Log In Sign Up
Models:
Amanda Davis
Amanda-D/
DeepPurpose
0
Downloads: 1
[4717e2]: / docs / build / doctrees / notes / encoder.doctree

Download this file

23 lines (23 with data), 15.8 kB 

Äēź=Ćdocutils.nodesĒĆdocumentĒďĒ)ĀĒ}Ē(Ć	rawsourceĒĆĒĆchildrenĒ]ĒhĆsectionĒďĒ)ĀĒ}Ē(hhh]Ē(hĆtitleĒďĒ)ĀĒ}Ē(hĆDrug/Target EncoderĒh]ĒhĆTextĒďĒĆDrug/Target EncoderĒÖĒĀĒ}Ē(hhĆparentĒhhhĆsourceĒNĆlineĒNubaĆ
attributesĒ}Ē(ĆidsĒ]ĒĆclassesĒ]ĒĆnamesĒ]ĒĆdupnamesĒ]ĒĆbackrefsĒ]ĒuĆtagnameĒhhhhhhĆO/Users/futianfan/Downloads/spring2020/DeepPurpose/docs/source/notes/encoder.rstĒhKubh
)ĀĒ}Ē(hhh]Ē(h)ĀĒ}Ē(hĆ
Drug encodingĒh]ĒhĆ
Drug encodingĒÖĒĀĒ}Ē(hh0hh.hhhNhNubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hhh+hhhh*hKubhĆtableĒďĒ)ĀĒ}Ē(hhh]ĒhĆtgroupĒďĒ)ĀĒ}Ē(hhh]Ē(hĆcolspecĒďĒ)ĀĒ}Ē(hhh]Ēh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆcolwidthĒKuh)hFhhCubhG)ĀĒ}Ē(hhh]Ēh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆcolwidthĒK3uh)hFhhCubhĆtheadĒďĒ)ĀĒ}Ē(hhh]ĒhĆrowĒďĒ)ĀĒ}Ē(hhh]Ē(hĆentryĒďĒ)ĀĒ}Ē(hhh]ĒhĆ	paragraphĒďĒ)ĀĒ}Ē(hĆDrug EncodingsĒh]ĒhĆDrug EncodingsĒÖĒĀĒ}Ē(hhohhmubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK	hhhubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhhcubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆDescriptionĒh]ĒhĆDescriptionĒÖĒĀĒ}Ē(hhÜhhĄubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK	hhĀubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhhcubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahh^ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)h\hhCubhĆtbodyĒďĒ)ĀĒ}Ē(hhh]Ē(hb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆMorganĒh]ĒhĆMorganĒÖĒĀĒ}Ē(hhĪhhĮubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhh¨ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhh©ubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ"Extended-Connectivity FingerprintsĒh]ĒhĆ"Extended-Connectivity FingerprintsĒÖĒĀĒ}Ē(hh»hh∆ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhh√ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhh©ubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahh¶ubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆPubchemĒh]ĒhĆPubchemĒÖĒĀĒ}Ē(hhŤhhśubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhh„ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhhŗubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ'Pubchem Substructure-based FingerprintsĒh]ĒhĆ'Pubchem Substructure-based FingerprintsĒÖĒĀĒ}Ē(hhˇhhżubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhhķubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhhŗubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahh¶ubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆDaylightĒh]ĒhĆDaylightĒÖĒĀĒ}Ē(hjhjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK
hjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆDaylight-type fingerprintsĒh]ĒhĆDaylight-type fingerprintsĒÖĒĀĒ}Ē(hj6hj4ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK
hj1ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahh¶ubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆrdkit_2d_normalizedĒh]ĒhĆrdkit_2d_normalizedĒÖĒĀĒ}Ē(hjVhjTubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjQubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjNubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆNormalized DescriptastorusĒh]ĒhĆNormalized DescriptastorusĒÖĒĀĒ}Ē(hjmhjkubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjhubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjNubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahh¶ubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆCNNĒh]ĒhĆCNNĒÖĒĀĒ}Ē(hjćhjčubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjąubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjÖubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ&Convolutional Neural Network on SMILESĒh]ĒhĆ&Convolutional Neural Network on SMILESĒÖĒĀĒ}Ē(hj§hjĘubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjüubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjÖubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahh¶ubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆCNN_RNNĒh]ĒhĆCNN_RNNĒÖĒĀĒ}Ē(hjńhj¬ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjŅubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjľubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ$A GRU/LSTM on top of a CNN on SMILESĒh]ĒhĆ$A GRU/LSTM on top of a CNN on SMILESĒÖĒĀĒ}Ē(hjŘhjŔubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhj÷ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjľubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahh¶ubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆTransformerĒh]ĒhĆTransformerĒÖĒĀĒ}Ē(hjŻhjýubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjŲubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjůubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆTransformer Encoder on ESPFĒh]ĒhĆTransformer Encoder on ESPFĒÖĒĀĒ}Ē(hjhjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhj
ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjůubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahh¶ubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆMPNNĒh]ĒhĆMPNNĒÖĒĀĒ}Ē(hj2hj0ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhj-ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj*ubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆMessage-passing neural networkĒh]ĒhĆMessage-passing neural networkĒÖĒĀĒ}Ē(hjIhjGubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjDubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj*ubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahh¶ubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)h§hhCubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆcolsĒKuh)hAhh>ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆalignĒĆdefaultĒuh)h<hh+hhhh*hNubeh}Ē(h]ĒĆ
drug-encodingĒah!]Ēh#]ĒĆ
drug encodingĒah%]Ēh']Ēuh)h	hhhhhh*hKubh
)ĀĒ}Ē(hhh]Ē(h)ĀĒ}Ē(hĆTarget encodingĒh]ĒhĆTarget encodingĒÖĒĀĒ}Ē(hjÉhjĀhhhNhNubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hhj~hhhh*hKubh=)ĀĒ}Ē(hhh]ĒhB)ĀĒ}Ē(hhh]Ē(hG)ĀĒ}Ē(hhh]Ēh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆcolwidthĒKuh)hFhjíubhG)ĀĒ}Ē(hhh]Ēh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆcolwidthĒK3uh)hFhjíubh])ĀĒ}Ē(hhh]Ēhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆTarget EncodingsĒh]ĒhĆTarget EncodingsĒÖĒĀĒ}Ē(hjīhj≤ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjĮubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj¨ubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆDescriptionĒh]ĒhĆDescriptionĒÖĒĀĒ}Ē(hjňhj…ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhj∆ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj¨ubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahj©ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)h\hjíubh•)ĀĒ}Ē(hhh]Ē(hb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆAACĒh]ĒhĆAACĒÖĒĀĒ}Ē(hjŰhjÚubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjÔubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjžubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ#Amino acid composition up to 3-mersĒh]ĒhĆ#Amino acid composition up to 3-mersĒÖĒĀĒ}Ē(hjhj	ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjžubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjťubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ	PseudoAACĒh]ĒhĆ	PseudoAACĒÖĒĀĒ}Ē(hj+hj)ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhj&ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj#ubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆPseudo amino acid compositionĒh]ĒhĆPseudo amino acid compositionĒÖĒĀĒ}Ē(hjBhj@ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhj=ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj#ubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjťubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆConjoint_triadĒh]ĒhĆConjoint_triadĒÖĒĀĒ}Ē(hjbhj`ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhj]ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjZubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆConjoint triad featuresĒh]ĒhĆConjoint triad featuresĒÖĒĀĒ}Ē(hjyhjwubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjtubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjZubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjťubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ	Quasi-seqĒh]ĒhĆ	Quasi-seqĒÖĒĀĒ}Ē(hjôhjóubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjĒubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjĎubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆQuasi-sequence order descriptorĒh]ĒhĆQuasi-sequence order descriptorĒÖĒĀĒ}Ē(hjįhjģubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hKhjęubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjĎubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjťubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆCNNĒh]ĒhĆCNNĒÖĒĀĒ}Ē(hj–hjőubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK hjňubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj»ubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ*Convolutional Neural Network on target seqĒh]ĒhĆ*Convolutional Neural Network on target seqĒÖĒĀĒ}Ē(hjÁhjŚubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK hj‚ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj»ubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjťubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆCNN_RNNĒh]ĒhĆCNN_RNNĒÖĒĀĒ}Ē(hjhjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK!hjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjˇubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ(A GRU/LSTM on top of a CNN on target seqĒh]ĒhĆ(A GRU/LSTM on top of a CNN on target seqĒÖĒĀĒ}Ē(hjhjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK!hjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjˇubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjťubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆTransformerĒh]ĒhĆTransformerĒÖĒĀĒ}Ē(hj>hj<ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK"hj9ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj6ubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆTransformer Encoder on ESPFĒh]ĒhĆTransformer Encoder on ESPFĒÖĒĀĒ}Ē(hjUhjSubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK"hjPubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj6ubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjťubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)h§hjíubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆcolsĒKuh)hAhjŹubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ējtjuuh)h<hj~hhhh*hNubeh}Ē(h]ĒĆtarget-encodingĒah!]Ēh#]ĒĆtarget encodingĒah%]Ēh']Ēuh)h	hhhhhh*hKubh
)ĀĒ}Ē(hhh]Ē(h)ĀĒ}Ē(hĆ
Encoder ModelĒh]ĒhĆ
Encoder ModelĒÖĒĀĒ}Ē(hjćhjčhhhNhNubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hhjąhhhh*hK'ubh=)ĀĒ}Ē(hhh]ĒhB)ĀĒ}Ē(hhh]Ē(hG)ĀĒ}Ē(hhh]Ēh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆcolwidthĒKuh)hFhjúubhG)ĀĒ}Ē(hhh]Ēh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆcolwidthĒKCuh)hFhjúubh])ĀĒ}Ē(hhh]Ēhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ
Encoder ModelĒh]ĒhĆ
Encoder ModelĒÖĒĀĒ}Ē(hjĺhjľubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK*hjĻubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj∂ubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆDescriptionĒh]ĒhĆDescriptionĒÖĒĀĒ}Ē(hj’hj”ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK*hj–ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj∂ubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahj≥ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)h\hjúubh•)ĀĒ}Ē(hhh]Ē(hb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆCNNĒh]ĒhĆCNNĒÖĒĀĒ}Ē(hjĢhjŁubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK,hjýubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjŲubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ&Convolutional Neural Network on SMILESĒh]ĒhĆ&Convolutional Neural Network on SMILESĒÖĒĀĒ}Ē(hjhjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK,hjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjŲubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjůubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆCNN_RNNĒh]ĒhĆCNN_RNNĒÖĒĀĒ}Ē(hj5hj3ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK-hj0ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj-ubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ$A GRU/LSTM on top of a CNN on SMILESĒh]ĒhĆ$A GRU/LSTM on top of a CNN on SMILESĒÖĒĀĒ}Ē(hjLhjJubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK-hjGubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj-ubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjůubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆTransformerĒh]ĒhĆTransformerĒÖĒĀĒ}Ē(hjlhjjubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK.hjgubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjdubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆTransformer Encoder on SMILESĒh]ĒhĆTransformer Encoder on SMILESĒÖĒĀĒ}Ē(hjÉhjĀubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK.hj~ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjdubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjůubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆMPNNĒh]ĒhĆMPNNĒÖĒĀĒ}Ē(hj£hj°ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK/hjěubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjõubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ1Message Passing Neural Network on Molecular GraphĒh]ĒhĆ1Message Passing Neural Network on Molecular GraphĒÖĒĀĒ}Ē(hjļhjłubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK/hjĶubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhjõubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjůubhb)ĀĒ}Ē(hhh]Ē(hg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆMLPĒh]ĒhĆMLPĒÖĒĀĒ}Ē(hjŕhjōubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK0hj’ubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj“ubhg)ĀĒ}Ē(hhh]Ēhl)ĀĒ}Ē(hĆ/MultiLayer Perceptron on fix-dim feature vectorĒh]ĒhĆ/MultiLayer Perceptron on fix-dim feature vectorĒÖĒĀĒ}Ē(hjŮhjÔubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK0hjžubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hfhj“ubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hahjůubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)h§hjúubeh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆcolsĒKuh)hAhjôubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ējtjuuh)h<hjąhhhh*hNubeh}Ē(h]ĒĆ
encoder-modelĒah!]Ēh#]ĒĆ
encoder modelĒah%]Ēh']Ēuh)h	hhhhhh*hK'ubh
)ĀĒ}Ē(hhh]Ē(h)ĀĒ}Ē(hĆTechnical DetailsĒh]ĒhĆTechnical DetailsĒÖĒĀĒ}Ē(hj)hj'hhhNhNubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hhj$hhhh*hK<ubhl)ĀĒ}Ē(hĆ?First, we describe the common modules we import in DeepPurpose.Ēh]ĒhĆ?First, we describe the common modules we import in DeepPurpose.ĒÖĒĀĒ}Ē(hj7hj5hhhNhNubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']Ēuh)hkhh*hK?hj$hhubhĆ
literal_blockĒďĒ)ĀĒ}Ē(hĆĆimport torch
from torch.autograd import Variable
import torch.nn.functional as F
from torch import nn
import numpy as np
import pandas as pdĒh]ĒhĆĆimport torch
from torch.autograd import Variable
import torch.nn.functional as F
from torch import nn
import numpy as np
import pandas as pdĒÖĒĀĒ}Ē(hhhjEubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆ	xml:spaceĒĆpreserveĒĆforceĒČĆlanguageĒĆpythonĒĆhighlight_argsĒ}Ēuh)jChh*hKChj$hhubhĆcompoundĒďĒ)ĀĒ}Ē(hhh]ĒĆsphinx.addnodesĒĆtoctreeĒďĒ)ĀĒ}Ē(hhh]Ēh}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒhĆ
notes/encoderĒĆentriesĒ]Ē(NĆnotes/encoders/transformerĒÜĒNĆnotes/encoders/mpnnĒÜĒNĆnotes/encoders/cnnrnnĒÜĒNĆnotes/encoders/cnnĒÜĒNĆnotes/encoders/mlpĒÜĒeĆincludefilesĒ]Ē(jnjpjrjtjveĆmaxdepthĒKĆcaptionĒĆ$Links of details of various encodersĒĆglobĒąĆhiddenĒČĆ
includehiddenĒČĆnumberedĒKĆ
titlesonlyĒČĆ
rawentriesĒ]ĒĆ
rawcaptionĒj|uh)j`hh*hKQhj\ubah}Ē(h]Ēh!]ĒĆtoctree-wrapperĒah#]Ēh%]Ēh']Ēuh)jZhj$hhhh*hNubeh}Ē(h]ĒĆtechnical-detailsĒah!]Ēh#]ĒĆtechnical detailsĒah%]Ēh']Ēuh)h	hhhhhh*hK<ubeh}Ē(h]ĒĆdrug-target-encoderĒah!]Ēh#]ĒĆdrug/target encoderĒah%]Ēh']Ēuh)h	hhhhhh*hKubah}Ē(h]Ēh!]Ēh#]Ēh%]Ēh']ĒĆsourceĒh*uh)hĆcurrent_sourceĒNĆcurrent_lineĒNĆsettingsĒĆdocutils.frontendĒĆValuesĒďĒ)ĀĒ}Ē(hNĆ	generatorĒNĆ	datestampĒNĆsource_linkĒNĆ
source_urlĒNĆ
toc_backlinksĒhfĆfootnote_backlinksĒKĆ
sectnum_xformĒKĆstrip_commentsĒNĆstrip_elements_with_classesĒNĆ
strip_classesĒNĆreport_levelĒKĆ
halt_levelĒKĆexit_status_levelĒKĆdebugĒNĆwarning_streamĒNĆ	tracebackĒąĆinput_encodingĒĆ	utf-8-sigĒĆinput_encoding_error_handlerĒĆstrictĒĆoutput_encodingĒĆutf-8ĒĆoutput_encoding_error_handlerĒjĺĆerror_encodingĒĆUTF-8ĒĆerror_encoding_error_handlerĒĆbackslashreplaceĒĆ
language_codeĒĆenĒĆrecord_dependenciesĒNĆconfigĒNĆ	id_prefixĒhĆauto_id_prefixĒĆidĒĆ
dump_settingsĒNĆdump_internalsĒNĆdump_transformsĒNĆdump_pseudo_xmlĒNĆexpose_internalsĒNĆstrict_visitorĒNĆ_disable_configĒNĆ_sourceĒh*Ć_destinationĒNĆ
_config_filesĒ]ĒĆpep_referencesĒNĆpep_base_urlĒĆ https://www.python.org/dev/peps/ĒĆpep_file_url_templateĒĆpep-%04dĒĆrfc_referencesĒNĆrfc_base_urlĒĆhttps://tools.ietf.org/html/ĒĆ	tab_widthĒKĆtrim_footnote_reference_spaceĒČĆfile_insertion_enabledĒąĆraw_enabledĒKĆsyntax_highlightĒĆlongĒĆsmart_quotesĒąĆsmartquotes_localesĒ]ĒĆcharacter_level_inline_markupĒČĆdoctitle_xformĒČĆ
docinfo_xformĒKĆsectsubtitle_xformĒČĆembed_stylesheetĒČĆcloak_email_addressesĒąĆenvĒNubĆreporterĒNĆindirect_targetsĒ]ĒĆsubstitution_defsĒ}ĒĆsubstitution_namesĒ}ĒĆrefnamesĒ}ĒĆrefidsĒ}ĒĆnameidsĒ}Ē(jôjĖj{jxjÖjāj!jjĎjéuĆ	nametypesĒ}Ē(jôNj{NjÖNj!NjĎNuh}Ē(jĖhjxh+jāj~jjąjéj$uĆ
footnote_refsĒ}ĒĆ
citation_refsĒ}ĒĆ
autofootnotesĒ]ĒĆautofootnote_refsĒ]ĒĆsymbol_footnotesĒ]ĒĆsymbol_footnote_refsĒ]ĒĆ	footnotesĒ]ĒĆ	citationsĒ]ĒĆautofootnote_startĒKĆsymbol_footnote_startĒKĆ
id_counterĒĆcollectionsĒĆCounterĒďĒ}ĒÖĒRĒĆparse_messagesĒ]ĒĆtransform_messagesĒ]ĒĆtransformerĒNĆ
decorationĒNhhub.