MiSTree: a Python package for constructing and analysing Minimum Spanning Trees

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</div> <form action="" method="post" id="official-pgr-form"> <input type="hidden" name="csrfmiddlewaretoken" value="a5H2bRfmR6q9InTl91zwui0v1df1Od4fMz4F6yH7C5XZsiaIq4D2NC5eUamMBsVX"> <input type="hidden" name="official_pgr_ids" id="official-pgr-ids" /> <div class="modal-body"> <div class="paper-implementations"> <div class="row align-items-center"> <div class="col-md-5"> <div class="paper-impl-cell"> <a href="https://github.com/knaidoo29/mistree" class="code-table-link"> <span class=" icon-wrapper icon-ion" data-name="logo-github"><svg xmlns="http://www.w3.org/2000/svg" width="512" height="512" viewBox="0 0 512 512"><path d="M256 32C132.3 32 32 134.9 32 261.7c0 101.5 64.2 187.5 153.2 217.9a17.56 17.56 0 0 0 3.8.4c8.3 0 11.5-6.1 11.5-11.4 0-5.5-.2-19.9-.3-39.1a102.4 102.4 0 0 1-22.6 2.7c-43.1 0-52.9-33.5-52.9-33.5-10.2-26.5-24.9-33.6-24.9-33.6-19.5-13.7-.1-14.1 1.4-14.1h.1c22.5 2 34.3 23.8 34.3 23.8 11.2 19.6 26.2 25.1 39.6 25.1a63 63 0 0 0 25.6-6c2-14.8 7.8-24.9 14.2-30.7-49.7-5.8-102-25.5-102-113.5 0-25.1 8.7-45.6 23-61.6-2.3-5.8-10-29.2 2.2-60.8a18.64 18.64 0 0 1 5-.5c8.1 0 26.4 3.1 56.6 24.1a208.21 208.21 0 0 1 112.2 0c30.2-21 48.5-24.1 56.6-24.1a18.64 18.64 0 0 1 5 .5c12.2 31.6 4.5 55 2.2 60.8 14.3 16.1 23 36.6 23 61.6 0 88.2-52.4 107.6-102.3 113.3 8 7.1 15.2 21.1 15.2 42.5 0 30.7-.3 55.5-.3 63 0 5.4 3.1 11.5 11.4 11.5a19.35 19.35 0 0 0 4-.4C415.9 449.2 480 363.1 480 261.7 480 134.9 379.7 32 256 32z"/></svg></span> knaidoo29/mistree <span class="badge badge-info is-official-code"><span class=" icon-wrapper icon-ion" data-name="checkmark-circle-outline"><svg xmlns="http://www.w3.org/2000/svg" width="512" height="512" viewBox="0 0 512 512"><path d="M448 256c0-106-86-192-192-192S64 150 64 256s86 192 192 192 192-86 192-192z" fill="none" stroke="#000" stroke-miterlimit="10" stroke-width="32"/><path fill="none" stroke="#000" stroke-linecap="round" stroke-linejoin="round" stroke-width="32" d="M352 176L217.6 336 160 272"/></svg></span> official</span> </a> </div> </div> <div class="col-md-3"> <div class="paper-impl-cell"> <span class=" icon-wrapper icon-ion" data-name="star"><svg xmlns="http://www.w3.org/2000/svg" width="512" height="512" viewBox="0 0 512 512"><path d="M394 480a16 16 0 0 1-9.39-3L256 383.76 127.39 477a16 16 0 0 1-24.55-18.08L153 310.35 23 221.2a16 16 0 0 1 9-29.2h160.38l48.4-148.95a16 16 0 0 1 30.44 0l48.4 149H480a16 16 0 0 1 9.05 29.2L359 310.35l50.13 148.53A16 16 0 0 1 394 480z"/></svg></span> 49 </div> </div> <div class="col-md-2"> <div class="paper-impl-cell"> </div> </div> <div class="col-md-2 text-center"> <input type="radio" name="official-pgr-radio" class="official-pgr-input official-pgr-radio radios-version-element" value="1677897" checked > <input type="checkbox" class="official-pgr-input official-pgr-checkbox checkboxes-version-element" value="1677897" checked > </div> </div> <div class="row align-items-center"> <div class="col-md-5"> <div class="paper-impl-cell"> <a 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134.9 379.7 32 256 32z"/></svg></span> meyerls/pc-skeletor </a> </div> </div> <div class="col-md-3"> <div class="paper-impl-cell"> <span class=" icon-wrapper icon-ion" data-name="star"><svg xmlns="http://www.w3.org/2000/svg" width="512" height="512" viewBox="0 0 512 512"><path d="M394 480a16 16 0 0 1-9.39-3L256 383.76 127.39 477a16 16 0 0 1-24.55-18.08L153 310.35 23 221.2a16 16 0 0 1 9-29.2h160.38l48.4-148.95a16 16 0 0 1 30.44 0l48.4 149H480a16 16 0 0 1 9.05 29.2L359 310.35l50.13 148.53A16 16 0 0 1 394 480z"/></svg></span> 169 </div> </div> <div class="col-md-2"> <div class="paper-impl-cell"> </div> </div> <div class="col-md-2 text-center"> <input type="radio" name="official-pgr-radio" class="official-pgr-input official-pgr-radio radios-version-element" value="2119362" > <input type="checkbox" class="official-pgr-input official-pgr-checkbox checkboxes-version-element" value="2119362" > </div> </div> <div class="radios-version-element"> <hr/> <div class="row align-items-center justify-content-between"> <div class="col-md-5"> <div class="paper-impl-cell"> There is no official implementation </div> </div> <div class="col-md-2 text-center"> <input type="radio" name="official-pgr-radio" value="" class="official-pgr-input official-pgr-radio" > </div> </div> </div> <hr/> <div class="row align-items-center justify-content-between"> <div class="col-md-5"> <div class="paper-impl-cell"> Multiple official implementations </div> </div> <div class="col-md-2 text-center"> <div class="custom-control custom-switch"> <input type="checkbox" class="custom-control-input" id="official-pgr-multiple-switch"> <label class="custom-control-label" for="official-pgr-multiple-switch" id="official-pgr-multiple-switch-label"></label> </div> </div> </div> </div> </div> <div class="modal-footer"> <button type="submit" class="btn btn-primary">Submit </button> </div> </form> </div> </div> </div>  <div class="modal fade" id="addRow" role="dialog" aria-labelledby="addRowLabel" aria-hidden="true"> <div class="modal-dialog" role="document"> <div class="modal-content"> <div class="modal-header"> <h5 class="modal-title" id="addRowLabel">Add a new evaluation result row</h5> <button type="button" class="close btn-close" data-bs-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="modal-body" style="padding-bottom:30px;"> To add evaluation results you first need to <a href="#addTask" data-bs-toggle="modal" data-bs-dismiss="modal">add a task to this paper</a>. </div> </div> </div> </div>  <div class="modal fade" id="removeRow" role="dialog" aria-labelledby="removeRowLabel" aria-hidden="true"> <div class="modal-dialog modal-lg" role="document"> <div class="modal-content"> <div class="modal-header"> <h5 class="modal-title" id="removeRowLabel">Add a new evaluation result row</h5> <button type="button" class="close btn-close" data-bs-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <form action="" method="post"> <div class="modal-body"> <div class="sota-table"> <table class="table-striped"> <tr> <th>TASK</th> <th>DATASET</th> <th>MODEL</th> <th>METRIC NAME</th> <th>METRIC VALUE</th> <th>GLOBAL RANK</th> <th>REMOVE</th> </tr> </table> </div> </div> </form> </div> </div> </div>  <div class="modal fade" id="addTask" role="dialog" aria-labelledby="addTaskLabel" aria-hidden="true"> <div class="modal-dialog" role="document"> <div class="modal-content"> <div class="modal-header"> <h5 class="modal-title" id="addTaskLabel">Add a task</h5> <button type="button" class="close btn-close" data-bs-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="modal-body"> <form action="" method="post"> <input type="hidden" name="csrfmiddlewaretoken" value="a5H2bRfmR6q9InTl91zwui0v1df1Od4fMz4F6yH7C5XZsiaIq4D2NC5eUamMBsVX"> <div id="div_id_task" class="form-group"> <label for="id_task" class=""> Add: </label> <div class=""> <select name="task" class="modelselect2 form-control" id="id_task" data-autocomplete-light-language="en" data-autocomplete-light-url="/task-autocomplete/" data-autocomplete-light-function="select2"> <option value="" selected>---------</option> </select> </div> </div> <div class="modal-help-text"> Not in the list?<br/> <a href="#" id="new-task-form-toggle"> <span class=" icon-wrapper icon-ion" data-name="add"><svg xmlns="http://www.w3.org/2000/svg" width="512" height="512" viewBox="0 0 512 512"><path fill="none" stroke="#000" stroke-linecap="round" stroke-linejoin="round" stroke-width="32" d="M256 112v288m144-144H112"/></svg></span> Create a new task</a>. </div> <div id="new-task-form" style="display: none"> <div id="div_id_new_task_name" class="form-group"> <label for="id_new_task_name" class=""> New task name: </label> <div class=""> <input type="text" name="new_task_name" maxlength="200" class="textinput textInput form-control" id="id_new_task_name"> </div> </div> <div id="div_id_new_task_area" class="form-group"> <label for="id_new_task_area" class=""> Top-level area: </label> <div class=""> <select name="new_task_area" class="select form-control" id="id_new_task_area"> <option value="" selected>---------</option> <option value="17">Adversarial</option> <option value="18">Audio</option> <option value="11">Computer Code</option> <option value="3">Computer Vision</option> <option value="9">Graphs</option> <option value="15">Knowledge Base</option> <option value="7">Medical</option> <option value="6">Methodology</option> <option value="5">Miscellaneous</option> <option value="12">Music</option> <option value="4">Natural Language Processing</option> <option value="13">Playing Games</option> <option value="14">Reasoning</option> <option value="16">Robots</option> <option value="10">Speech</option> <option value="8">Time Series</option> </select> </div> </div> <div id="div_id_new_task_parent" class="form-group"> <label for="id_new_task_parent" class=""> Parent task (if any): </label> <div class=""> <select name="new_task_parent" class="modelselect2 form-control" id="id_new_task_parent" data-autocomplete-light-language="en" data-autocomplete-light-url="/task-and-tag-autocomplete/" data-autocomplete-light-function="select2"> <option value="" selected>---------</option> </select> </div> </div> <div id="div_id_new_task_desc" class="form-group"> <label for="id_new_task_desc" class=""> Description: </label> <div class=""> <textarea name="new_task_desc" cols="40" rows="3" class="textarea form-control" id="id_new_task_desc"> </textarea> </div> </div> </div> <div class="modal-footer"> <button type="submit" class="btn btn-primary"> Submit </button> </div> </form> </div> </div> </div> </div>  <div class="modal fade" id="removeTask" tabindex="-1" role="dialog" aria-labelledby="removeTaskLabel" aria-hidden="true"> <div class="modal-dialog" role="document"> <div class="modal-content"> <div class="modal-header"> <h5 class="modal-title" id="removeTaskLabel">Remove a task</h5> <button type="button" class="close btn-close" data-bs-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <form action="" method="post"> <div class="modal-body"> </div> </form> </div> </div> </div>  <div class="modal fade" id="addMethod" role="dialog" aria-labelledby="addMethodLabel" aria-hidden="true"> <div class="modal-dialog" role="document"> <div class="modal-content"> <div class="modal-header"> <h5 class="modal-title" id="addMethodLabel">Add a method</h5> <button type="button" class="close btn-close" data-bs-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="modal-body"> <form action="" method="post"> <input type="hidden" name="csrfmiddlewaretoken" value="a5H2bRfmR6q9InTl91zwui0v1df1Od4fMz4F6yH7C5XZsiaIq4D2NC5eUamMBsVX"> <div id="div_id_method" class="form-group"> <label for="id_method" class=""> Add: </label> <div class=""> <select name="method" class="modelselect2 form-control" id="id_method" data-autocomplete-light-language="en" data-autocomplete-light-url="/method-autocomplete/" data-autocomplete-light-function="select2"> <option value="" selected>---------</option> </select> </div> </div> <div class="modal-help-text"> Not in the list?<br/> <a href="#" id="new-method-form-toggle"> <span class=" icon-wrapper icon-ion" data-name="add"><svg xmlns="http://www.w3.org/2000/svg" width="512" height="512" viewBox="0 0 512 512"><path fill="none" stroke="#000" stroke-linecap="round" stroke-linejoin="round" stroke-width="32" d="M256 112v288m144-144H112"/></svg></span> Create a new method</a>. </div> <div id="new-method-form" style="display: none"> <div id="div_id_new_method_name" class="form-group"> <label for="id_new_method_name" class=""> <b>New method name</b> (e.g. ReLU): </label> <div class=""> <input type="text" name="new_method_name" maxlength="200" minlength="2" class="textinput textInput form-control" id="id_new_method_name"> </div> </div> <div id="div_id_new_method_full_name" class="form-group"> <label for="id_new_method_full_name" class=""> <b>New method full name</b> (e.g. Rectified Linear Unit): </label> <div class=""> <input type="text" name="new_method_full_name" maxlength="200" minlength="2" class="textinput textInput form-control" id="id_new_method_full_name"> </div> </div> <div id="div_id_new_method_paper" class="form-group"> <label for="id_new_method_paper" class=""> <b>Paper where method was first introduced</b>: </label> <div class=""> <select name="new_method_paper" class="modelselect2 form-control" id="id_new_method_paper" data-autocomplete-light-language="en" data-autocomplete-light-url="/paper-autocomplete/" data-autocomplete-light-function="select2"> <option value="" selected>---------</option> </select> </div> </div> <div id="div_id_new_method_collection" class="form-group"> <label for="id_new_method_collection" class=""> <b>Method category</b> (e.g. Activation Functions): <i>If no match, add something for now then you can add a new category afterwards.</i> </label> <div class=""> <select name="new_method_collection" class="modelselect2 form-control" id="id_new_method_collection" data-autocomplete-light-language="en" data-autocomplete-light-url="/method-collection-autocomplete/" data-autocomplete-light-function="select2"> <option value="" selected>---------</option> </select> </div> </div> <div id="div_id_new_method_desc" class="form-group"> <label for="id_new_method_desc" class=""> <b>Markdown description</b> (optional; $\LaTeX$ enabled): <i>You can edit this later, so feel free to start with something succinct.</i> </label> <div class=""> <textarea name="new_method_desc" cols="40" rows="10" class="textarea form-control" id="id_new_method_desc"> </textarea> </div> </div> </div> <div class="modal-footer"> <button type="submit" class="btn btn-primary"> Submit </button> </div> </form> </div> </div> </div> </div>  <div class="modal fade" id="removeMethod" tabindex="-1" role="dialog" aria-labelledby="removeMethodLabel" aria-hidden="true"> <div class="modal-dialog" role="document"> <div class="modal-content"> <div class="modal-header"> <h5 class="modal-title" id="removeMethodLabel">Remove a method</h5> <button type="button" class="close btn-close" data-bs-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <form action="" method="post"> <div class="modal-body"> </div> </form> </div> </div> </div>  <div class="modal fade" id="badgeModal" tabindex="-1" role="dialog" aria-labelledby="badgeModalLabel" aria-hidden="true" > <div class="modal-dialog modal-lg" role="document"> <div class="modal-content modal-badge"> </div> </div> </div>  <div class="modal fade" id="editDatasets" role="dialog" aria-labelledby="editDatasetsLabel" aria-hidden="true"> <div class="modal-dialog" role="document"> <div class="modal-content"> <div class="modal-header"> <h5 class="modal-title" id="editDatasetsLabel">Edit Datasets</h5> <button type="button" class="close btn-close" data-bs-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <form action="" method="post"> <div class="modal-body paper-page-edit-dataset-modal"> <input type="hidden" name="csrfmiddlewaretoken" value="a5H2bRfmR6q9InTl91zwui0v1df1Od4fMz4F6yH7C5XZsiaIq4D2NC5eUamMBsVX"> <div id="div_id_introduced" class="form-group"> <label for="id_introduced" class=""> Add or remove datasets <b>introduced</b> in this paper: </label> <div class=""> <select name="introduced" data-container-css-class="" data-allow-clear="false" style="width: 100%" class="modelselect2multiple form-control" id="id_introduced" data-autocomplete-light-language="en" data-autocomplete-light-url="/dataset-autocomplete/" data-autocomplete-light-function="select2" multiple> </select><div style="display:none" class="dal-forward-conf" id="dal-forward-conf-for_id_introduced"><script type="text/dal-forward-conf">[{"type": "const", "val": true, "dst": "canonical_only"}, {"type": 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icon-wrapper icon-fa icon-fa-solid" data-name="plus-circle"><svg viewBox="0 0 512 514.999" xmlns="http://www.w3.org/2000/svg"><path d="M256 9.998c137 0 248 111 248 248s-111 248-248 248-248-111-248-248 111-248 248-248zm144 276v-56c0-6.6-5.4-12-12-12h-92v-92c0-6.6-5.4-12-12-12h-56c-6.6 0-12 5.4-12 12v92h-92c-6.6 0-12 5.4-12 12v56c0 6.6 5.4 12 12 12h92v92c0 6.6 5.4 12 12 12h56c6.6 0 12-5.4 12-12v-92h92c6.6 0 12-5.4 12-12z"/></svg></span> Add a new dataset here </a> </div> </div> </div> <div class="modal-footer"> <button type="submit" class="btn btn-primary" name="edit-datasets"> Save </button> </div> </form> </div> </div> </div> </template> <div class="container content content-buffer astro-buffer"> <main> <div class="paper-title"> <div class="row"> <div class="col-md-12"> <h1> MiSTree: a Python package for constructing and analysing Minimum Spanning Trees </h1> <div class="authors"> <p> <span class="author-span">18 Oct 2019</span>  路  <span class="author-span"> Naidoo Krishna</span> <span class="hidden-element">路 </span><button type="button" class="badge-edit" data-bs-toggle="modal" data-bs-toggle="modal" data-bs-target="#loginModal"> <span class=" icon-wrapper icon-fa icon-fa-solid" data-name="edit"><svg viewBox="0 0 576 514.999" xmlns="http://www.w3.org/2000/svg"><path d="M402.6 85.198l90.2 90.2c3.8 3.8 3.8 10 0 13.8l-218.399 218.4-92.8 10.3c-12.4 1.4-22.9-9.1-21.5-21.5l10.3-92.8 218.4-218.4c3.799-3.8 10-3.8 13.799 0zm162-22.9c15.2 15.2 15.2 39.9 0 55.2l-35.4 35.4c-3.8 3.8-10 3.8-13.8 0l-90.2-90.2c-3.8-3.8-3.8-10 0-13.8l35.4-35.4c15.3-15.2 40-15.2 55.2 0zM384 348.198c0-3.2 1.3-6.2 3.5-8.5l40-40c7.6-7.5 20.5-2.2 20.5 8.5v157.8c0 26.5-21.5 48-48 48H48c-26.5 0-48-21.5-48-48v-352c0-26.5 21.5-48 48-48h285.8c10.7 0 16.1 12.9 8.5 20.5l-40 40c-2.3 2.2-5.3 3.5-8.5 3.5H64v320h320v-101.8z"/></svg></span> <span>Edit social preview</span> </button> </p> </div> </div> </div> </div> <div class="paper-abstract"> <div class="row"> <div class="col-md-12"> <p> The minimum spanning tree (MST), a graph constructed from a distribution of points, draws lines between pairs of points so that all points are linked in a single skeletal structure that contains no loops and has minimal total edge length. The MST has been used in a broad range of scientific fields such as particle physics (to distinguish classes of events in collider collisions), in astronomy (to detect mass segregation in star clusters) and cosmology (to search for filaments in the cosmic web). Its success in these fields has been driven by its sensitivity to the spatial distribution of points and the patterns within. MiSTree, a public Python package, allows a user to construct the MST in a variety of coordinates systems, including Celestial coordinates used in astronomy. The package enables the MST to be constructed quickly by initially using a k-nearest neighbour graph (kNN, rather than a matrix of pairwise distances) which is then fed to Kruskal's algorithm to construct the MST. MiSTree enables a user to measure the statistics of the MST and provides classes for binning the MST statistics (into histograms) and plotting the distributions. Applying the MST will enable the inclusion of high-order statistics information from the cosmic web which can provide additional information to improve cosmological parameter constraints. This information has not been fully exploited due to the computational cost of calculating N-point statistics. MiSTree was designed to be used in cosmology but could be used in any field which requires extracting non-Gaussian information from point distributions. 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