graphembed-rs 0.1.2__cp38-cp38-macosx_10_12_x86_64.whl

graphembed_rs/__init__.py

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+from importlib import import_module as _imp
+from graphembed_rs import *      
+
+# add the helper into the same namespace
+from .load_utils import *                   
+
+del _imp    

graphembed_rs/load_utils.py

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+import numpy as np
+from pathlib import Path
+### install pymongo with pip install pymongo
+# -- pymongo is a BSON decoder, not a BSON encoder --
+from bson import decode_file_iter
+
+
+def _dtype_from_type_name(tname: str):
+    """Map the Rust type-name string to a NumPy dtype."""
+    if tname == "f32":
+        return np.float32
+    if tname == "f64":
+        return np.float64
+    if tname == "usize":                 # stored as i64 in BSON
+        return np.int64
+    raise ValueError(f"Unknown type_name {tname!r} in BSON header")
+
+
+def load_embedding_bson(path: str | Path, *, want_in: bool = False):
+    """
+    Parameters
+    ----------
+    path : str | pathlib.Path
+        File written by graphembed::io::bson_dump(...)
+    want_in : bool, default False
+        • False … always return the OUT/source embedding (shape = (n, d))  
+        • True  … additionally return the IN/target embedding when
+          the dump is *asymmetric* (tuple(out, in_)).  For symmetric
+          dumps the second item is None.
+
+    Returns
+    -------
+    np.ndarray            (sym. dump or want_in=False)
+    OR (out_emb, in_emb)  (want_in=True)
+    """
+    path = Path(path)
+    with path.open("rb") as fh:
+        docs = decode_file_iter(fh)
+
+        # -- header ----------------------------------------------------
+        header = next(docs)["header"]
+        n      = int(header["nbdata"])
+        d      = int(header["dimension"])
+        sym    = bool(header["symetric"])
+        dtype  = _dtype_from_type_name(header["type_name"])
+        out_emb = np.empty((n, d), dtype=dtype)
+        in_emb  = None if sym or not want_in else np.empty((n, d), dtype=dtype)
+
+        # --OUT part --------------------------------------------------
+        for _ in range(n):
+            doc = next(docs)
+            key, vec = next(iter(doc.items()))            # only 1 (key,val)
+            idx, tag = map(int, key.split(","))
+            assert tag == 0, f"expected tag 0, got {tag}"
+            out_emb[idx] = np.asarray(vec, dtype=dtype)
+
+        # -- IN part (if any) -----------------------------------------
+        if not sym:
+            for _ in range(n):
+                doc = next(docs)
+                key, vec = next(iter(doc.items()))
+                idx, tag = map(int, key.split(","))
+                assert tag == 1, f"expected tag 1, got {tag}"
+                if in_emb is not None:                    # want_in == True
+                    in_emb[idx] = np.asarray(vec, dtype=dtype)
+                # else: silently drop it
+
+        # -- optional indexation doc – skip for now --------------------
+        # (decode_file_iter stops automatically at EOF)
+
+    return (out_emb, in_emb) if want_in else out_emb

graphembed_rs-0.1.2.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: graphembed_rs
+Version: 0.1.2
+Requires-Dist: numpy>=2.2.5
+Requires-Dist: pymongo>=4.12.1
+License-File: LICENSE-MIT
+Summary: Python bindings for the high‑performance Rust graph/network embedding library graphembed
+Keywords: graph,embedding,hash
+Author: Jianshu Zhao
+Author-email: jeanpierre.both@gmail.com
+License: MIT OR Apache-2.0
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Source Code, https://github.com/jean-pierreBoth/graphembed
+
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/graphembed/README.html)
+![](https://anaconda.org/bioconda/graphembed/badges/license.svg)
+![](https://anaconda.org/bioconda/graphembed/badges/version.svg)
+![](https://anaconda.org/bioconda/graphembed/badges/latest_release_relative_date.svg)
+![](https://anaconda.org/bioconda/graphembed/badges/platforms.svg)
+[![install with conda](https://anaconda.org/bioconda/graphembed/badges/downloads.svg)](https://anaconda.org/bioconda/graphembed)
+
+<div align="center">
+  <img width="35%" src ="GraphEmbed_log.jpg">
+</div>
+
+# GraphEmbed: Efficient and Robust Network Embedding via High-Order Proximity Preservation or Recursive Sketching
+
+This crate provides an executable and a library for embedding of directed or undirected graphs with positively weighted edges. We engineered and optimized current network embedding algorithms for large-scale network embedding, especially biological network. This crate was developed by [Jianshu Zhao](https://gitlab.com/Jianshu_Zhao) and Jean-Pierre Both [jpboth](https://gitlab.com/jpboth). We have a copy here in [Github](https://github.com/jianshu93/graphembed)
+
+
+  - For simple graphs, without data attached to nodes, there are 2 modules **nodesketch** and **atp**. A simple executable with a validation option based on link prediction is also provided.
+
+## Quick Install
+
+### Pre-built binaries on Linux
+```bash
+wget https://gitlab.com/-/project/64961144/uploads/9d7d0b038140cb67c584f01cd6dafac9/graphembed_Linux_x86-64_v0.1.6.zip
+unzip graphembed_Linux_x86-64_v0.1.6.zip
+chmod a+x ./graphembed
+./graphembed -h
+```
+
+### Bioconda on Linux/MacOS
+```bash
+conda install -c conda-forge -c bioconda graphembed
+```
+
+### Homebrew on MacOS
+```bash
+brew tap jianshu93/graphembed
+brew update
+brew install graphembed
+```
+
+
+### In Python (Please install python>=3.9 first)
+```bash
+pip install graphembed_rs
+
+### or you can build from source (Linux) after installing maturin
+git clone https://gitlab.com/Jianshu_Zhao/graphembed
+cd graphembed
+pip install maturin
+### note: for macOS, you need to change the line "features = ["pyo3/extension-module", "intel-mkl-static", "simdeez_f"]" in pyporject.toml to "features = ["pyo3/extension-module","openblas-system","stdsimd"]", you also need to Install OpenBLAS and add to system library path via Homebrew
+maturin develop --release
+
+#### Prepare some data
+wget https://gitlab.com/-/project/64961144/uploads/4e341383d62d86d1dd66e668e91b2c07/BlogCatalog.txt
+```
+
+```python
+import os
+os.environ["RUST_LOG"] = "info"
+import graphembed_rs.graphembed_rs as ge
+import graphembed_rs.load_utils as ge_utils
+help(ge)
+help(ge_utils)
+### HOPE
+ge.embed_hope_rank("BlogCatalog.txt", target_rank=128, nbiter=4,output="embedding_output")
+out_vectors=ge_utils.load_embedding_bson("embedding_output.bson")
+print("OUT embedding shape :", out_vectors.shape)
+print("first OUT vector    :", out_vectors[0])
+
+### Sketching
+### sketching only
+ge.embed_sketching("BlogCatalog.txt", decay=0.3, dim=128, nbiter=5, symetric=True, output="embedding_output")
+out_vectors=ge_utils.load_embedding_bson("embedding_output.bson")
+print("OUT embedding shape :", out_vectors.shape)
+print("first OUT vector    :", out_vectors[0])
+
+
+### validate accuracy
+auc_scores = ge.validate_sketching("BlogCatalog.txt",decay=0.3, dim=128, nbiter=3, nbpass=1, skip_frac=0.2,symetric=True, centric=True)
+print("Standard AUC per pass:", auc_scores)
+```
+
+## Methods
+### The embedding algorithms used in this crate are based on the following papers
+
+- **nodesketch**
+
+*NodeSketch : Highly-Efficient Graph Embeddings via Recursive Sketching KDD 2019*.  see [nodesketch](https://dl.acm.org/doi/10.1145/3292500.3330951)  
+    D. Yang,P. Rosso,Bin-Li, P. Cudre-Mauroux.
+
+It is based on multi hop neighbourhood identification via sensitive hashing based on the recent algorithm **probminhash**. See [arxiv](https://arxiv.org/abs/1911.00675) or  [ieee-2022](https://ieeexplore.ieee.org/document/9185081).
+
+The algorithm associates a probability distribution on neighbours of each point depending on edge weights and distance to the point.
+Then this distribution is hashed to build a (discrete) embedding vector consisting in nodes identifiers.  
+The distance between embedded vectors is the Jaccard distance so we get
+a real distance on the embedding space for the symetric embedding.  
+
+An extension of the paper is also implemented to get asymetric embedding for directed graph. The similarity is also based on the hash of sets (nodes going to or from) a given node but then the dissimilarity is no more a distance (no symetry and some discrepancy with the triangular inequality).
+
+**The orkut graph with 3 millions nodes and 100 millions of edge is embedded in 5' with a 24 core i9 laptop with this algorithm giving an AUC of 0.95**.
+
+
+- **atp**
+
+*Asymetric Transitivity Preserving Graph Embedding 2016*.
+    M. Ou, P Cui, J. Pei, Z. Zhang and W. Zhu. See [hope](https://dl.acm.org/doi/10.1145/2939672.2939751).
+
+The objective is to provide an asymetric graph embedding and get estimate of the precision of the embedding in function of its dimension.  
+
+We use the Adamic-Adar matricial representation of the graph. (It must be noted that the ponderation of a node by the number of couples joined by it is called Resource Allocation in the Graph Kernel litterature).
+The asymetric embedding is obtained from the left and right singular eigenvectors of the Adamic-Adar representation of the graph.
+Source node are related to left singular vectors and target nodes to the right ones.  
+The similarity measure is the dot product, so it is not a norm.  
+The svd is approximated by randomization as described in Halko-Tropp 2011 as implemented in the [annembed crate](https://crates.io/crates/annembed).
+
+## Validation
+
+Validation of embeddings is assessed via standard Auc with random deletion of edges. See documentation in the *link* module and *embed* binary.
+We give also a variation based on centric quality assessment as explained at [cauc](http://github.com/jean-pierreBoth/linkauc)
+## Some data sets
+
+Small datasets are given in the Data subdirectory (with 7z compression) to run tests.  
+Larger datasets can be downloaded from the SNAP data collections <https://snap.stanford.edu/data>
+
+#### Some small test graphs are provided in a Data subdirectory
+
+- Symetric graphs
+
+  - Les miserables  <http://konect.cc/networks/moreno_lesmis>.  
+    This is the graph of co-occurence of characters in Victor Hugo's novel 'Les Misérables'.
+
+- Asymetric graphs
+
+  - wiki-vote <https://snap.stanford.edu/data/wiki-Vote.html>
+         7115 nodes 103689 edges
+
+  - Cora : <http://konect.cc/networks/subelj_cora>
+        citation network 23166 nodes 91500 edges
+
+#### Some larger data tests for user to download
+
+These graphs were used in results see below.
+
+Beware of the possible need to convert from Windows to Linux End Of Line, see the dos2unix utility.  
+Possibly some data can need to be converted from Tsv format to Csv, before being read by the program.
+
+- Symetric
+
+  - Amazon.   Nodes: 334 863   Edges: 925 872  <https://snap.stanford.edu/data/amazon0601.html>
+  - youtube.  Nodes: 1 134 890 Edges: 2 987 624 <https://snap.stanford.edu/data/com-Youtube.html>
+  - orkut.    Nodes: 3 072 441 Edges: 117 185 083 <https://snap.stanford.edu/data/com-Orkut.html>
+
+- Asymetric
+
+  - twitter as tested in Hope  <http://konect.cc/networks/munmun_twitter_social>
+        465017 nodes 834797 edges
+
+## Some results
+
+### results for the *atp* and *nodesketch* modules
+
+Embedding and link prediction evaluation for the above data sets are given in file [resultats.md](./resultats.md)
+A more global analysis of the embedding with the nodesketch module is done for the orkut graph in file [orkut.md](./orkut.md)
+
+A preliminary of node centric quality estimation is provided in the validation module (see documentation in validation::link).  
+
+### Some qualitative comments
+
+- For the embedding using the randomized svd, increasing the embedding dimension is interesting as far as the corresponding eigenvalues continue to decrease significantly.
+
+- The munmun_twitter_social graph shows that treating a directed graph as an undirected graph give significantly different results in terms of link prediction AUC.
+
+
+## Generalized Svd
+
+An implementation of Generalized Svd comes as a by-product in module [gsvd](./src/atp/gsvd.rs).
+
+## Detailed Installation and Usage
+
+### Installation
+
+The crate provides features (with a default configuration), required by the *annembed* dependency, to specify which version of lapack you want to use or the choice of simd implementation.
+- For example compilation is done by :
+*cargo build --release --features="openblas-system"* to  use a dynamic link with openblas.
+The choice of one feature is mandatory to provide required linear algebra library.  
+- On Intel the simdeez_f feature can be used. On other cpus the stdsimd feature can be chosen but it requires compiler >= 1.79
+
+### Usage
+
+The embed module can be generated with the standard : cargo doc --no-deps --bin embed.  
+
+- The Hope embedding relying on matrices computations limits the size of the graph to some hundred thousands nodes.
+It is intrinsically asymetric in nature. It nevertheless gives access to the spectrum of Adamic Adar matrix representing the graph and
+so to the required dimension to get a valid embedding in $R^{n}$.  
+
+- The Sketching embedding is much faster for large graphs but embeds in a space consisting in sequences of node id equipped with the Jaccard distance. It is particularly efficient in low degrees graph.
+
+- The *embed* module takes embedding and possibly validation commands (link prediction task) in one directive.  
+The general syntax is :
+
+    graphembed file_description [validation_command --validation_arguments] sketching mode  --embedding_arguments  
+    for example:  
+
+  For a symetric graph we get:
+
+- just embedding:
+        graphembed --csv ./Data/Graphs/Orkut/com-orkut.ungraph.txt --symetric  sketching --decay 0.2  --dim 200 --nbiter 
+
+- embedding and validation:
+ 
+        graphembed --csv ./Data/Graphs/Orkut/com-orkut.ungraph.txt  --symetric  validation --nbpass 5 --skip 0.15 sketching --decay 0.2  --dim 200 --nbiter 5
+
+For an asymetric graph we get 
+
+       graphembed --csv ./Data/Graphs/asymetric.csv  validation --nbpass 5 --skip 0.15 sketching --decay 0.2  --dim 200 --nbiter 5 
+
+
+    More details can be found in docs of the embed module. Use cargo doc --no-dep --bin embed (and cargo doc --no-dep) as usual.
+
+- Use the environment variable RUST_LOG gives access to some information at various level (debug, info, error)  via the **log** and **env_logger** crates.
+
+## License
+
+Licensed under either of
+
+* Apache License, Version 2.0, [LICENSE-APACHE](LICENSE-APACHE) or <http://www.apache.org/licenses/LICENSE-2.0>
+* MIT license [LICENSE-MIT](LICENSE-MIT) or <http://opensource.org/licenses/MIT>
+
+at your option.
+

graphembed_rs-0.1.2.dist-info/RECORD

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graphembed_rs-0.1.2.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: maturin (1.8.3)
+Root-Is-Purelib: false
+Tag: cp38-cp38-macosx_10_12_x86_64

graphembed_rs-0.1.2.dist-info/licenses/LICENSE-MIT

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+Copyright (c) 2022 jean-pierre.both and Jianshu Zhao
+
+Permission is hereby granted, free of charge, to any
+person obtaining a copy of this software and associated
+documentation files (the "Software"), to deal in the
+Software without restriction, including without
+limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software
+is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice
+shall be included in all copies or substantial portions
+of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF
+ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
+TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
+SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
+IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.