├── .github └── workflows │ └── deploy.yml ├── .gitignore ├── CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── README.md ├── environment.yml ├── network_machine_learning_in_python ├── Images │ ├── anascombe.jpeg │ ├── jupyter.jpg │ ├── jupyter.png │ ├── jupyter_grasp.png │ ├── mase1.jpeg │ ├── mcc_3.jpeg │ ├── network_models.jpg │ ├── two-truths.jpeg │ ├── two_truths_fig_1.jpg │ ├── umap_pedigo_small.jpg │ └── vnsgm.png ├── _config.yml ├── _toc.yml ├── appendix │ ├── ch11 │ │ ├── alt-reps.ipynb │ │ └── ch11.ipynb │ ├── ch12 │ │ ├── background.ipynb │ │ ├── ch12.ipynb │ │ ├── ers.ipynb │ │ ├── foundation.ipynb │ │ ├── rdpgs.ipynb │ │ └── sbms.ipynb │ ├── ch13 │ │ ├── ase.ipynb │ │ ├── ch13.ipynb │ │ ├── lse.ipynb │ │ ├── mle-theory.ipynb │ │ └── spectral-theory.ipynb │ └── ch14 │ │ ├── bayes.ipynb │ │ ├── ch14.ipynb │ │ ├── hypothesis.ipynb │ │ └── unsupervised.ipynb ├── applications │ ├── ch7 │ │ ├── Images │ │ │ ├── applications.ai │ │ │ └── applications.png │ │ ├── ch7.ipynb │ │ ├── community-detection.ipynb │ │ ├── model-selection.ipynb │ │ ├── out-of-sample.ipynb │ │ ├── testing-differences.ipynb │ │ └── vertex-nomination.ipynb │ ├── ch8 │ │ ├── ch8.ipynb │ │ ├── gm_1.png │ │ ├── gm_2.png │ │ ├── gm_3.png │ │ ├── grad_desc.png │ │ ├── graph-matching-vertex.ipynb │ │ ├── multiple-vertex-nomination.ipynb │ │ ├── significant-communities.ipynb │ │ └── two-sample-hypothesis.ipynb │ └── ch9 │ │ ├── anomaly-detection.ipynb │ │ ├── ch9.ipynb │ │ ├── significant-edges.ipynb │ │ └── significant-vertices.ipynb ├── coverpage.md ├── foundations │ ├── ch1 │ │ ├── Images │ │ │ ├── apply.ai │ │ │ ├── apply.png │ │ │ ├── ase_ex.ai │ │ │ ├── ase_ex.png │ │ │ ├── causal_dag.ai │ │ │ ├── causal_dag.png │ │ │ ├── cboy.ai │ │ │ ├── cboy.png │ │ │ ├── crossnetattr_ex.ai │ │ │ ├── crossnetattr_ex.png │ │ │ ├── edgeattr_ex.ai │ │ │ ├── edgeattr_ex.png │ │ │ ├── errorful_obs.ai │ │ │ ├── errorful_obs.png │ │ │ ├── many_networks.ai │ │ │ ├── many_networks.png │ │ │ ├── ml_ex.ai │ │ │ ├── ml_ex.png │ │ │ ├── netattr_ex.ai │ │ │ ├── netattr_ex.png │ │ │ ├── nml-high-level.ai │ │ │ ├── nml-high-level.png │ │ │ ├── nodeattr_ex.ai │ │ │ ├── nodeattr_ex.png │ │ │ ├── nodes.ai │ │ │ ├── nodes.png │ │ │ ├── nonattr_ex.ai │ │ │ ├── nonattr_ex.png │ │ │ ├── pca_ex.ai │ │ │ └── pca_ex.png │ │ ├── ch1.ipynb │ │ ├── challenges-of-nml.ipynb │ │ ├── examples-of-applications.ipynb │ │ ├── types-nml-problems.ipynb │ │ ├── what-is-a-network.ipynb │ │ └── why-study-networks.ipynb │ ├── ch2 │ │ ├── Images │ │ │ ├── bold.jpg │ │ │ ├── fmri_bold.ai │ │ │ ├── fmri_bold.png │ │ │ └── lobes.png │ │ ├── big-picture.ipynb │ │ ├── ch2.ipynb │ │ ├── datasets │ │ │ └── dice.py │ │ ├── discover-and-visualize.ipynb │ │ ├── fine-tune.ipynb │ │ ├── get-the-data.ipynb │ │ ├── prepare-the-data.ipynb │ │ └── select-and-train.ipynb │ └── ch3 │ │ ├── big-picture.ipynb │ │ ├── ch3.ipynb │ │ ├── discover-and-visualize.ipynb │ │ ├── get-the-data.ipynb │ │ └── prepare-the-data.ipynb ├── introduction │ ├── Images │ │ ├── this_book.ai │ │ └── this_book.png │ ├── preface.ipynb │ └── terminology.ipynb ├── logo.png ├── next │ └── ch10 │ │ ├── Images │ │ ├── epoch_compute.ai │ │ ├── epoch_compute.png │ │ ├── forward_pass.ai │ │ ├── forward_pass.png │ │ ├── full_process.ai │ │ ├── full_process.png │ │ ├── gnn.ai │ │ ├── gnn.png │ │ ├── graphstats_fig.ai │ │ ├── molecule_repr.png │ │ ├── nn_epoch.ai │ │ ├── nn_epoch.png │ │ ├── water_molecule.ai │ │ └── water_molecule.png │ │ ├── ch10.ipynb │ │ ├── gnn.ipynb │ │ ├── random-walk-diffusion-methods.ipynb │ │ └── sparsity.ipynb ├── references.bib └── representations │ ├── ch4 │ ├── ch4.ipynb │ ├── img │ │ ├── network_reps.ai │ │ ├── network_reps.png │ │ └── newyork.png │ ├── matrix-representations.ipynb │ ├── network-representations.ipynb │ ├── properties-of-networks.ipynb │ └── regularization.ipynb │ ├── ch5 │ ├── Images │ │ ├── network_modelling.ai │ │ ├── network_modelling.png │ │ ├── unify.ai │ │ ├── unify_sn.ai │ │ └── 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