ssakg 0.0.1__tar.gz

ssakg-0.0.1/LICENSE

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ssakg-0.0.1/MANIFEST.in

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+include README_PYPI.md

ssakg-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: ssakg
+Version: 0.0.1
+Summary: Sequential Structural Associative Knowledge Graph (ssakg)
+Home-page: https://github.com/PrzemyslawStok/ssakg
+Author: Przemysław Stokłosa
+Author-email: przemyslaw.stoklosa@gmail.com
+License: Apache 2.0
+Keywords: semantic memory,structural graphs,graph density,sequence storage,sequence retrieval,context based memory,graph based memory
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy~=1.26.2
+Requires-Dist: networkx~=3.2.1
+Requires-Dist: matplotlib~=3.8.2
+Requires-Dist: pandas~=2.2.0
+Requires-Dist: tabulate~=0.9.0
+Requires-Dist: PyPrind~=2.11.3
+Requires-Dist: seaborn~=0.13.2
+
+# SSAKG
+
+Sequential Structural Associative Knowledge Graph (SSAKG) is a semantic memory.
+It can memorize sequences and then read them using a context. 
+The context contains random sequence elements. The elements of the context are not ordered.
+## Requirements
+
+- **Minimum Python Version:** 3.10
+## Installation
+
+Use the package manager [pip](https://pip.pypa.io/en/stable/) to install ssakg.
+
+```bash
+pip install ssakg
+```
+
+## Usage
+
+```python
+from ssakg import SSAKG
+
+# This basic example creates very simple ssakg, and stores two sequences.
+# The program shows how sequences are stored in Associative Knowledge Graph.
+
+ssakg = SSAKG(number_of_symbols=10, sequence_length=3, graphs_to_drawing=True)
+ssakg.insert([1, 2, 3])
+ssakg.insert([2, 4, 5])
+ssakg.show()
+```
+
+## Examples
+Examples of the use of the program:
+
+[Basics](https://github.com/PrzemyslawStok/ssakg/blob/main/examples/ssakg_basic.ipynb)\
+[Reading sequences](https://github.com/PrzemyslawStok/ssakg/blob/main/examples/ssakg_reading.ipynb)  
+[SSAKG memory](https://github.com/PrzemyslawStok/ssakg/blob/main/examples/ssakg_tests.ipynb)  
+
+## Requirements
+
+- **Minimum Python Version:** 3.10
+
+## License
+
+[Apache 2.0](LICENSE)

ssakg-0.0.1/README.md

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+# SSAKG
+
+Sequential Structural Associative Knowledge Graph (SSAKG) is a semantic memory.
+It can memorize sequences and then read them using a context. 
+The context contains random sequence elements. The elements of the context are not ordered.
+## Requirements
+
+- **Minimum Python Version:** 3.10
+## Installation
+
+Use the package manager [pip](https://pip.pypa.io/en/stable/) to install ssakg.
+
+```bash
+pip install ssakg
+```
+
+## Usage
+
+```python
+from ssakg import SSAKG
+
+# This basic example creates very simple ssakg, and stores two sequences.
+# The program shows how sequences are stored in Associative Knowledge Graph.
+
+ssakg = SSAKG(number_of_symbols=10, sequence_length=3, graphs_to_drawing=True)
+ssakg.insert([1, 2, 3])
+ssakg.insert([2, 4, 5])
+ssakg.show()
+```
+
+## Examples
+Examples of the use of the program:
+
+[Basics](examples/ssakg_basic.ipynb)\
+[Reading sequences](examples/ssakg_reading.ipynb)  
+[SSAKG memory](examples/ssakg_tests.ipynb)  
+
+## License
+
+[Apache 2.0](LICENSE)

ssakg-0.0.1/README_PYPI.md

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+# SSAKG
+
+Sequential Structural Associative Knowledge Graph (SSAKG) is a semantic memory.
+It can memorize sequences and then read them using a context. 
+The context contains random sequence elements. The elements of the context are not ordered.
+## Requirements
+
+- **Minimum Python Version:** 3.10
+## Installation
+
+Use the package manager [pip](https://pip.pypa.io/en/stable/) to install ssakg.
+
+```bash
+pip install ssakg
+```
+
+## Usage
+
+```python
+from ssakg import SSAKG
+
+# This basic example creates very simple ssakg, and stores two sequences.
+# The program shows how sequences are stored in Associative Knowledge Graph.
+
+ssakg = SSAKG(number_of_symbols=10, sequence_length=3, graphs_to_drawing=True)
+ssakg.insert([1, 2, 3])
+ssakg.insert([2, 4, 5])
+ssakg.show()
+```
+
+## Examples
+Examples of the use of the program:
+
+[Basics](https://github.com/PrzemyslawStok/ssakg/blob/main/examples/ssakg_basic.ipynb)\
+[Reading sequences](https://github.com/PrzemyslawStok/ssakg/blob/main/examples/ssakg_reading.ipynb)  
+[SSAKG memory](https://github.com/PrzemyslawStok/ssakg/blob/main/examples/ssakg_tests.ipynb)  
+
+## Requirements
+
+- **Minimum Python Version:** 3.10
+
+## License
+
+[Apache 2.0](LICENSE)

ssakg-0.0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

ssakg-0.0.1/setup.py

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+from setuptools import setup, find_packages
+
+VERSION = '0.0.1'
+DESCRIPTION = 'Sequential Structural Associative Knowledge Graph (ssakg)'
+LONG_DESCRIPTION = open('README_PYPI.md').read()
+
+setup(
+    name='ssakg',
+    version=VERSION,
+    description=DESCRIPTION,
+    long_description=LONG_DESCRIPTION,
+    long_description_content_type='text/markdown',
+    packages=find_packages(),
+    include_package_data=True,
+    install_requires=['numpy~=1.26.2', "networkx~=3.2.1", "matplotlib~=3.8.2", "pandas~=2.2.0", "tabulate~=0.9.0",
+                      "PyPrind~=2.11.3", "seaborn~=0.13.2"],
+    url='https://github.com/PrzemyslawStok/ssakg',
+    license='Apache 2.0',
+    author='Przemysław Stokłosa',
+    author_email='przemyslaw.stoklosa@gmail.com',
+    classifiers=[
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Science/Research",
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: Apache Software License",
+        "Operating System :: OS Independent",
+    ],
+    keywords=["semantic memory", "structural graphs", "graph density", "sequence storage", "sequence retrieval",
+              "context based memory", "graph based memory"],
+    python_requires='>=3.10',
+)

ssakg-0.0.1/ssakg/__init__.py

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+from .ssakg import SSAKG
+from .utils.sequence_generator import SequenceGenerator
+from .utils.ssakg_tester import SSAKG_Tester

ssakg-0.0.1/ssakg/anakg.py

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+# Copyright 2024 The SSAKG Authors. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import os
+
+import numpy as np
+
+import warnings
+
+import pandas as pd
+import seaborn as sns
+
+import matplotlib.pyplot as plot
+
+from ssakg.anakg_view import GraphView, create_dir
+from ssakg.sequence_translator import SequenceTranslator
+
+from tabulate import tabulate
+
+
+class ANAKG:
+    def __init__(self, graph_dim: int = 10, subgraph_dim: int = 5, dtype=np.int16, graphs_to_drawing=False,
+                 remove_diagonals=True, weighted_edges=True):
+
+        # The parameter graphs_to_drawing is only for draw colorfully graph to examples.
+        # Do not use it for other purposes.
+
+        self.graph_dim = graph_dim
+        self.subgraph_dim = subgraph_dim
+        self.dtype = dtype
+
+        self.sequence_translator = SequenceTranslator(sequence_matrix_dim=graph_dim, dtype=self.dtype)
+
+        self.subgraph_pattern = self.create_upper_triangular(self.graph_dim, remove_diagonals=remove_diagonals,
+                                                                     weighted_edges=weighted_edges, dtype=self.dtype)
+
+        self.graph = self.crate_graph()
+        self.sequences = []
+
+        self.graphs_to_drawing = graphs_to_drawing
+        self.graph_matrices = []
+
+    @staticmethod
+    def create_upper_triangular(dim: int, remove_diagonals=False, weighted_edges=True, dtype=np.int16) -> np.array:
+
+        array = np.ones([dim, dim], dtype=dtype)
+
+        if weighted_edges:
+            mul = np.arange(1, dim + 1, dtype=dtype)
+        else:
+            mul = np.ones(dim, dtype=dtype)
+
+        upper_triangular_matrix = (np.tril(array) * mul).transpose()
+
+        if remove_diagonals:
+            upper_triangular_matrix = upper_triangular_matrix - np.eye(dim, dtype=dtype) * mul
+
+        return upper_triangular_matrix
+
+    @staticmethod
+    def create_square(dim: int, remove_diagonals=False, weighted_edges=False, dtype=np.int16) -> np.array:
+        if weighted_edges:
+            mul = np.arange(1, dim + 1, dtype=dtype)
+        else:
+            mul = np.ones(dim, dtype=dtype)
+
+        square_matrix = (np.ones([dim, dim], dtype=dtype) * mul).transpose()
+
+        if remove_diagonals:
+            square_matrix = square_matrix - np.eye(dim, dtype=dtype) * mul
+
+        return square_matrix
+
+    def set_subgraph_pattern(self, subgraph_pattern: np.array):
+        self.subgraph_pattern = subgraph_pattern
+
+    def crate_graph(self):
+        dim = self.graph_dim
+
+        return np.zeros([dim, dim], dtype=self.dtype)
+
+    def add_subgraph(self, i: int, j: int):
+        subgraph = self.subgraph_pattern.copy()
+
+        temp_graph = np.zeros(self.graph.shape, dtype=self.dtype)
+        temp_graph[i:i + self.subgraph_dim, j:j + self.subgraph_dim] = subgraph
+        if self.graphs_to_drawing:
+            self.graph_matrices.append(temp_graph)
+
+        self.graph = self.graph + temp_graph
+
+    def add_random_subgraph(self):
+        rand_min = 0
+        rand_max = len(self.graph) - self.subgraph_dim + 1
+        i = np.random.randint(rand_min, rand_max)
+        j = np.random.randint(rand_min, rand_max)
+
+        self.add_subgraph(i, j)
+
+    def add_dim_to_graph(self, dim_to_add: int):
+        self.graph_dim += dim_to_add
+        self.graph = np.pad(self.graph, (0, dim_to_add), 'constant')
+
+        for i in range(len(self.graph_matrices)):
+            self.graph_matrices[i] = np.pad(self.graph_matrices[i], (0, dim_to_add), 'constant')
+
+    def sequence_to_subgraph(self, sequence: np.ndarray) -> np.ndarray:
+        temp_graph = np.zeros(self.graph.shape, dtype=self.dtype)
+
+        for i in range(self.subgraph_dim):
+            for j in range(self.subgraph_dim):
+                temp_graph[sequence[i], sequence[j]] = self.subgraph_pattern[i, j]
+
+        return temp_graph
+
+    def insert_sequence(self, sequence: np.ndarray) -> np.ndarray | None:
+        if len(sequence) != self.subgraph_dim:
+            warnings.warn(f"Sequence has incorrect length {len(sequence)}. Subgraph not inserted.")
+            return None
+
+        new_sequence, dims_to_add = self.sequence_translator.translate_sequence(sequence)
+
+        if dims_to_add > 0:
+            self.add_dim_to_graph(dims_to_add)
+
+        self.sequences.append(new_sequence)
+        temp_graph = self.sequence_to_subgraph(new_sequence)
+
+        if self.graphs_to_drawing:
+            self.graph_matrices.append(temp_graph)
+
+        self.graph = self.graph + temp_graph
+
+        return new_sequence
+
+    def insert(self, sequences: np.ndarray):
+        if np.ndim(sequences) == 1:
+            return self.insert_sequence(sequences)
+        else:
+            for sequence in sequences:
+                self.insert_sequence(sequence)
+
+    def get_subgraph_from_sequence(self, sequence: np.ndarray) -> np.ndarray | None:
+        if len(sequence) > self.subgraph_dim:
+            warn = f"Sequence has incorrect length {len(sequence)}. Subgraph not created."
+            warnings.warn(warn)
+            return None
+
+        temp_graph = np.zeros([len(sequence), len(sequence)], dtype=self.dtype)
+
+        for i in range(len(sequence)):
+            for j in range(len(sequence)):
+                temp_graph[i, j] = self.graph[sequence[i], sequence[j]]
+
+        return temp_graph
+
+    def __str__(self):
+        graph_size = self.graph.nbytes
+        sequences_no = len(self.graph_matrices)
+        sequences_size = 0
+        for sequence in self.graph_matrices:
+            sequences_size += sequence.nbytes
+
+        density = self.density()
+
+        return (f"graph_size: {graph_size} B\ngraph density: {density:.2f}\nstored sequences: "
+                f"{sequences_no}\nstored sequences size: {sequences_size}B\n")
+
+    def get_subgraph(self):
+        return self.subgraph_pattern
+
+    def get_graph(self):
+        return self.graph
+
+    def create_graph_view(self, to_print=False):
+        graph_view = GraphView()
+        graph_view.graph_from_matrix(np.zeros(self.graph.shape), color="gray", to_print=to_print)
+
+        last_matrix = np.zeros(self.graph.shape, dtype=self.dtype)
+
+        for graph_matrix in self.graph_matrices:
+            last_matrix += graph_matrix
+
+        graph_view.graph_from_matrix(last_matrix, add_empty_nodes=False, color="orange", to_print=to_print)
+
+        return graph_view
+
+    def density(self) -> float:
+        n = self.graph_dim
+        non_zeros = np.nonzero(self.graph)
+        m = len(non_zeros[0])
+
+        return m / n / (n - 1)
+
+    def show(self, to_print=False):
+        if not self.graphs_to_drawing:
+            warnings.warn("Sequences are not stored. Graph view is empty.")
+            return
+
+        graph_view = self.create_graph_view(to_print=to_print)
+        graph_view.draw(title=None, to_print=to_print)
+
+    def save_fig(self, title: (str, str), output_dir: str = None, output_file: str = None, to_print=True):
+        if not self.graphs_to_drawing:
+            warnings.warn("Sequences are not stored. Graph view is empty.")
+
+        graph_view = self.create_graph_view(to_print=to_print)
+        graph_view.draw(show=False, output_dir=output_dir, output_file=output_file, title=title, to_print=to_print)
+
+    def save_matrix(self, output_dir: str = None, output_file: str = None):
+        if not self.graphs_to_drawing:
+            warnings.warn("Sequences are not stored. Matrix is empty.")
+
+        if output_file is not None and output_dir is not None:
+            create_dir(output_dir)
+            file = open(os.path.join(output_dir, output_file), "w")
+            file.write(tabulate(self.graph, tablefmt="latex", floatfmt=".0f"))
+            file.close()
+
+    def translate_sequence(self, sequence: np.ndarray):
+        return self.sequence_translator.translate_sequence(sequence, add_to_dictionary=False)[0]
+
+    def decode_sequence(self, sequence: np.ndarray):
+        return self.sequence_translator.decode_sentence(sequence)
+
+    def check_context_correctness(self, context: np.ndarray):
+        pass
+
+    def sequence_from_placeholders(self, sequence: list[str]) -> np.ndarray:
+        return self.sequence_translator.sequence_from_placeholders(sequence)
+
+    def translate_context(self, context: np.ndarray):
+        return self.sequence_translator.translate_sequence(context, add_to_dictionary=False)[0]
+
+    def clear(self):
+        self.graph = self.crate_graph()
+        self.sequences = []
+        self.sequence_translator = SequenceTranslator(sequence_matrix_dim=self.graph_dim, dtype=self.dtype)
+        self.graph_matrices = []
+
+    def draw_density(self, title=None, x_label=None, y_label=None, circle_size: int = 2):
+        dim = self.graph_dim
+
+        graph_1d = self.graph.reshape(dim * dim)
+
+        non_zeros = np.nonzero(graph_1d)[0]
+        x = np.mod(non_zeros, dim)
+        y = np.floor_divide(non_zeros, dim)
+        non_zeros_values = graph_1d[non_zeros]
+
+        dataframe = pd.DataFrame({"x": x, "y": y, "z": non_zeros_values})
+
+        palette = sns.color_palette("dark:#5A9_r", as_cmap=True)
+        joint_grid = sns.JointGrid(data=dataframe, x="x", y="y", hue="z", palette=palette)
+        joint_grid.plot_joint(sns.scatterplot, s=circle_size)
+        joint_grid.plot_marginals(sns.histplot, kde=False, bins=100)
+        joint_grid.ax_joint.legend().remove()
+
+        if title is not None:
+            joint_grid.fig.suptitle("ssakg - local density")
+
+        if x_label is not None:
+            joint_grid.ax_joint.set_xlabel(x_label)
+        else:
+            joint_grid.ax_joint.set_xlabel("")
+
+        if y_label is not None:
+            joint_grid.ax_joint.set_ylabel(y_label)
+        else:
+            joint_grid.ax_joint.set_ylabel("")
+
+        joint_grid.fig.tight_layout()
+
+        plot.show()