multipers 2.2.3__cp311-cp311-win_amd64.whl → 2.3.0__cp311-cp311-win_amd64.whl

multipers/data/graphs.py

@@ -1,466 +1,466 @@
-import numpy as np
-from os.path import expanduser, exists
-import networkx as nx
-from warnings import warn
-import pickle
-from joblib import Parallel, delayed
-from tqdm import tqdm
-from sklearn.preprocessing import LabelEncoder
-from scipy.spatial import distance_matrix
-from sklearn.base import BaseEstimator, TransformerMixin, clone
-import multipers as mp
-from typing import Iterable, List, Optional
-from numpy.typing import ArrayLike
-
-DATASET_PATH = expanduser("~/Datasets/")
-
-
-def _check_installed(dataset: str):
-    from warnings import warn
-    from os.path import exists
-
-    assert dataset.startswith(
-        "graphs/"
-    ), "Graph datasets have to be of the form graphs/<name>"
-    if exists(DATASET_PATH + dataset):
-        return
-    else:
-        warn(
-            f"""
-Dataset {dataset} not installed.
-You can find it in https://networkrepository.com
-Then (optinally) configure multipers.data.graphs.DATASET_PATH, which is currently
-> {DATASET_PATH=}
-and puts this dataset in $DATASET_PATH/{dataset}
-"""
-        )
-        raise ValueError("Unknown dataset.")
-
-
-def get(dataset: str, filtration: Optional[str] = None):
-    if filtration is None:
-        return get_graphs(dataset)
-    graphs, labels = get_graphs(dataset)
-    try:
-        for g in graphs:
-            for node in g.nodes:
-                g.nodes[node][filtration]
-    except:
-        print(
-            f"Filtration {filtration} not computed, trying to compute it ...",
-            flush=True,
-        )
-        compute_filtration(dataset, filtration)
-    return get_graphs(dataset)
-
-
-def get_from_file_old(dataset: str, label="lb"):
-    from os import walk
-    from scipy.io import loadmat
-    from warnings import warn
-
-    path = DATASET_PATH + dataset + "/mat/"
-    labels: list[int] = []
-    gs: list[nx.Graph] = []
-    for root, dir, files in walk(path):
-        for file in files:
-            file_ppties = file.split("_")
-            gid = file_ppties[5]
-            i = 0
-            while i + 1 < len(file_ppties) and file_ppties[i] != label:
-                i += 1
-            if i + 1 >= len(file_ppties):
-                warn(f"Cannot find label {label} on file {file}.")
-            else:
-                labels += [file_ppties[i + 1]]
-            adj_mat = np.array(loadmat(path + file)["A"], dtype=np.float32)
-            gs.append(nx.Graph(adj_mat))
-    return gs, labels
-
-
-def get_from_file(dataset: str):
-    from os.path import expanduser, exists
-
-    path = DATASET_PATH + f"{dataset}/{dataset[7:]}."
-    try:
-        graphs_ids = np.loadtxt(path + "graph_idx")
-    except:
-        return get_from_file_old(dataset=dataset)
-    labels: list[int] = LabelEncoder().fit_transform(np.loadtxt(path + "graph_labels"))
-    edges = np.loadtxt(path + "edges", delimiter=",", dtype=int) - 1
-    has_intrinsic_filtration = exists(path + "node_attrs")
-    graphs: list[nx.Graph] = []
-    if has_intrinsic_filtration:
-        F = np.loadtxt(path + "node_attrs", delimiter=",")
-    for graph_id in tqdm(np.unique(graphs_ids), desc="Reading graphs from file"):
-        (nodes,) = np.where(graphs_ids == graph_id)
-
-        def graph_has_edge(u: int, v: int) -> bool:
-            if u in nodes or v in nodes:
-                assert u in nodes and v in nodes, f"Nodes\
-                {u} and {v} are not in the same graph"
-                return True
-            return False
-
-        graph_edges = [(u, v) for u, v in edges if graph_has_edge(u, v)]
-        g = nx.Graph(graph_edges)
-        if has_intrinsic_filtration:
-            node_attrs = {node: F[node] for node in nodes}
-            nx.set_node_attributes(g, node_attrs, "intrinsic")
-        graphs.append(g)
-    return graphs, labels
-
-
-def get_graphs(dataset: str, N: int | str = "") -> tuple[list[nx.Graph], list[int]]:
-    _check_installed(dataset)
-    graphs_path = f"{DATASET_PATH}{dataset}/graphs{N}.pkl"
-    labels_path = f"{DATASET_PATH}{dataset}/labels{N}.pkl"
-    if not exists(graphs_path) or not exists(labels_path):
-        if dataset.startswith("3dshapes/"):
-            return get_from_file_old(
-                dataset,
-            )
-
-        graphs, labels = get_from_file(
-            dataset,
-        )
-        print("Saving graphs at :", graphs_path)
-        set_graphs(graphs=graphs, labels=labels, dataset=dataset)
-    else:
-        graphs = pickle.load(open(graphs_path, "rb"))
-        labels = pickle.load(open(labels_path, "rb"))
-    from sklearn.preprocessing import LabelEncoder
-
-    return graphs, LabelEncoder().fit_transform(labels)
-
-
-# saves graphs (and filtration values) into a file
-def set_graphs(graphs: list[nx.Graph], labels: list, dataset: str, N: int | str = ""):
-    graphs_path = f"{DATASET_PATH}{dataset}/graphs{N}.pkl"
-    labels_path = f"{DATASET_PATH}{dataset}/labels{N}.pkl"
-    pickle.dump(graphs, open(graphs_path, "wb"))
-    pickle.dump(labels, open(labels_path, "wb"))
-    return
-
-
-def reset_graphs(dataset: str, N=None):  # Resets filtrations values on graphs
-    graphs, labels = get_from_file(dataset)
-    set_graphs(graphs, labels, dataset)
-    return
-
-
-def compute_ricci(graphs: list[nx.Graph], alpha=0.5, progress=1):
-    from GraphRicciCurvature.OllivierRicci import OllivierRicci
-
-    def ricci(graph, alpha=alpha):
-        return OllivierRicci(graph, alpha=alpha).compute_ricci_curvature()
-
-    graphs = [
-        ricci(g) for g in tqdm(graphs, disable=not progress, desc="Computing ricci")
-    ]
-
-    def push_back_node(graph):
-        # for node in graph.nodes:
-        # graph.nodes[node]['ricciCurvature'] = np.min([graph[node][node2]['ricciCurvature'] for node2 in graph[node]] + [graph.nodes[node]['ricciCurvature']])
-        node_filtrations = {
-            node: -1
-            if len(graph[node]) == 0
-            else np.min([graph[node][node2]["ricciCurvature"] for node2 in graph[node]])
-            for node in graph.nodes
-        }
-        nx.set_node_attributes(graph, node_filtrations, "ricciCurvature")
-        return graph
-
-    graphs = [push_back_node(g) for g in graphs]
-    return graphs
-
-
-def compute_cc(graphs: list[nx.Graph], progress=1):
-    def _cc(g):
-        cc = nx.closeness_centrality(g)
-        nx.set_node_attributes(g, cc, "cc")
-        edges_cc = {(u, v): max(cc[u], cc[v]) for u, v in g.edges}
-        nx.set_edge_attributes(g, edges_cc, "cc")
-        return g
-
-    graphs = Parallel(n_jobs=1, prefer="threads")(
-        delayed(_cc)(g) for g in tqdm(graphs, disable=not progress, desc="Computing cc")
-    )
-    return graphs
-    # for g in tqdm(graphs, desc="Computing cc"):
-    # 	_cc(g)
-    # return graphs
-
-
-def compute_degree(graphs: list[nx.Graph], progress=1):
-    def _degree(g):
-        degrees = {i: 1.1 if degree == 0 else 1 / degree for i, degree in g.degree}
-        nx.set_node_attributes(g, degrees, "degree")
-        edges_dg = {(u, v): max(degrees[u], degrees[v]) for u, v in g.edges}
-        nx.set_edge_attributes(g, edges_dg, "degree")
-        return g
-
-    graphs = Parallel(n_jobs=1, prefer="threads")(
-        delayed(_degree)(g)
-        for g in tqdm(graphs, disable=not progress, desc="Computing degree")
-    )
-    return graphs
-    # for g in tqdm(graphs, desc="Computing degree"):
-    # 	_degree(g)
-    # return graphs
-
-
-# TODO : make it compatible with non-connexe graphs
-def compute_fiedler(graphs: list[nx.Graph], progress=1):
-    def _fiedler(g):
-        connected_graphs = [
-            nx.subgraph(g, nodes) for nodes in nx.connected_components(g)
-        ]
-        fiedler_vectors = [
-            nx.fiedler_vector(g) ** 2
-            if g.number_of_nodes() > 2
-            else np.zeros(
-                g.number_of_nodes(
-                    # order of nx.fiedler_vector correspond to nx.laplacian -> g.nodes
-                )
-            )
-            for g in connected_graphs
-        ]
-        fiedler_dict = {
-            node: fiedler_vector[node_index]
-            for g, fiedler_vector in zip(connected_graphs, fiedler_vectors)
-            for node_index, node in enumerate(list(g.nodes))
-        }
-        nx.set_node_attributes(g, fiedler_dict, "fiedler")
-        edges_fiedler = {
-            (u, v): max(fiedler_dict[u], fiedler_dict[v]) for u, v in g.edges
-        }
-        nx.set_edge_attributes(g, edges_fiedler, "fiedler")
-        return g
-
-    graphs = Parallel(n_jobs=1, prefer="threads")(
-        delayed(_fiedler)(g)
-        for g in tqdm(graphs, disable=not progress, desc="Computing fiedler")
-    )
-    return graphs
-    # for g in tqdm(graphs, desc="Computing fiedler"):
-    # 	_fiedler(g)
-    # return graphs
-
-
-def compute_hks(graphs: list[nx.Graph], t: float, progress=1):
-    def _hks(g: nx.Graph):
-        w, vps = np.linalg.eig(
-            nx.laplacianmatrix.normalized_laplacian_matrix(
-                g, nodelist=g.nodes()
-            ).toarray()
-        )  # order is given by g.nodes order
-        w = w.view(dtype=float)
-        vps = vps.view(dtype=float)
-        node_hks = {
-            node: np.sum(np.exp(-t * w) * np.square(vps[node_index, :]))
-            for node_index, node in enumerate(g.nodes)
-        }
-        nx.set_node_attributes(g, node_hks, f"hks_{t}")
-        edges_hks = {(u, v): max(node_hks[u], node_hks[v]) for u, v in g.edges}
-        nx.set_edge_attributes(g, edges_hks, f"hks_{t}")
-        return g
-
-    graphs = Parallel(n_jobs=1, prefer="threads")(
-        delayed(_hks)(g)
-        for g in tqdm(graphs, disable=not progress, desc=f"Computing hks_{t}")
-    )
-    return graphs
-
-
-def compute_geodesic(graphs: list[nx.Graph], progress=1):
-    def _f(g: nx.Graph):
-        try:
-            nodes_intrinsic = {i: n["intrinsic"] for i, n in g.nodes.data()}
-        except:
-            warn(
-                "This graph doesn't have an intrinsic filtration, will use 0 instead ..."
-            )
-            nodes_intrinsic = {i: 0 for i, n in g.nodes.data()}
-            # return g
-        node_geodesic = {i: 0 for i in g.nodes}
-        nx.set_node_attributes(g, node_geodesic, f"geodesic")
-        edges_geodesic = {
-            (u, v): np.linalg.norm(nodes_intrinsic[u] - nodes_intrinsic[v])
-            for u, v in g.edges
-        }
-        nx.set_edge_attributes(g, edges_geodesic, f"geodesic")
-        return g
-
-    graphs = Parallel(n_jobs=1, prefer="threads")(
-        delayed(_f)(g)
-        for g in tqdm(
-            graphs, disable=not progress, desc=f"Computing geodesic distances on graphs"
-        )
-    )
-    return graphs
-
-
-def compute_intrinsic(graphs: list[nx.Graph], progress=1, nowarning=False):
-    def _f(g: nx.Graph):
-        try:
-            nodes_intrinsic = {i: n["intrinsic"] for i, n in g.nodes.data()}
-        except:
-            if not nowarning:
-                raise ValueError("This graph doesn't have an intrinsic filtration.")
-            else:
-                return g
-        edges_intrinsic = {
-            (u, v): np.max([nodes_intrinsic[u], nodes_intrinsic[v]], axis=0)
-            for u, v in g.edges
-        }
-        nx.set_edge_attributes(g, edges_intrinsic, "intrinsic")
-        return g
-
-    graphs = Parallel(n_jobs=1, prefer="threads")(
-        delayed(_f)(g)
-        for g in tqdm(
-            graphs, disable=not progress, desc="Computing geodesic distances on graphs"
-        )
-    )
-    return graphs
-
-
-def compute_filtration(dataset: str, filtration: str = "ALL", **kwargs):
-    if filtration == "ALL":
-        reset_graphs(dataset)  # not necessary
-        graphs, labels = get_graphs(dataset, **kwargs)
-        graphs = compute_intrinsic(graphs, nowarning=True)
-        graphs = compute_geodesic(graphs)
-        graphs = compute_cc(graphs)
-        graphs = compute_degree(graphs)
-        graphs = compute_ricci(graphs)
-        graphs = compute_fiedler(graphs)
-        graphs = compute_hks(graphs, 10)
-        set_graphs(graphs=graphs, labels=labels, dataset=dataset)
-        return
-    graphs, labels = get_graphs(dataset, **kwargs)
-    if filtration == "dijkstra":
-        return
-    elif filtration == "cc":
-        graphs = compute_cc(graphs)
-    elif filtration == "degree":
-        graphs = compute_degree(graphs)
-    elif filtration == "ricciCurvature":
-        graphs = compute_ricci(graphs)
-    elif filtration == "fiedler":
-        graphs = compute_fiedler(graphs)
-    elif filtration == "geodesic":
-        graphs = compute_geodesic(graphs)
-    elif filtration.startswith("hks_"):
-        # don't want do deal with floats, makes dots in title...
-        t = int(filtration[4:])
-        graphs = compute_hks(graphs=graphs, t=t)
-    else:
-        warn(f"Filtration {filtration} not implemented !")
-        return
-    set_graphs(graphs=graphs, labels=labels, dataset=dataset)
-    return
-
-
-class Graph2SimplexTrees(BaseEstimator, TransformerMixin):
-    """
-    Transforms a list of networkx graphs into a list of simplextree multi
-
-    Usual Filtrations
-    -----------------
-    - "cc" closeness centrality
-    - "geodesic" if the graph provides data to compute it, e.g., BZR, COX2, PROTEINS
-    - "degree"
-    - "ricciCurvature" the ricci curvature
-    - "fiedler" the square of the fiedler vector
-    """
-
-    def __init__(
-        self,
-        filtrations=[],
-        delayed=False,
-        num_collapses=100,
-        progress: bool = False,
-    ):
-        super().__init__()
-        self.filtrations = filtrations  # filtration to search in graph
-        self.delayed = delayed  # reverses the filtration #TODO
-        self.num_collapses = num_collapses
-        self.progress = progress
-        self.num_parameters: int = len(filtrations)
-
-    def fit(self, X, y=None):
-        if len(X) == 0:
-            return self
-        self.num_parameters = len(self.filtrations)
-        if "intrinsic" in self.filtrations:
-            intrinsic_size = len(X[0].nodes[0]["intrinsic"])
-            self.num_parameters += intrinsic_size - 1
-        return self
-
-    def transform(self, X: list[nx.Graph]):
-        def todo(graph, filtrations=self.filtrations) -> list[mp.SimplexTreeMulti]:
-            st = mp.SimplexTreeMulti(num_parameters=self.num_parameters)
-            nodes = np.asarray(graph.nodes, dtype=int).reshape(1, -1)
-            nodes_filtrations = np.asarray(
-                [
-                    [
-                        filtration
-                        for filtration_ in filtrations
-                        for filtration in np.asarray(
-                            graph.nodes[node][filtration_]
-                        ).reshape(-1)
-                        # this reshape is for attributes that are vectors
-                    ]
-                    for node in graph.nodes
-                ],
-                dtype=np.float32,
-            )
-            st.insert_batch(nodes, nodes_filtrations)
-            edges = np.asarray(graph.edges, dtype=int).T
-            edges_filtrations = np.asarray(
-                [
-                    [
-                        filtration
-                        for filtration_ in filtrations
-                        for filtration in np.asarray(graph[u][v][filtration_]).reshape(
-                            -1
-                        )
-                        # this reshape is for attributes that are vectors
-                    ]
-                    for u, v in graph.edges
-                ],
-                dtype=np.float32,
-            )
-            st.insert_batch(edges, edges_filtrations)
-            if st.num_parameters == 2:
-                # TODO : wait for a filtration domination update
-                st.collapse_edges(num=self.num_collapses)
-            # st.make_filtration_non_decreasing() ## Ricci is not safe ...
-            # same output for each pipelines, some have a supplementary axis.
-            return [st]
-
-        return (
-            [delayed(todo)(graph) for graph in X]
-            if self.delayed
-            # memory bound imo
-            else [
-                todo(graph=graph)
-                for graph in tqdm(
-                    X,
-                    desc="Computing simplextrees from graphs",
-                    disable=not self.progress,
-                )
-            ]
-            #                     #         ,
-            #     )
-            # else Parallel(n_jobs=-1, prefer="threads")(
-            #     delayed(todo)(graph)
-            #     for graph in tqdm(
-            #         X,
-            #         desc="Computing simplextrees from graphs",
-            #         disable=not self.progress,
-            #     )
-            # )
-        )
+import numpy as np
+from os.path import expanduser, exists
+import networkx as nx
+from warnings import warn
+import pickle
+from joblib import Parallel, delayed
+from tqdm import tqdm
+from sklearn.preprocessing import LabelEncoder
+from scipy.spatial import distance_matrix
+from sklearn.base import BaseEstimator, TransformerMixin, clone
+import multipers as mp
+from typing import Iterable, List, Optional
+from numpy.typing import ArrayLike
+
+DATASET_PATH = expanduser("~/Datasets/")
+
+
+def _check_installed(dataset: str):
+    from warnings import warn
+    from os.path import exists
+
+    assert dataset.startswith(
+        "graphs/"
+    ), "Graph datasets have to be of the form graphs/<name>"
+    if exists(DATASET_PATH + dataset):
+        return
+    else:
+        warn(
+            f"""
+Dataset {dataset} not installed.
+You can find it in https://networkrepository.com
+Then (optinally) configure multipers.data.graphs.DATASET_PATH, which is currently
+> {DATASET_PATH=}
+and puts this dataset in $DATASET_PATH/{dataset}
+"""
+        )
+        raise ValueError("Unknown dataset.")
+
+
+def get(dataset: str, filtration: Optional[str] = None):
+    if filtration is None:
+        return get_graphs(dataset)
+    graphs, labels = get_graphs(dataset)
+    try:
+        for g in graphs:
+            for node in g.nodes:
+                g.nodes[node][filtration]
+    except:
+        print(
+            f"Filtration {filtration} not computed, trying to compute it ...",
+            flush=True,
+        )
+        compute_filtration(dataset, filtration)
+    return get_graphs(dataset)
+
+
+def get_from_file_old(dataset: str, label="lb"):
+    from os import walk
+    from scipy.io import loadmat
+    from warnings import warn
+
+    path = DATASET_PATH + dataset + "/mat/"
+    labels: list[int] = []
+    gs: list[nx.Graph] = []
+    for root, dir, files in walk(path):
+        for file in files:
+            file_ppties = file.split("_")
+            gid = file_ppties[5]
+            i = 0
+            while i + 1 < len(file_ppties) and file_ppties[i] != label:
+                i += 1
+            if i + 1 >= len(file_ppties):
+                warn(f"Cannot find label {label} on file {file}.")
+            else:
+                labels += [file_ppties[i + 1]]
+            adj_mat = np.array(loadmat(path + file)["A"], dtype=np.float32)
+            gs.append(nx.Graph(adj_mat))
+    return gs, labels
+
+
+def get_from_file(dataset: str):
+    from os.path import expanduser, exists
+
+    path = DATASET_PATH + f"{dataset}/{dataset[7:]}."
+    try:
+        graphs_ids = np.loadtxt(path + "graph_idx")
+    except:
+        return get_from_file_old(dataset=dataset)
+    labels: list[int] = LabelEncoder().fit_transform(np.loadtxt(path + "graph_labels"))
+    edges = np.loadtxt(path + "edges", delimiter=",", dtype=int) - 1
+    has_intrinsic_filtration = exists(path + "node_attrs")
+    graphs: list[nx.Graph] = []
+    if has_intrinsic_filtration:
+        F = np.loadtxt(path + "node_attrs", delimiter=",")
+    for graph_id in tqdm(np.unique(graphs_ids), desc="Reading graphs from file"):
+        (nodes,) = np.where(graphs_ids == graph_id)
+
+        def graph_has_edge(u: int, v: int) -> bool:
+            if u in nodes or v in nodes:
+                assert u in nodes and v in nodes, f"Nodes\
+                {u} and {v} are not in the same graph"
+                return True
+            return False
+
+        graph_edges = [(u, v) for u, v in edges if graph_has_edge(u, v)]
+        g = nx.Graph(graph_edges)
+        if has_intrinsic_filtration:
+            node_attrs = {node: F[node] for node in nodes}
+            nx.set_node_attributes(g, node_attrs, "intrinsic")
+        graphs.append(g)
+    return graphs, labels
+
+
+def get_graphs(dataset: str, N: int | str = "") -> tuple[list[nx.Graph], list[int]]:
+    _check_installed(dataset)
+    graphs_path = f"{DATASET_PATH}{dataset}/graphs{N}.pkl"
+    labels_path = f"{DATASET_PATH}{dataset}/labels{N}.pkl"
+    if not exists(graphs_path) or not exists(labels_path):
+        if dataset.startswith("3dshapes/"):
+            return get_from_file_old(
+                dataset,
+            )
+
+        graphs, labels = get_from_file(
+            dataset,
+        )
+        print("Saving graphs at :", graphs_path)
+        set_graphs(graphs=graphs, labels=labels, dataset=dataset)
+    else:
+        graphs = pickle.load(open(graphs_path, "rb"))
+        labels = pickle.load(open(labels_path, "rb"))
+    from sklearn.preprocessing import LabelEncoder
+
+    return graphs, LabelEncoder().fit_transform(labels)
+
+
+# saves graphs (and filtration values) into a file
+def set_graphs(graphs: list[nx.Graph], labels: list, dataset: str, N: int | str = ""):
+    graphs_path = f"{DATASET_PATH}{dataset}/graphs{N}.pkl"
+    labels_path = f"{DATASET_PATH}{dataset}/labels{N}.pkl"
+    pickle.dump(graphs, open(graphs_path, "wb"))
+    pickle.dump(labels, open(labels_path, "wb"))
+    return
+
+
+def reset_graphs(dataset: str, N=None):  # Resets filtrations values on graphs
+    graphs, labels = get_from_file(dataset)
+    set_graphs(graphs, labels, dataset)
+    return
+
+
+def compute_ricci(graphs: list[nx.Graph], alpha=0.5, progress=1):
+    from GraphRicciCurvature.OllivierRicci import OllivierRicci
+
+    def ricci(graph, alpha=alpha):
+        return OllivierRicci(graph, alpha=alpha).compute_ricci_curvature()
+
+    graphs = [
+        ricci(g) for g in tqdm(graphs, disable=not progress, desc="Computing ricci")
+    ]
+
+    def push_back_node(graph):
+        # for node in graph.nodes:
+        # graph.nodes[node]['ricciCurvature'] = np.min([graph[node][node2]['ricciCurvature'] for node2 in graph[node]] + [graph.nodes[node]['ricciCurvature']])
+        node_filtrations = {
+            node: -1
+            if len(graph[node]) == 0
+            else np.min([graph[node][node2]["ricciCurvature"] for node2 in graph[node]])
+            for node in graph.nodes
+        }
+        nx.set_node_attributes(graph, node_filtrations, "ricciCurvature")
+        return graph
+
+    graphs = [push_back_node(g) for g in graphs]
+    return graphs
+
+
+def compute_cc(graphs: list[nx.Graph], progress=1):
+    def _cc(g):
+        cc = nx.closeness_centrality(g)
+        nx.set_node_attributes(g, cc, "cc")
+        edges_cc = {(u, v): max(cc[u], cc[v]) for u, v in g.edges}
+        nx.set_edge_attributes(g, edges_cc, "cc")
+        return g
+
+    graphs = Parallel(n_jobs=1, prefer="threads")(
+        delayed(_cc)(g) for g in tqdm(graphs, disable=not progress, desc="Computing cc")
+    )
+    return graphs
+    # for g in tqdm(graphs, desc="Computing cc"):
+    # 	_cc(g)
+    # return graphs
+
+
+def compute_degree(graphs: list[nx.Graph], progress=1):
+    def _degree(g):
+        degrees = {i: 1.1 if degree == 0 else 1 / degree for i, degree in g.degree}
+        nx.set_node_attributes(g, degrees, "degree")
+        edges_dg = {(u, v): max(degrees[u], degrees[v]) for u, v in g.edges}
+        nx.set_edge_attributes(g, edges_dg, "degree")
+        return g
+
+    graphs = Parallel(n_jobs=1, prefer="threads")(
+        delayed(_degree)(g)
+        for g in tqdm(graphs, disable=not progress, desc="Computing degree")
+    )
+    return graphs
+    # for g in tqdm(graphs, desc="Computing degree"):
+    # 	_degree(g)
+    # return graphs
+
+
+# TODO : make it compatible with non-connexe graphs
+def compute_fiedler(graphs: list[nx.Graph], progress=1):
+    def _fiedler(g):
+        connected_graphs = [
+            nx.subgraph(g, nodes) for nodes in nx.connected_components(g)
+        ]
+        fiedler_vectors = [
+            nx.fiedler_vector(g) ** 2
+            if g.number_of_nodes() > 2
+            else np.zeros(
+                g.number_of_nodes(
+                    # order of nx.fiedler_vector correspond to nx.laplacian -> g.nodes
+                )
+            )
+            for g in connected_graphs
+        ]
+        fiedler_dict = {
+            node: fiedler_vector[node_index]
+            for g, fiedler_vector in zip(connected_graphs, fiedler_vectors)
+            for node_index, node in enumerate(list(g.nodes))
+        }
+        nx.set_node_attributes(g, fiedler_dict, "fiedler")
+        edges_fiedler = {
+            (u, v): max(fiedler_dict[u], fiedler_dict[v]) for u, v in g.edges
+        }
+        nx.set_edge_attributes(g, edges_fiedler, "fiedler")
+        return g
+
+    graphs = Parallel(n_jobs=1, prefer="threads")(
+        delayed(_fiedler)(g)
+        for g in tqdm(graphs, disable=not progress, desc="Computing fiedler")
+    )
+    return graphs
+    # for g in tqdm(graphs, desc="Computing fiedler"):
+    # 	_fiedler(g)
+    # return graphs
+
+
+def compute_hks(graphs: list[nx.Graph], t: float, progress=1):
+    def _hks(g: nx.Graph):
+        w, vps = np.linalg.eig(
+            nx.laplacianmatrix.normalized_laplacian_matrix(
+                g, nodelist=g.nodes()
+            ).toarray()
+        )  # order is given by g.nodes order
+        w = w.view(dtype=float)
+        vps = vps.view(dtype=float)
+        node_hks = {
+            node: np.sum(np.exp(-t * w) * np.square(vps[node_index, :]))
+            for node_index, node in enumerate(g.nodes)
+        }
+        nx.set_node_attributes(g, node_hks, f"hks_{t}")
+        edges_hks = {(u, v): max(node_hks[u], node_hks[v]) for u, v in g.edges}
+        nx.set_edge_attributes(g, edges_hks, f"hks_{t}")
+        return g
+
+    graphs = Parallel(n_jobs=1, prefer="threads")(
+        delayed(_hks)(g)
+        for g in tqdm(graphs, disable=not progress, desc=f"Computing hks_{t}")
+    )
+    return graphs
+
+
+def compute_geodesic(graphs: list[nx.Graph], progress=1):
+    def _f(g: nx.Graph):
+        try:
+            nodes_intrinsic = {i: n["intrinsic"] for i, n in g.nodes.data()}
+        except:
+            warn(
+                "This graph doesn't have an intrinsic filtration, will use 0 instead ..."
+            )
+            nodes_intrinsic = {i: 0 for i, n in g.nodes.data()}
+            # return g
+        node_geodesic = {i: 0 for i in g.nodes}
+        nx.set_node_attributes(g, node_geodesic, f"geodesic")
+        edges_geodesic = {
+            (u, v): np.linalg.norm(nodes_intrinsic[u] - nodes_intrinsic[v])
+            for u, v in g.edges
+        }
+        nx.set_edge_attributes(g, edges_geodesic, f"geodesic")
+        return g
+
+    graphs = Parallel(n_jobs=1, prefer="threads")(
+        delayed(_f)(g)
+        for g in tqdm(
+            graphs, disable=not progress, desc=f"Computing geodesic distances on graphs"
+        )
+    )
+    return graphs
+
+
+def compute_intrinsic(graphs: list[nx.Graph], progress=1, nowarning=False):
+    def _f(g: nx.Graph):
+        try:
+            nodes_intrinsic = {i: n["intrinsic"] for i, n in g.nodes.data()}
+        except:
+            if not nowarning:
+                raise ValueError("This graph doesn't have an intrinsic filtration.")
+            else:
+                return g
+        edges_intrinsic = {
+            (u, v): np.max([nodes_intrinsic[u], nodes_intrinsic[v]], axis=0)
+            for u, v in g.edges
+        }
+        nx.set_edge_attributes(g, edges_intrinsic, "intrinsic")
+        return g
+
+    graphs = Parallel(n_jobs=1, prefer="threads")(
+        delayed(_f)(g)
+        for g in tqdm(
+            graphs, disable=not progress, desc="Computing geodesic distances on graphs"
+        )
+    )
+    return graphs
+
+
+def compute_filtration(dataset: str, filtration: str = "ALL", **kwargs):
+    if filtration == "ALL":
+        reset_graphs(dataset)  # not necessary
+        graphs, labels = get_graphs(dataset, **kwargs)
+        graphs = compute_intrinsic(graphs, nowarning=True)
+        graphs = compute_geodesic(graphs)
+        graphs = compute_cc(graphs)
+        graphs = compute_degree(graphs)
+        graphs = compute_ricci(graphs)
+        graphs = compute_fiedler(graphs)
+        graphs = compute_hks(graphs, 10)
+        set_graphs(graphs=graphs, labels=labels, dataset=dataset)
+        return
+    graphs, labels = get_graphs(dataset, **kwargs)
+    if filtration == "dijkstra":
+        return
+    elif filtration == "cc":
+        graphs = compute_cc(graphs)
+    elif filtration == "degree":
+        graphs = compute_degree(graphs)
+    elif filtration == "ricciCurvature":
+        graphs = compute_ricci(graphs)
+    elif filtration == "fiedler":
+        graphs = compute_fiedler(graphs)
+    elif filtration == "geodesic":
+        graphs = compute_geodesic(graphs)
+    elif filtration.startswith("hks_"):
+        # don't want do deal with floats, makes dots in title...
+        t = int(filtration[4:])
+        graphs = compute_hks(graphs=graphs, t=t)
+    else:
+        warn(f"Filtration {filtration} not implemented !")
+        return
+    set_graphs(graphs=graphs, labels=labels, dataset=dataset)
+    return
+
+
+class Graph2SimplexTrees(BaseEstimator, TransformerMixin):
+    """
+    Transforms a list of networkx graphs into a list of simplextree multi
+
+    Usual Filtrations
+    -----------------
+    - "cc" closeness centrality
+    - "geodesic" if the graph provides data to compute it, e.g., BZR, COX2, PROTEINS
+    - "degree"
+    - "ricciCurvature" the ricci curvature
+    - "fiedler" the square of the fiedler vector
+    """
+
+    def __init__(
+        self,
+        filtrations=[],
+        delayed=False,
+        num_collapses=100,
+        progress: bool = False,
+    ):
+        super().__init__()
+        self.filtrations = filtrations  # filtration to search in graph
+        self.delayed = delayed  # reverses the filtration #TODO
+        self.num_collapses = num_collapses
+        self.progress = progress
+        self.num_parameters: int = len(filtrations)
+
+    def fit(self, X, y=None):
+        if len(X) == 0:
+            return self
+        self.num_parameters = len(self.filtrations)
+        if "intrinsic" in self.filtrations:
+            intrinsic_size = len(X[0].nodes[0]["intrinsic"])
+            self.num_parameters += intrinsic_size - 1
+        return self
+
+    def transform(self, X: list[nx.Graph]):
+        def todo(graph, filtrations=self.filtrations) -> list[mp.SimplexTreeMulti]:
+            st = mp.SimplexTreeMulti(num_parameters=self.num_parameters)
+            nodes = np.asarray(graph.nodes, dtype=int).reshape(1, -1)
+            nodes_filtrations = np.asarray(
+                [
+                    [
+                        filtration
+                        for filtration_ in filtrations
+                        for filtration in np.asarray(
+                            graph.nodes[node][filtration_]
+                        ).reshape(-1)
+                        # this reshape is for attributes that are vectors
+                    ]
+                    for node in graph.nodes
+                ],
+                dtype=np.float32,
+            )
+            st.insert_batch(nodes, nodes_filtrations)
+            edges = np.asarray(graph.edges, dtype=int).T
+            edges_filtrations = np.asarray(
+                [
+                    [
+                        filtration
+                        for filtration_ in filtrations
+                        for filtration in np.asarray(graph[u][v][filtration_]).reshape(
+                            -1
+                        )
+                        # this reshape is for attributes that are vectors
+                    ]
+                    for u, v in graph.edges
+                ],
+                dtype=np.float32,
+            )
+            st.insert_batch(edges, edges_filtrations)
+            if st.num_parameters == 2:
+                # TODO : wait for a filtration domination update
+                st.collapse_edges(num=self.num_collapses)
+            # st.make_filtration_non_decreasing() ## Ricci is not safe ...
+            # same output for each pipelines, some have a supplementary axis.
+            return [st]
+
+        return (
+            [delayed(todo)(graph) for graph in X]
+            if self.delayed
+            # memory bound imo
+            else [
+                todo(graph=graph)
+                for graph in tqdm(
+                    X,
+                    desc="Computing simplextrees from graphs",
+                    disable=not self.progress,
+                )
+            ]
+            #                     #         ,
+            #     )
+            # else Parallel(n_jobs=-1, prefer="threads")(
+            #     delayed(todo)(graph)
+            #     for graph in tqdm(
+            #         X,
+            #         desc="Computing simplextrees from graphs",
+            #         disable=not self.progress,
+            #     )
+            # )
+        )