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mackelab
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sbi-for-connectomics-data

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Christian Tomm, J-C Floyd Sarria, Carl C H Petersen", "title": "The Excitatory Neuronal Network of the C2 Barrel Column in Mouse Primary Somatosensory Cortex", "journal": "Neuron. 2009 Jan 29;61(2):301-16.", "year": "2009", "DOI": "10.1016/j.neuron.2008.12.020", "PMID": "19186171", "pre_layer": "L5B", "pre_type": "EXC", "post_layer": "L6", "post_type": "EXC", "only_septum": "no", "cp_empirical": 7, "species": "mouse", "area": "barrel", "samples": 100}, {"ID": "fc1aee04-2083-477d-8cd2-bedbbacaa9d5", "type": "connection_probability_invitro", "authors": "Sandrine Lefort, Christian Tomm, J-C Floyd Sarria, Carl C H Petersen", "title": "The Excitatory Neuronal Network of the C2 Barrel Column in Mouse Primary Somatosensory Cortex", "journal": "Neuron. 2009 Jan 29;61(2):301-16.", "year": "2009", "DOI": "10.1016/j.neuron.2008.12.020", "PMID": "19186171", "pre_layer": "L6", "pre_type": "EXC", "post_layer": "L2", "post_type": "EXC", "only_septum": "no", "cp_empirical": 0, "species": "mouse", "area": "barrel", "samples": 50}, {"ID": "f362cd36-1c0a-45c6-903b-63aceb4828ab", "type": "connection_probability_invitro", "authors": "Sandrine Lefort, Christian Tomm, J-C Floyd Sarria, Carl C H Petersen", "title": "The Excitatory Neuronal Network of the C2 Barrel Column in Mouse Primary Somatosensory Cortex", "journal": "Neuron. 2009 Jan 29;61(2):301-16.", "year": "2009", "DOI": "10.1016/j.neuron.2008.12.020", "PMID": "19186171", "pre_layer": "L6", "pre_type": "EXC", "post_layer": "L3", "post_type": "EXC", "only_septum": "no", "cp_empirical": 0, "species": "mouse", "area": "barrel", "samples": 64}, {"ID": "c0d19eaa-44ee-4cac-84cb-7fd670ab0b73", "type": "connection_probability_invitro", "authors": "Sandrine Lefort, Christian Tomm, J-C Floyd Sarria, Carl C H Petersen", "title": "The Excitatory Neuronal Network of the C2 Barrel Column in Mouse Primary Somatosensory Cortex", "journal": "Neuron. 2009 Jan 29;61(2):301-16.", "year": "2009", "DOI": "10.1016/j.neuron.2008.12.020", "PMID": "19186171", "pre_layer": "L6", "pre_type": "EXC", "post_layer": "L4", "post_type": "EXC", "only_septum": "no", "cp_empirical": 0, "species": "mouse", "area": "barrel", "samples": 94}, {"ID": "ba05ff59-0a83-4062-8bc6-1ee0356072e0", "type": "connection_probability_invitro", "authors": "Sandrine Lefort, Christian Tomm, J-C Floyd Sarria, Carl C H Petersen", "title": "The Excitatory Neuronal Network of the C2 Barrel Column in Mouse Primary Somatosensory Cortex", "journal": "Neuron. 2009 Jan 29;61(2):301-16.", "year": "2009", "DOI": "10.1016/j.neuron.2008.12.020", "PMID": "19186171", "pre_layer": "L6", "pre_type": "EXC", "post_layer": "L5A", "post_type": "EXC", "only_septum": "no", "cp_empirical": 1, "species": "mouse", "area": "barrel", "samples": 160}, {"ID": "c972e68f-e04a-443f-bed1-e14a00b1f5f4", "type": "connection_probability_invitro", "authors": "Sandrine Lefort, Christian Tomm, J-C Floyd Sarria, Carl C H Petersen", "title": "The Excitatory Neuronal Network of the C2 Barrel Column in Mouse Primary Somatosensory Cortex", "journal": "Neuron. 2009 Jan 29;61(2):301-16.", "year": "2009", "DOI": "10.1016/j.neuron.2008.12.020", "PMID": "19186171", "pre_layer": "L6", "pre_type": "EXC", "post_layer": "L5B", "post_type": "EXC", "only_septum": "no", "cp_empirical": 2, "species": "mouse", "area": "barrel", "samples": 100}, {"ID": "c24cd3e7-e10c-46f5-9b04-6a42e16e63c5", "type": "connection_probability_invitro", "authors": "Sandrine Lefort, Christian Tomm, J-C Floyd Sarria, Carl C H Petersen", "title": "The Excitatory Neuronal Network of the C2 Barrel Column in Mouse Primary Somatosensory Cortex", "journal": "Neuron. 2009 Jan 29;61(2):301-16.", "year": "2009", "DOI": "10.1016/j.neuron.2008.12.020", "PMID": "19186171", "pre_layer": "L6", "pre_type": "EXC", "post_layer": "L6", "post_type": "EXC", "only_septum": "no", "cp_empirical": 3, "species": "mouse", "area": "barrel", "samples": 532}, {"ID": "8d94a164-88ac-454c-a0f7-0eea455fc270", "type": "connection_probability_invitro", "authors": "H Markram, J L\u00fcbke, M Frotscher, A Roth, B Sakmann", "title": "Physiology and Anatomy of Synaptic Connections Between Thick Tufted Pyramidal Neurones in the Developing Rat Neocortex", "journal": "J Physiol. 1997 Apr 15;500 ( Pt 2)(Pt 2):409-40.", "year": "1997", "DOI": "10.1113/jphysiol.1997.sp022031", "PMID": "9147328", "pre_layer": "L5", "pre_type": "EXC", "post_layer": "L5", "post_type": "EXC", "only_septum": "no", "cp_empirical": 10, "species": "rat", "area": "SS", "samples": 500}, {"ID": "ae04d7f5-5c09-4d3a-a0c8-994d1b9b2b98", "type": "connection_probability_invitro", "authors": "Audrey Mercer, David C West, Oliver T Morris, Sarah Kirchhecker, Jane E Kerkhoff, Alex M Thomson", "title": "Excitatory Connections Made by Presynaptic Cortico-Cortical Pyramidal Cells in Layer 6 of the Neocortex", "journal": "Cereb Cortex. 2005 Oct;15(10):1485-96.", "year": "2005", "DOI": "10.1093/cercor/bhi027", "PMID": "15647524", "pre_layer": "L6", "pre_type": "EXC", "post_layer": "L6", "post_type": "EXC", "only_septum": "no", "cp_empirical": 4, "species": "rat", "area": "SS, VS", "samples": 27}, {"ID": "8cb7701b-ed14-4743-9ba3-d4a84d3b585d", "type": "connection_probability_invitro", "authors": "Rodrigo Perin, Thomas K Berger, Henry Markram", "title": "A Synaptic Organizing Principle for Cortical Neuronal Groups", "journal": "Proc Natl Acad Sci U S A. 2011 Mar 29;108(13):5419-24.", "year": "2011", "DOI": "10.1073/pnas.1016051108", "PMID": "21383177", "pre_layer": "L5", "pre_type": "L5PT", "post_layer": "L5", "post_type": "L5PT", "only_septum": "no", "cp_empirical": 13, "species": "rat", "area": "SS", "samples": 3446}, {"ID": "107c2b45-4df2-4311-a007-38b40756aa63", "type": "connection_probability_invitro", "authors": "Carl C H Petersen, Bert Sakmann", "title": "The Excitatory Neuronal Network of Rat Layer 4 Barrel Cortex", "journal": "J Neurosci. 2000 Oct 15;20(20):7579-86.", "year": "2000", "DOI": "10.1523/JNEUROSCI.20-20-07579.2000", "PMID": "11027217", "pre_layer": "L4", "pre_type": "L4ss", "post_layer": "L4", "post_type": "L4ss", "only_septum": "no", "cp_empirical": 36, "species": "rat", "area": "barrel", "samples": 146}, {"ID": "745d65c1-5831-4bb9-b28c-619e5893b3a7", "type": "connection_probability_invitro", "authors": "Gilad Silberberg, Henry Markram", "title": "Disynaptic Inhibition Between Neocortical Pyramidal Cells Mediated by Martinotti Cells", "journal": "Neuron. 2007 Mar 1;53(5):735-46.", "year": "2007", "DOI": "10.1016/j.neuron.2007.02.012", "PMID": "17329212", "pre_layer": "L5", "pre_type": "EXC", "post_layer": "L5", "post_type": "EXC", "only_septum": "no", "cp_empirical": 12, "species": "rat", "area": "SS", "samples": 1450}, {"ID": "2a01488f-6fba-4efc-bbdb-9a50a4bf003d", "type": "connection_probability_invitro", "authors": "Sen Song, Per Jesper Sj\u00f6str\u00f6m, Markus Reigl, Sacha Nelson, Dmitri B Chklovskii", "title": "Highly Nonrandom Features of Synaptic Connectivity in Local Cortical Circuits", "journal": "PLoS Biol. 2005 Mar;3(3):e68.", "year": "2005", "DOI": "10.1371/journal.pbio.0030068", "PMID": "15737062", "pre_layer": "L5", "pre_type": "L5PT", "post_layer": "L5", "post_type": "L5PT", "only_septum": "no", "cp_empirical": 12, "species": "rat", "area": "VC", "samples": 8050}, {"ID": "dabe08c5-2260-40eb-ab2a-585446ee7615", "type": "connection_probability_invitro", "authors": "Qian-Quan Sun, John R Huguenard, David A Prince", "title": "Barrel Cortex Microcircuits: Thalamocortical Feedforward Inhibition in Spiny Stellate Cells Is Mediated by a Small Number of Fast-Spiking Interneurons", "journal": "J Neurosci. 2006 Jan 25;26(4):1219-30.", "year": "2006", "DOI": "10.1523/JNEUROSCI.4727-04.2006", "PMID": "16436609", "pre_layer": "L4", "pre_type": "L4sp", "post_layer": "L4", "post_type": "L4sp", "only_septum": "no", "cp_empirical": 21, "species": "rat", "area": "barrel", "samples": 24}, {"ID": "e1302174-b50c-4f7f-bafb-993fd7c9a678", "type": "connection_probability_invitro", "authors": "Qian-Quan Sun, John R Huguenard, David A Prince", "title": "Barrel Cortex Microcircuits: Thalamocortical Feedforward Inhibition in Spiny Stellate Cells Is Mediated by a Small Number of Fast-Spiking Interneurons", "journal": "J Neurosci. 2006 Jan 25;26(4):1219-30.", "year": "2006", "DOI": "10.1523/JNEUROSCI.4727-04.2006", "PMID": "16436609", "pre_layer": "L4", "pre_type": "L4ss", "post_layer": "L4", "post_type": "L4ss", "only_septum": "no", "cp_empirical": 21, "species": "rat", "area": "barrel", "samples": 24}, {"ID": "3410f9b8-f11a-49c2-b033-f63eb98b2dc9", "type": "connection_probability_invitro", "authors": "Alex M Thomson, David C West, Yun Wang, A Peter Bannister", "title": "Synaptic Connections and Small Circuits Involving Excitatory and Inhibitory Neurons in Layers 2-5 of Adult Rat and Cat Neocortex: Triple Intracellular Recordings and Biocytin Labelling in Vitro", "journal": "Cereb Cortex. 2002 Sep;12(9):936-53.", "year": "2002", "DOI": "10.1093/cercor/12.9.936", "PMID": "12183393", "pre_layer": "L23", "pre_type": "EXC", "post_layer": "L23", "post_type": "EXC", "only_septum": "no", "cp_empirical": 26, "species": "rat", "area": "SM", "samples": 247}, {"ID": "a0e90a58-2fa3-4f0c-a024-76ff113b4f13", "type": "connection_probability_invitro", "authors": "Alex M Thomson, David C West, Yun Wang, A Peter Bannister", "title": "Synaptic Connections and Small Circuits Involving Excitatory and Inhibitory Neurons in Layers 2-5 of Adult Rat and Cat Neocortex: Triple Intracellular Recordings and Biocytin Labelling in Vitro", "journal": "Cereb Cortex. 2002 Sep;12(9):936-53.", "year": "2002", "DOI": "10.1093/cercor/12.9.936", "PMID": "12183393", "pre_layer": "L3", "pre_type": "EXC", "post_layer": "L5", "post_type": "EXC", "only_septum": "no", "cp_empirical": 55, "species": "rat", "area": "SM", "samples": 29}, {"ID": "459f83ca-9039-4f30-8952-79fa7f0c259b", "type": "connection_probability_invitro", "authors": "Alex M Thomson, David C West, Yun Wang, A Peter Bannister", "title": "Synaptic Connections and Small Circuits Involving Excitatory and Inhibitory Neurons in Layers 2-5 of Adult Rat and Cat Neocortex: Triple Intracellular Recordings and Biocytin Labelling in Vitro", "journal": "Cereb Cortex. 2002 Sep;12(9):936-53.", "year": "2002", "DOI": "10.1093/cercor/12.9.936", "PMID": "12183393", "pre_layer": "L4", "pre_type": "EXC", "post_layer": "L3", "post_type": "EXC", "only_septum": "no", "cp_empirical": 28, "species": "rat", "area": "SM", "samples": 25}, {"ID": "04b3dd80-0954-4dee-8cce-d32c9d798ac5", "type": "connection_probability_invitro", "authors": "Alex M Thomson, David C West, Yun Wang, A Peter Bannister", "title": "Synaptic Connections and Small Circuits Involving Excitatory and Inhibitory Neurons in Layers 2-5 of Adult Rat and Cat Neocortex: Triple Intracellular Recordings and Biocytin Labelling in Vitro", "journal": "Cereb Cortex. 2002 Sep;12(9):936-53.", "year": "2002", "DOI": "10.1093/cercor/12.9.936", "PMID": "12183393", "pre_layer": "L5", "pre_type": "EXC", "post_layer": "L5", "post_type": "EXC", "only_septum": "no", "cp_empirical": 9, "species": "rat", "area": "SM", "samples": 163}, {"ID": "a8bc6716-4189-49dc-aaf9-081e530fc536", "type": "connection_probability_invitro", "authors": "Alex M Thomson, David C West, Yun Wang, A Peter Bannister", "title": "Synaptic Connections and Small Circuits Involving Excitatory and Inhibitory Neurons in Layers 2-5 of Adult Rat and Cat Neocortex: Triple Intracellular Recordings and Biocytin Labelling in Vitro", "journal": "Cereb Cortex. 2002 Sep;12(9):936-53.", "year": "2002", "DOI": "10.1093/cercor/12.9.936", "PMID": "12183393", "pre_layer": "L5", "pre_type": "EXC", "post_layer": "L3", "post_type": "EXC", "only_septum": "no", "cp_empirical": 3, "species": "rat", "area": "SM", "samples": 29}, {"ID": "dd748df9-12cd-4183-879d-3d4a01648842", "type": "connection_probability_invitro", "authors": "Yumiko Yoshimura, Jami L M Dantzker, Edward M Callaway", "title": "Excitatory Cortical Neurons Form Fine-Scale Functional Networks", "journal": "Nature. 2005 Feb 24;433(7028):868-73.", "year": "2005", "DOI": "10.1038/nature03252", "PMID": "15729343", "pre_layer": "L23", "pre_type": "EXC", "post_layer": "L23", "post_type": "EXC", "only_septum": "no", "cp_empirical": 20, "species": "rat", "area": "VC", "samples": 112}, {"ID": "ab3dd055-4a4b-4e8f-8a32-4793c7016da6", "type": "connection_probability_invitro", "authors": "Yumiko Yoshimura, Jami L M Dantzker, Edward M Callaway", "title": "Excitatory Cortical Neurons Form Fine-Scale Functional Networks", "journal": "Nature. 2005 Feb 24;433(7028):868-73.", "year": "2005", "DOI": "10.1038/nature03252", "PMID": "15729343", "pre_layer": "L4", "pre_type": "EXC", "post_layer": "L23", "post_type": "EXC", "only_septum": "no", "cp_empirical": 20, "species": "rat", "area": "VC", "samples": 50}, {"ID": "2c91035c-ab5f-4d17-87bc-3bd0d50b5655", "type": "connection_probability_invivo", "authors": "Jean-S\u00e9bastien Jouhanneau, Jens Kremkow, James F A Poulet", "title": "Single Synaptic Inputs Drive High-Precision Action Potentials in Parvalbumin Expressing GABA-ergic Cortical Neurons in Vivo", "journal": "Nat Commun. 2018 Apr 18;9(1):1540.", "year": "2018", "DOI": "10.1038/s41467-018-03995-2", "PMID": "29670095", "pre_layer": "L23", "pre_type": "EXC", "post_layer": "L23", "post_type": "EXC", "only_septum": "no", "cp_empirical": 7, "species": "mouse", "area": "barrel", "samples": 774}, {"ID": "751f5584-c779-46ab-a5ef-9622095c0634", "type": "connection_probability_invitro", "authors": "Sonja B Hofer, Ho Ko, Bruno Pichler, Joshua Vogelstein, Hana Ros, Hongkui Zeng, Ed Lein, Nicholas A Lesica, Thomas D Mrsic-Flogel", "title": "Differential Connectivity and Response Dynamics of Excitatory and Inhibitory Neurons in Visual Cortex", "journal": "Nat Neurosci. 2011 Jul 17;14(8):1045-52.", "year": "2011", "DOI": "10.1038/nn.2876", "PMID": "21765421", "pre_layer": "L23", "pre_type": "EXC", "post_layer": "L23", "post_type": "EXC", "only_septum": "no", "cp_empirical": 19, "species": "mouse", "area": "VC", "samples": 235}, {"ID": "f1ba71df-15b6-4fc4-8587-319290fed8d5", "type": "connection_probability_invivo", "authors": "Jean-S\u00e9bastien Jouhanneau, Jens Kremkow, Anja L Dorrn, James F A Poulet", "title": "In Vivo Monosynaptic Excitatory Transmission Between Layer 2 Cortical Pyramidal Neurons", "journal": "Cell Rep. 2015 Dec 15;13(10):2098-106.", "year": "2015", "DOI": "10.1016/j.celrep.2015.11.011", "PMID": "26670044", "pre_layer": "L2", "pre_type": "EXC", "post_layer": "L2", "post_type": "EXC", "only_septum": "no", "cp_empirical": 7, "species": "mouse", "area": "barrel", "samples": 878}]

data/structural_model/empirical_data_2020-07-13.json DELETED Viewed

@@ -1 +0,0 @@

data/structural_model/inference_experiments_local.json DELETED Viewed

@@ -1,24 +0,0 @@
-[
-    {
-        "name": "pre-pst-pstAll",
-        "identifier": "default_rule_invivo",
-        "description": "invivo: VPM to C2 column, 7 empirical measurements",
-        "rule" : "default_rule",
-        "feature-set" : "set-3",
-        "prior" : {
-            "low" : [0.5, 0.5, -1.5],
-            "high" : [1.5, 1.5, -0.5]
-        },
-        "numSimulations" : 1000,
-        "constraints": [
-            "897f7fba-714c-4e2e-9f9c-552e3815fb34",
-            "8bbcab58-cd1e-48ac-b7ef-583e8a077a9f",
-            "7d6ff52f-0810-4ff8-8bad-e41173c5d2ff",
-            "1c32cfac-828a-46ce-acaa-8de786e6c22f",
-            "1d0687e0-bb9e-4cb1-9ed5-fcc00cd29c4d",
-            "fe21fc12-9bda-45c9-857a-385b418a1116",
-            "2eab5e02-e8da-485e-8989-41554deae0c1"
-        ]
-    }
-]

data/subcellular_features/empirical_data_2020-07-13.json DELETED Viewed

@@ -1 +0,0 @@

data/subcellular_features/inference_experiments_local.json DELETED Viewed

@@ -1,31 +0,0 @@
-[
-    {
-        "name": "meet_in_cube",
-        "identifier": "peters-subcellular",
-        "description": "invivo: VPM to C2 column, 7 empirical measurements",
-        "rule": "bernoulli",
-        "feature-set": "set-7",
-        "prior": {
-            "low": [
-                0.5,
-                0.5,
-                -1.5
-            ],
-            "high": [
-                1.5,
-                1.5,
-                -0.5
-            ]
-        },
-        "numSimulations": 1000,
-        "constraints": [
-            "897f7fba-714c-4e2e-9f9c-552e3815fb34",
-            "8bbcab58-cd1e-48ac-b7ef-583e8a077a9f",
-            "7d6ff52f-0810-4ff8-8bad-e41173c5d2ff",
-            "1c32cfac-828a-46ce-acaa-8de786e6c22f",
-            "1d0687e0-bb9e-4cb1-9ed5-fcc00cd29c4d",
-            "fe21fc12-9bda-45c9-857a-385b418a1116",
-            "2eab5e02-e8da-485e-8989-41554deae0c1"
-        ]
-    }
-]

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figures/plotting_settings.mplstyle DELETED Viewed

@@ -1,12 +0,0 @@
-font.sans-serif : arial
-font.family : sans-serif
-axes.spines.top : False
-axes.spines.right : False
-axes.labelsize : 17
-xtick.labelsize : 15
-ytick.labelsize : 15
-legend.frameon : False
-legend.fontsize : 17
-font.size : 17
-text.usetex: false

figures/plotting_utils.py DELETED Viewed

@@ -1,72 +0,0 @@
-import matplotlib.pyplot as plt
-import numpy as np
-# short fun to colorize boxplots
-def color_boxplot(thos, bp, colors, alpha=0.7):
-    for key in ["boxes", "medians"]:
-        for i, b in enumerate(bp[key]):
-            b.set(color=colors[i], alpha=alpha)
-    for idx, patch in enumerate(bp["boxes"]):
-        patch.set_facecolor(colors[idx])
-        patch.set_alpha(alpha)
-    for key in ["whiskers", "caps"]:
-        for i in range(thos.shape[1]):
-            bp[key][2 * i].set(color=colors[i], alpha=alpha)
-            bp[key][2 * i + 1].set(color=colors[i], alpha=alpha)
-# plotting 1D marginals, e.g., for showing posterior predictives.
-def custom_marginal_plot(
-    ax,
-    x,
-    points,
-    x_label,
-    points_label,
-    color,
-    show_xlabels=True,
-    labels=None,
-    num_bins=10,
-    alpha=0.8,
-    histtype="stepfilled",
-    plot_legend=True,
-    handlelength=0.8,
-    bbox_to_anchor=(1, 1),
-    points_line_style="-",
-):
-    # Cross validation
-    assert x.shape[1] == 7
-    assert isinstance(x, np.ndarray)
-    assert not show_xlabels or labels
-    for idx in range(x.shape[1]):
-        axi = ax[idx]
-        plt.sca(axi)
-        axi.spines["right"].set_visible(False)
-        axi.spines["top"].set_visible(False)
-        axi.spines["left"].set_visible(False)
-        plt.yticks([])
-        if points is not None:
-            plt.axvline(
-                x=points[0, idx], color="k", label=points_label, ls=points_line_style
-            )
-        plt.xlim([0, 1])
-        plt.xticks([0, 1])
-        _, bins, _ = plt.hist(
-            x[:1000, idx],
-            bins=num_bins,
-            alpha=alpha,
-            color=color,
-            label=x_label,
-            histtype=histtype,
-        )
-        if show_xlabels:
-            plt.xlabel(labels[idx])
-        # plt.sca(ax[-1, -1])
-        # plt.axis("off")
-        # plt.sca(ax[-1, -2])
-        if idx == 6 and plot_legend:
-            plt.legend(handlelength=handlelength, bbox_to_anchor=bbox_to_anchor)

figures/supplementary_figures/plotting_settings.mplstyle DELETED Viewed

@@ -1,12 +0,0 @@
-font.sans-serif : arial
-font.family : sans-serif
-axes.spines.top : False
-axes.spines.right : False
-axes.labelsize : 17
-xtick.labelsize : 15
-ytick.labelsize : 15
-legend.frameon : False
-legend.fontsize : 17
-font.size : 17
-text.usetex: false

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figures/supplementary_figures/supp_fig2-3_predictives_and_conditionals.ipynb DELETED Viewed

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results/benchmark_poisson_glm_snpe_samples/.hydra/config.yaml DELETED Viewed

@@ -1,24 +0,0 @@
-compute_metrics: true
-device: ${algorithm.device}
-seed: null
-algorithm:
-  name: SNPE
-  run: sbi.snpe.run
-  device: cpu
-  params:
-    num_rounds: 10
-    neural_net: mdn
-    hidden_features: 50
-    simulation_batch_size: 1000
-    training_batch_size: 1000
-    num_atoms: 5
-    automatic_transforms_enabled: false
-    z_score_x: false
-    z_score_theta: true
-    stop_after_epochs: 100
-task:
-  name: poisson_glm
-  num_simulations: 1000000
-  num_observation: 5
-joblib:
-  n_jobs: 20

results/benchmark_poisson_glm_snpe_samples/.hydra/hydra.yaml DELETED Viewed

@@ -1,142 +0,0 @@
-hydra:
-  run:
-    dir: outputs/${now:%Y-%m-%d}/${now:%H-%M-%S}
-  sweep:
-    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
-    subdir: ${hydra.job.num}
-  hydra_logging:
-    version: 1
-    formatters:
-      simple:
-        format: '[%(asctime)s][HYDRA] %(message)s'
-    handlers:
-      console:
-        class: logging.StreamHandler
-        formatter: simple
-        stream: ext://sys.stdout
-    root:
-      level: INFO
-      handlers:
-      - console
-    loggers:
-      logging_example:
-        level: DEBUG
-    disable_existing_loggers: false
-  job_logging:
-    version: 1
-    formatters:
-      simple:
-        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
-    handlers:
-      console:
-        class: logging.StreamHandler
-        formatter: simple
-        stream: ext://sys.stdout
-      file:
-        class: logging.FileHandler
-        formatter: simple
-        filename: ${hydra.job.name}.log
-    root:
-      level: INFO
-      handlers:
-      - console
-      - file
-    disable_existing_loggers: false
-  sweeper:
-    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
-    max_batch_size: null
-  launcher:
-    _target_: hydra_plugins.hydra_joblib_launcher.joblib_launcher.JoblibLauncher
-    n_jobs: -1
-    backend: null
-    prefer: processes
-    require: null
-    verbose: 0
-    timeout: null
-    pre_dispatch: 2*n_jobs
-    batch_size: auto
-    temp_folder: null
-    max_nbytes: null
-    mmap_mode: r
-  help:
-    app_name: ${hydra.job.name}
-    header: '${hydra.help.app_name} is powered by Hydra.
-      '
-    footer: 'Powered by Hydra (https://hydra.cc)
-      Use --hydra-help to view Hydra specific help
-      '
-    template: '${hydra.help.header}
-      == Configuration groups ==
-      Compose your configuration from those groups (group=option)
-      $APP_CONFIG_GROUPS
-      == Config ==
-      Override anything in the config (foo.bar=value)
-      $CONFIG
-      ${hydra.help.footer}
-      '
-  hydra_help:
-    hydra_help: ???
-    template: 'Hydra (${hydra.runtime.version})
-      See https://hydra.cc for more info.
-      == Flags ==
-      $FLAGS_HELP
-      == Configuration groups ==
-      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
-      to command line)
-      $HYDRA_CONFIG_GROUPS
-      Use ''--cfg hydra'' to Show the Hydra config.
-      '
-  output_subdir: .hydra
-  overrides:
-    hydra:
-    - hydra/launcher=joblib
-    task:
-    - task=poisson_glm
-    - task.num_observation=5
-    - task.num_simulations=1000000
-    - algorithm=snpe
-    - +joblib.n_jobs=20
-  job:
-    name: run
-    override_dirname: +joblib.n_jobs=20,algorithm=snpe,task.num_observation=5,task.num_simulations=1000000,task=poisson_glm
-    id: run_79
-    num: 79
-    config_name: config
-    env_set: {}
-    env_copy: []
-    config:
-      override_dirname:
-        kv_sep: '='
-        item_sep: ','
-        exclude_keys: []
-  runtime:
-    version: 1.0.3
-    cwd: /home/janfb/qode/benchmarking_sbi
-  verbose: false

results/benchmark_poisson_glm_snpe_samples/.hydra/overrides.yaml DELETED Viewed

@@ -1,5 +0,0 @@
-- task=poisson_glm
-- task.num_observation=5
-- task.num_simulations=1000000
-- algorithm=snpe
-- +joblib.n_jobs=20

results/benchmark_poisson_glm_snpe_samples/log_prob_true_parameters.csv DELETED Viewed

	@@ -1 +0,0 @@
1	- 2.731577634811401367e+00

results/benchmark_poisson_glm_snpe_samples/metrics.csv DELETED Viewed

	@@ -1,2 +0,0 @@
1	- C2ST,C2ST_Z,MMD,MMD_Z,KSD_GAUSS,MEDDIST,C2ST_1K,C2ST_1K_Z,MMD_1K,MMD_1K_Z,KSD_GAUSS_1K,MEDDIST_1K,NLTP,RT
2	- 0.52315,0.53165,0.0002142191,0.00024402142,1897984.8,8.888194,0.4885,0.4945,-0.00052678585,-0.0005502701,195861.8,9.0,-2.7315776,93883.83

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	@@ -1 +0,0 @@
1	- 1.000000000000000000e+06

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@@ -1,24 +0,0 @@
-algorithm:
-  device: cpu
-  name: SNPE
-  params:
-    automatic_transforms_enabled: false
-    hidden_features: 50
-    neural_net: mdn
-    num_atoms: 5
-    num_rounds: 10
-    simulation_batch_size: 1000
-    stop_after_epochs: 100
-    training_batch_size: 1000
-    z_score_theta: true
-    z_score_x: false
-  run: sbi.snpe.run
-compute_metrics: true
-device: cpu
-joblib:
-  n_jobs: 20
-seed: 3191617583
-task:
-  name: poisson_glm
-  num_observation: 5
-  num_simulations: 1000000

results/benchmark_poisson_glm_snpe_samples/runtime.csv DELETED Viewed

	@@ -1 +0,0 @@
1	- 9.388382812500000000e+04

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