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ÇĽîdocutils.nodesöîdocumentöôö)üö}ö(î	rawsourceöîöîchildrenö]öhîsectionöôö)üö}ö(hhh]ö(hîtitleöôö)üö}ö(hî%Message Passing Neural Network (MPNN)öh]öhîTextöôöî%Message Passing Neural Network (MPNN)öůöüö}ö(hhîparentöhhhîsourceöNîlineöNubaî
attributesö}ö(îidsö]öîclassesö]öînamesö]öîdupnamesö]öîbackrefsö]öuîtagnameöhhhhhhîL/Users/futianfan/Downloads/spring2020/DeepPurpose/docs/source/notes/mpnn.rstöhKubhî
literal_blocköôö)üö}ö(hî,class DeepPurpose.models.MPNN(nn.Sequential)öh]öhî,class DeepPurpose.models.MPNN(nn.Sequential)öůöüö}ö(hhhh-ubah}ö(h]öh!]öh#]öh%]öh']öî	xml:spaceöîpreserveöîforceöëîlanguageöîpythonöîhighlight_argsö}öuh)h+hh*hKhhhhubhî	paragraphöôö)üö}ö(hîä`Message Passing Neural Network (MPNN) <https://www.biorxiv.org/content/10.1101/684662v3>`_ encode drug in its graph representation.öh]ö(hî	referenceöôö)üö}ö(hî[`Message Passing Neural Network (MPNN) <https://www.biorxiv.org/content/10.1101/684662v3>`_öh]öhî%Message Passing Neural Network (MPNN)öůöüö}ö(hî%Message Passing Neural Network (MPNN)öhhJubah}ö(h]öh!]öh#]öh%]öh']öînameöî%Message Passing Neural Network (MPNN)öîrefuriöî0https://www.biorxiv.org/content/10.1101/684662v3öuh)hHhhDubhîtargetöôö)üö}ö(hî3 <https://www.biorxiv.org/content/10.1101/684662v3>öh]öh}ö(h]öîid1öah!]öh#]öî%message passing neural network (mpnn)öah%]öh']öîrefuriöh\uh)h]î
referencedöKhhDubhî) encode drug in its graph representation.öůöüö}ö(hî) encode drug in its graph representation.öhhDhhhNhNubeh}ö(h]öh!]öh#]öh%]öh']öuh)hBhh*hKhhhhubhC)üö}ö(hî"**constructor** create MPNN class.öh]ö(hîstrongöôö)üö}ö(hî**constructor**öh]öhîconstructoröůöüö}ö(hhhh~ubah}ö(h]öh!]öh#]öh%]öh']öuh)h|hhxubhî create MPNN class.öůöüö}ö(hî create MPNN class.öhhxhhhNhNubeh}ö(h]öh!]öh#]öh%]öh']öuh)hBhh*hKhhhhubh,)üö}ö(hî,__init__(self, mpnn_hidden_size, mpnn_depth)öh]öhî,__init__(self, mpnn_hidden_size, mpnn_depth)öůöüö}ö(hhhhŚubah}ö(h]öh!]öh#]öh%]öh']öh;h<h=ëh>îpythonöh@}öuh)h+hh*hKhhhhubhîbullet_listöôö)üö}ö(hhh]ö(hî	list_itemöôö)üö}ö(hîe**mpnn_hidden_size** (int) - specify dimension of hidden layer in MPNN, e.g,  mpnn_hidden_size = 256.öh]öhC)üö}ö(hh░h]ö(h})üö}ö(hî**mpnn_hidden_size**öh]öhîmpnn_hidden_sizeöůöüö}ö(hhhhÁubah}ö(h]öh!]öh#]öh%]öh']öuh)h|hh▓ubhîQ (int) - specify dimension of hidden layer in MPNN, e.g,  mpnn_hidden_size = 256.öůöüö}ö(hîQ (int) - specify dimension of hidden layer in MPNN, e.g,  mpnn_hidden_size = 256.öhh▓ubeh}ö(h]öh!]öh#]öh%]öh']öuh)hBhh*hKhh«ubah}ö(h]öh!]öh#]öh%]öh']öuh)hČhhęhhhh*hNubhş)üö}ö(hîF**mpnn_depth** (int) - specify depth of MPNN, e.g.,  mpnn_depth = 3.

öh]öhC)üö}ö(hîD**mpnn_depth** (int) - specify depth of MPNN, e.g.,  mpnn_depth = 3.öh]ö(h})üö}ö(hî**mpnn_depth**öh]öhî
mpnn_depthöůöüö}ö(hhhh▄ubah}ö(h]öh!]öh#]öh%]öh']öuh)h|hhěubhî6 (int) - specify depth of MPNN, e.g.,  mpnn_depth = 3.öůöüö}ö(hî6 (int) - specify depth of MPNN, e.g.,  mpnn_depth = 3.öhhěubeh}ö(h]öh!]öh#]öh%]öh']öuh)hBhh*hKhhďubah}ö(h]öh!]öh#]öh%]öh']öuh)hČhhęhhhh*hNubeh}ö(h]öh!]öh#]öh%]öh']öîbulletöî*öuh)hžhh*hKhhhhubhC)üö}ö(hîB**Calling functions** implement the feedforward procedure of MPNN.öh]ö(h})üö}ö(hî**Calling functions**öh]öhîCalling functionsöůöüö}ö(hhhjubah}ö(h]öh!]öh#]öh%]öh']öuh)h|hjubhî- implement the feedforward procedure of MPNN.öůöüö}ö(hî- implement the feedforward procedure of MPNN.öhjhhhNhNubeh}ö(h]öh!]öh#]öh%]öh']öuh)hBhh*hKhhhhubh,)üö}ö(hîforward(self, feature)öh]öhîforward(self, feature)öůöüö}ö(hhhj ubah}ö(h]öh!]öh#]öh%]öh']öh;h<h=ëh>îpythonöh@}öuh)h+hh*hKhhhhubhĘ)üö}ö(hhh]öhş)üö}ö(hî>**feature** (tuple of length 5)
      * **todo**
      *





öh]öhîdefinition_listöôö)üö}ö(hhh]öhîdefinition_list_itemöôö)üö}ö(hî2**feature** (tuple of length 5)
* **todo**
*





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definitionöôö)üö}ö(hhh]öhĘ)üö}ö(hhh]ö(hş)üö}ö(hî**todo**öh]öhC)üö}ö(hjkh]öh})üö}ö(hjkh]öhîtodoöůöüö}ö(hhhjpubah}ö(h]öh!]öh#]öh%]öh']öuh)h|hjmubah}ö(h]öh!]öh#]öh%]öh']öuh)hBhh*hK#hjiubah}ö(h]öh!]öh#]öh%]öh']öuh)hČhjfubhş)üö}ö(hhh]öh}ö(h]öh!]öh#]öh%]öh']öuh)hČhjfubeh}ö(h]öh!]öh#]öh%]öh']öjjuh)hžhh*hK#hjcubah}ö(h]öh!]öh#]öh%]öh']öuh)jahj>ubeh}ö(h]öh!]öh#]öh%]öh']öuh)j<hh*hK)hj9ubah}ö(h]öh!]öh#]öh%]öh']öuh)j7hj3ubah}ö(h]öh!]öh#]öh%]öh']öuh)hČhj0hhhNhNubah}ö(h]öh!]öh#]öh%]öh']öjjuh)hžhh*hK"hhhhubeh}ö(h]öî#message-passing-neural-network-mpnnöah!]öh#]öh%]öhhah']öuh)h	hhhhhh*hKhlKubah}ö(h]öh!]öh#]öh%]öh']öîsourceöh*uh)hîcurrent_sourceöNîcurrent_lineöNîsettingsöîdocutils.frontendöîValuesöôö)üö}ö(hNî	generatoröNî	datestampöNîsource_linköNî
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language_codeöîenöîrecord_dependenciesöNîconfigöNî	id_prefixöhîauto_id_prefixöîidöî
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_config_filesö]öîpep_referencesöNîpep_base_urlöî https://www.python.org/dev/peps/öîpep_file_url_templateöîpep-%04döîrfc_referencesöNîrfc_base_urlöîhttps://tools.ietf.org/html/öî	tab_widthöKîtrim_footnote_reference_spaceöëîfile_insertion_enabledöłîraw_enabledöKîsyntax_highlightöîlongöîsmart_quotesöłîsmartquotes_localesö]öîcharacter_level_inline_markupöëîdoctitle_xformöëî
docinfo_xformöKîsectsubtitle_xformöëîembed_stylesheetöëîcloak_email_addressesöłîenvöNubîreporteröNîindirect_targetsö]öîsubstitution_defsö}öîsubstitution_namesö}öîrefnamesö}öîrefidsö}öînameidsö}öî%message passing neural network (mpnn)öhesî	nametypesö}öjłsh}ö(jŞhheh_uî
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autofootnotesö]öîautofootnote_refsö]öîsymbol_footnotesö]öîsymbol_footnote_refsö]öî	footnotesö]öî	citationsö]öîautofootnote_startöKîsymbol_footnote_startöKî
id_counteröîcollectionsöîCounteröôö}öjţKsůöRöîparse_messagesö]öhîsystem_messageöôö)üö}ö(hhh]öhC)üö}ö(hîHDuplicate implicit target name: "message passing neural network (mpnn)".öh]öhîLDuplicate implicit target name: ÔÇťmessage passing neural network (mpnn)ÔÇŁ.öůöüö}ö(hhhjCubah}ö(h]öh!]öh#]öh%]öh']öuh)hBhj@ubah}ö(h]öh!]öh#]öh%]öh']öheaîlevelöKîtypeöîINFOöîsourceöh*îlineöKuh)j>hhhhhh*hK
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