one shard after another pool = None result = imap(query_shard, args) return pool, result
def __getitem__(self, query): """Get similarities of document `query` to all documents in the corpus. **or** If `query` is a corpus (iterable of documents), return a matrix of similarities of all query documents vs. all corpus document. This batch query is more efficient than computing the similarities one document after another. """ self.close_shard() # no-op if no documents added to index since last query # reset num_best and normalize parameters, in case they were changed dynamically for shard in self.shards: shard.num_best = self.num_best shard.normalize = self.norm # there are 4 distinct code paths, depending on whether input `query` is # a corpus (or numpy/scipy matrix) or a single document, and whether the # similarity result should be a full array or only num_best most similar # documents. pool, shard_results = self.query_shards(query) if self.num_best is None: # user asked for all documents => just stack the sub-results into a single matrix # (works for both corpus / single doc query) result = numpy.hstack(shard_results) else: # the following uses a lot of lazy evaluation and (optionally) parallel # processing, to improve query latency and minimize memory footprint. offsets = numpy.cumsum([0] + [len(shard) for shard in self.shards]) convert = lambda doc, shard_no: [(doc_index + offsets[shard_no], sim) for doc_index, sim in doc] is_corpus, query = utils.is_corpus(query) is_corpus = is_corpus or hasattr(query, 'ndim') and query.ndim > 1 and query.shape[0] > 1 if not is_corpus: # user asked for num_best most similar and query is a single doc results = (convert(result, shard_no) for shard_no, result in enumerate(shard_results)) result = heapq.nlargest(self.num_best, itertools.chain(*results), key=lambda item: item[1]) else: # the trickiest combination: returning num_best results when query was a corpus results = [] for shard_no, result in enumerate(shard_results): shard_result = [convert(doc, shard_no) for doc in result] results.append(shard_result) result = [] for parts in izip(*results): merged = heapq.nlargest(self.num_best, itertools.chain(*parts), key=lambda item: item[1]) result.append(merged) if pool: # gc doesn't seem to collect the Pools, eventually leading to # "IOError 24: too many open files". so let's terminate it manually. pool.terminate() return result
[docs] def vector_by_id(self, docpos): """ Return indexed vector corresponding to the document at position `docpos`. """ self.close_shard() # no-op if no documents added to index since last query pos = 0 for shard in self.shards: pos += len(shard) if docpos < pos: break if not self.shards or docpos < 0 or docpos >= pos: raise ValueError("invalid document position: %s (must be 0 <= x < %s)" % (docpos, len(self))) result = shard.get_document_id(docpos - pos + len(shard)) return result
[docs] def similarity_by_id(self, docpos): """ Return similarity of the given document only. `docpos` is the position of the query document within index. """ query = self.vector_by_id(docpos) norm, self.norm = self.norm, False result = self[query] self.norm = norm return result
def __iter__(self): """ For each index document, compute cosine similarity against all other documents in the index and yield the result. """ # turn off query normalization (vectors in the index are already normalized, save some CPU) norm, self.norm = self.norm, False for chunk in self.iter_chunks(): if chunk.shape[0] > 1: for sim in self[chunk]: yield sim else: yield self[chunk] self.norm = norm # restore normalization
[docs] def iter_chunks(self, chunksize=None): """ Iteratively yield the index as chunks of documents, each of size <= chunksize. The chunk is returned in its raw form (matrix or sparse matrix slice). The size of the chunk may be smaller than requested; it is up to the caller to check the result for real length, using `chunk.shape[0]`. """ self.close_shard() if chunksize is None: # if not explicitly specified, use the chunksize from the constructor chunksize = self.chunksize for shard in self.shards: query = shard.get_index().index for chunk_start in xrange(0, query.shape[0], chunksize): # scipy.sparse doesn't allow slicing beyond real size of the matrix # (unlike numpy). so, clip the end of the chunk explicitly to make # scipy.sparse happy chunk_end = min(query.shape[0], chunk_start + chunksize) chunk = query[chunk_start: chunk_end] # create a view yield chunk
[docs] def check_moved(self): """ Update shard locations, in case the server directory has moved on filesystem. """ dirname = os.path.dirname(self.output_prefix) for shard in self.shards: shard.dirname = dirname
[docs] def save(self, fname=None, *args, **kwargs): """ Save the object via pickling (also see load) under filename specified in the constructor. Calls `close_shard` internally to spill any unfinished shards to disk first. """ self.close_shard() if fname is None: fname = self.output_prefix super(Similarity, self).save(fname, *args, **kwargs)
[docs] def destroy(self): """ Delete all files under self.output_prefix. Object is not usable after calling this method anymore. Use with care! """ import glob for fname in glob.glob(self.output_prefix + '*'):"deleting %s", fname) os.remove(fname)
#endclass Similarity
[docs]class MatrixSimilarity(interfaces.SimilarityABC): """ Compute similarity against a corpus of documents by storing the index matrix in memory. The similarity measure used is cosine between two vectors. Use this if your input corpus contains dense vectors (such as documents in LSI space) and fits into RAM. The matrix is internally stored as a *dense* numpy array. Unless the entire matrix fits into main memory, use `Similarity` instead. See also `Similarity` and `SparseMatrixSimilarity` in this module. """
[docs] def __init__(self, corpus, num_best=None, dtype=numpy.float32, num_features=None, chunksize=256, corpus_len=None): """ `num_features` is the number of features in the corpus (will be determined automatically by scanning the corpus if not specified). See `Similarity` class for description of the other parameters. """ if num_features is None: logger.warning("scanning corpus to determine the number of features (consider setting `num_features` explicitly)") num_features = 1 + utils.get_max_id(corpus) self.num_features = num_features self.num_best = num_best self.normalize = True self.chunksize = chunksize if corpus_len is None: corpus_len = len(corpus) if corpus is not None: if self.num_features <= 0: raise ValueError("cannot index a corpus with zero features (you must specify either `num_features` or a non-empty corpus in the constructor)")"creating matrix with %i documents and %i features", corpus_len, num_features) self.index = numpy.empty(shape=(corpus_len, num_features), dtype=dtype) # iterate over corpus, populating the numpy index matrix with (normalized) # document vectors for docno, vector in enumerate(corpus): if docno % 1000 == 0: logger.debug("PROGRESS: at document #%i/%i", docno, corpus_len) # individual documents in fact may be in numpy.scipy.sparse format as well. # it's not documented because other it's not fully supported throughout. # the user better know what he's doing (no normalization, must # explicitly supply num_features etc). if isinstance(vector, numpy.ndarray): pass elif scipy.sparse.issparse(vector): vector = vector.toarray().flatten() else: vector = matutils.unitvec(matutils.sparse2full(vector, num_features)) self.index[docno] = vector
def __len__(self): return self.index.shape[0]
[docs] def get_similarities(self, query): """ Return similarity of sparse vector `query` to all documents in the corpus, as a numpy array. If `query` is a collection of documents, return a 2D array of similarities of each document in `query` to all documents in the corpus (=batch query, faster than processing each document in turn). **Do not use this function directly; use the self[query] syntax instead.** """ is_corpus, query = utils.is_corpus(query) if is_corpus: query = numpy.asarray( [matutils.sparse2full(vec, self.num_features) for vec in query], dtype=self.index.dtype) else: if scipy.sparse.issparse(query): query = query.toarray() # convert sparse to dense elif isinstance(query, numpy.ndarray): pass else: # default case: query is a single vector in sparse gensim format query = matutils.sparse2full(query, self.num_features) query = numpy.asarray(query, dtype=self.index.dtype) # do a little transposition dance to stop numpy from making a copy of # self.index internally in (very slow). result =, query.T).T # return #queries x #index return result # XXX: removed casting the result from array to list; does anyone care?
def __str__(self): return "%s<%i docs, %i features>" % (self.__class__.__name__, len(self), self.index.shape[1])
#endclass MatrixSimilarity
[docs]class WmdSimilarity(interfaces.SimilarityABC): """ Document similarity (like MatrixSimilarity) that uses the negative of WMD as a similarity measure. See gensim.models.word2vec.wmdistance for more information. When a `num_best` value is provided, only the most similar documents are retrieved. When using this code, please consider citing the following papers: .. Ofir Pele and Michael Werman, "A linear time histogram metric for improved SIFT matching". .. Ofir Pele and Michael Werman, "Fast and robust earth mover's distances". .. Matt Kusner et al. "From Word Embeddings To Document Distances". Example: # See Tutorial Notebook for more examples >>> # Given a document collection "corpus", train word2vec model. >>> model = word2vec(corpus) >>> instance = WmdSimilarity(corpus, model, num_best=10) >>> # Make query. >>> query = 'Very good, you should seat outdoor.' >>> sims = instance[query] """
[docs] def __init__(self, corpus, w2v_model, num_best=None, normalize_w2v_and_replace=True, chunksize=256): """ corpus: List of lists of strings, as in gensim.models.word2vec. w2v_model: A trained word2vec model. num_best: Number of results to retrieve. normalize_w2v_and_replace: Whether or not to normalize the word2vec vectors to length 1. """ self.corpus = corpus self.w2v_model = w2v_model self.num_best = num_best self.chunksize = chunksize # Normalization of features is not possible, as corpus is a list (of lists) of strings. self.normalize = False # index is simply an array from 0 to size of corpus. self.index = numpy.array(range(len(corpus))) if normalize_w2v_and_replace: # Normalize vectors in word2vec class to length 1. w2v_model.init_sims(replace=True)
def __len__(self): return len(self.corpus)
[docs] def get_similarities(self, query): """ **Do not use this function directly; use the self[query] syntax instead.** """ if isinstance(query, numpy.ndarray): # Convert document indexes to actual documents. query = [self.corpus[i] for i in query] if not isinstance(query[0], list): query = [query] n_queries = len(query) result = [] for qidx in range(n_queries): # Compute similarity for each query. qresult = [self.w2v_model.wmdistance(document, query[qidx]) for document in self.corpus] qresult = numpy.array(qresult) qresult = 1./(1.+qresult) # Similarity is the negative of the distance. # Append single query result to list of all results. result.append(qresult) if len(result) == 1: # Only one query. result = result[0] else: result = numpy.array(result) return result
def __str__(self): return "%s<%i docs, %i features>" % (self.__class__.__name__, len(self), self.w2v_model.syn0.shape[1])
#endclass WmdSimilarity
[docs]class SparseMatrixSimilarity(interfaces.SimilarityABC): """ Compute similarity against a corpus of documents by storing the sparse index matrix in memory. The similarity measure used is cosine between two vectors. Use this if your input corpus contains sparse vectors (such as documents in bag-of-words format) and fits into RAM. The matrix is internally stored as a `scipy.sparse.csr` matrix. Unless the entire matrix fits into main memory, use `Similarity` instead. Takes an optional `maintain_sparsity` argument, setting this to True causes `get_similarities` to return a sparse matrix instead of a dense representation if possible. See also `Similarity` and `MatrixSimilarity` in this module. """
[docs] def __init__(self, corpus, num_features=None, num_terms=None, num_docs=None, num_nnz=None, num_best=None, chunksize=500, dtype=numpy.float32, maintain_sparsity=False): self.num_best = num_best self.normalize = True self.chunksize = chunksize self.maintain_sparsity = maintain_sparsity if corpus is not None:"creating sparse index") # iterate over input corpus, populating the sparse index matrix try: # use the more efficient corpus generation version, if the input # `corpus` is MmCorpus-like (knows its shape and number of non-zeroes). num_terms, num_docs, num_nnz = corpus.num_terms, corpus.num_docs, corpus.num_nnz logger.debug("using efficient sparse index creation") except AttributeError: # no MmCorpus, use the slower version (or maybe user supplied the # num_* params in constructor) pass if num_features is not None: # num_terms is just an alias for num_features, for compatibility with MatrixSimilarity num_terms = num_features if num_terms is None: raise ValueError("refusing to guess the number of sparse features: specify num_features explicitly") corpus = (matutils.scipy2sparse(v) if scipy.sparse.issparse(v) else (matutils.full2sparse(v) if isinstance(v, numpy.ndarray) else matutils.unitvec(v)) for v in corpus) self.index = matutils.corpus2csc( corpus, num_terms=num_terms, num_docs=num_docs, num_nnz=num_nnz, dtype=dtype, printprogress=10000).T # convert to Compressed Sparse Row for efficient row slicing and multiplications self.index = self.index.tocsr() # currently no-op, CSC.T is already CSR"created %r", self.index)
def __len__(self): return self.index.shape[0]
[docs] def get_similarities(self, query): """ Return similarity of sparse vector `query` to all documents in the corpus, as a numpy array. If `query` is a collection of documents, return a 2D array of similarities of each document in `query` to all documents in the corpus (=batch query, faster than processing each document in turn). **Do not use this function directly; use the self[query] syntax instead.** """ is_corpus, query = utils.is_corpus(query) if is_corpus: query = matutils.corpus2csc(query, self.index.shape[1], dtype=self.index.dtype) else: if scipy.sparse.issparse(query): query = query.T # convert documents=rows to documents=columns elif isinstance(query, numpy.ndarray): if query.ndim == 1: query.shape = (1, len(query)) query = scipy.sparse.csr_matrix(query, dtype=self.index.dtype).T else: # default case: query is a single vector, in sparse gensim format query = matutils.corpus2csc([query], self.index.shape[1], dtype=self.index.dtype) # compute cosine similarity against every other document in the collection result = self.index * query.tocsc() # N x T * T x C = N x C if result.shape[1] == 1 and not is_corpus: # for queries of one document, return a 1d array result = result.toarray().flatten() elif self.maintain_sparsity: # avoid converting to dense array if maintaining sparsity result = result.T else: # otherwise, return a 2d matrix (#queries x #index) result = result.toarray().T return result
#endclass SparseMatrixSimilarity