Docs v2

docs/HAT.rst

@@ -12,42 +12,42 @@ Hypergraph Class
    :undoc-members:
    :show-inheritance:
 
-Graph Interface
----------------------
+Tensor Representations
+----------------------
 
-.. automodule:: HAT.graph
+.. automodule:: HAT.tensors
    :members:
    :undoc-members:
    :show-inheritance:
 
-Hypergraph Metrics
----------------------
+Laplacians
+----------------------
 
-.. automodule:: HAT.metrics
+.. automodule:: HAT.laplacian
    :members:
    :undoc-members:
    :show-inheritance:
 
-Dynamics and Control
+Graph Interface
 ---------------------
 
-.. automodule:: HAT.dynamics
+.. automodule:: HAT.graph
    :members:
    :undoc-members:
    :show-inheritance:
 
-Tensor Representations
-----------------------
+Hypergraph Metrics
+---------------------
 
-.. automodule:: HAT.tensors
+.. automodule:: HAT.metrics
    :members:
    :undoc-members:
    :show-inheritance:
 
-Laplacians
-----------------------
+Dynamics and Control
+---------------------
 
-.. automodule:: HAT.laplacian
+.. automodule:: HAT.dynamics
    :members:
    :undoc-members:
    :show-inheritance:
@@ -60,7 +60,6 @@ HAT.HAT module
    :undoc-members:
    :show-inheritance:
 
-
 HAT.draw module
 ---------------
 

docs/index.rst

@@ -9,33 +9,52 @@ Hypergraph Analysis Toolbox
 .. image:: _static/index_dyadic_decomp.png
     :align: center
 
-Introduction
-============
-Hypergraph Analysis Toolbox (HAT) is a software suite for the analysis and visualization of hypergraphs and
-higher order structures. Motivated to investigate Pore-C data, HAT is intended as a general prupose, versatile
-software for hypergraph construction, visualization, and analysis. HAT addresses the following hypergraph
-problems:
+Hypergraph Analysis Toolbox (HAT) is a software for the analysis and visualization of hypergraphs and
+higher-order structures. HAT implements tensor-based methods for the analysis of higher-order observability/controllability,
+coupling, similarity measures, and other structural properties. HAT contains methods for the following hypergraph tasks:
 
 1. Construction
 2. Visualization
 3. Expansion and numeric representation
-4. Structral Properties
-5. Controllability
+4. Structural Properties
+5. Observability/Controllability
 6. Similarity Measures
 
-The capabilities and use cases of HAT are outlined in `this notice <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011190>`_. 
+This software was designed to analyze higher-order biological data, such as chromatin structures observed with Pore-C. The capabilities and use cases of HAT are outlined in `this PLOS Computational Biology article <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011190>`_. 
 
-Contributors
-************
+Contributors and Related Papers
+*******************************
 Joshua Pickard, Can Chen, Rahmy Salman, Cooper Stansbury, Sion Kim, Amit Surana, Anthony Bloch, and Indika Rajapakse
 
+**Software Paper**
+
+8. Joshua Pickard, Can Chen, Rahmy Salman, Cooper Stansbury, Sion Kim, Amit Surana, Anthony Bloch, and Indika Rajapakse. "HAT: Hypergraph analysis toolbox." PLOS Computational Biology 19, no. 6 (2023): e1011190.
+
+**Methods Papers**
+
+7. Joshua Pickard, Anthony M. Bloch, and Indika Rajapakse. "Scalable Hypergraphs Algorithms for Observability of Gene Regulation." In 2025 23rd European Control Conference (ECC) `[PDF] <https://drive.google.com/file/d/1WWkUyEWZEstOhsKrHBNEU680IBE8Kn0K/view?usp=sharing>`_
+
+6. Joshua Pickard, Can Chen, Cooper Stansbury, Amit Surana, Anthony M. Bloch, and Indika Rajapakse. "Kronecker product of tensors and hypergraphs: structure and dynamics." SIAM Journal on Matrix Analysis and Applications 45, no. 3 (2024): 1621-1642. `[PDF] <https://drive.google.com/file/d/1Nr3o1rr1O-32e-Qsl1RRNNUcLGoRkdJ9/view>`_
+
+5. Joshua Pickard, Cooper Stansbury, Amit Surana, Indika Rajapakse, and Anthony Bloch. "Geometric aspects of observability of hypergraphs." IFAC-PapersOnLine 58, no. 6 (2024): 321-326. `[PDF] <https://drive.google.com/file/d/1-5AL_rOvAm-aUClSfyy9MpED7h7_L76o/view>`_
+
+4. Joshua Pickard, Amit Surana, Anthony Bloch, and Indika Rajapakse. "Observability of hypergraphs." In 2023 62nd IEEE Conference on Decision and Control (CDC), pp. 2445-2451. IEEE, 2023. `[PDF] <https://drive.google.com/file/d/1FQxRj5VdPkY-P64ek7rq4lp9jQW9MLFP/view>`_
+
+3. Amit Surana, Can Chen, and Indika Rajapakse. "Hypergraph similarity measures." IEEE Transactions on Network Science and Engineering 10, no. 2 (2022): 658-674. `[PDF] <https://drive.google.com/file/d/1Dc4nSkkZyk4axOAshdRDXo8Gx24h4M-d/view>`_
+
+2. Can Chen, Amit Surana, Anthony M. Bloch, and Indika Rajapakse. "Controllability of hypergraphs." IEEE Transactions on Network Science and Engineering 8, no. 2 (2021): 1646-1657. `[PDF] <https://drive.google.com/file/d/12aReE7mE4MVbycZUxUYdtICgrAYlzg8o/view>`_
+
+1. Can Chen, and Indika Rajapakse. "Tensor entropy for uniform hypergraphs." IEEE Transactions on Network Science and Engineering 7, no. 4 (2020): 2889-2900. `[PDF] <https://drive.google.com/file/d/1-d4uR5KT3iDpOd69aCQVjNZzMyILXp5E/view>`_
+
+
+
 Bug Reporting
 -------------
 Please report all bugs or defects in HAT to `this page <https://github.com/Jpickard1/Hypergraph-Analysis-Toolbox/issues>`_.
 
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Contents:
 
    install.rst