Tags: ur-whitelab/exmol
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Easier usage of lime_explain (#105) * Fixed doc string * MACCS is default, saving is default behavior for plotting * descriptor_type is inferred for plotting * fixed svg display * only throw an error for ecfp * not saving for maccs and classic * fixed mypy complains * Made it still possible to save a figure * ran pre-commit * Bumpbed version Co-authored-by: Andrew White <white.d.andrew@gmail.com>
Add LIME explanations (#78) * Initial pass at getting descriptors * Removed redundant imports * Added a linear model with WLS, not sure if correct * Modifying RF notebook for LIME implementation, a long way to go.. * Added weighted t-statistic surrogate lime * Lime with counterfactuals, we need a regression example * LIME with CFs * Plot tstats * Added plotting code but doesn't work yet * Added plotting code that doesn't work yet * Added MACCS keys description, need to return MACCSfps in explain_lime * fixed MACCS key indexing, not assigning to examples yet * Refactored and added new svg code * Wrote new svg code * Added test for different sizes * Added SVG support to CFS * Refactored descriptors * Basic example working * Reworked svg code to be more robust * Removed debugging code * Added tuples to svg tests * Actual descriptor plots in _descriptor_layout * Features calculated as difference from base, plotting successful :) * Added two descriptor types, MACCS key description complete * Solubility model trained, shorter MACCS descriptions * tstat significance * Working notebooks * MACCSkeys read accurately * Updated MACCS descriptions and notebook plots * Fixed the sign for beta * removed descriptor plotting * ignoring temp images * LIME with updated weights * Sigmoid weights for lime * Using SVD with pseudo-inverse for xinv in WLS * method working - needs cleaning up! * MACCS key annotations * Added doc string for LIME functions * Will clean up on local computer * Remove nonzero weights and add plot descriptors function * Fixed scipy import * progress in notebook cleaning * Cleaned up notebooks * svg=False for _mol_images * Ran precommit * remove extra files * Replaced mordred descriptors with rdkit descriptors * fized return types and reading of atom_pols * fixed data file imports, using pickled file for maccs svgs * Added import-libresources to setup * add files to be installed? * Fixed how package data is installed - I think * changed as per setuptools instructions - might work? * CI has a problem with everything! * fixed most mypy issues * fixed modt mypy issues - forgot this file * Fixed ALLL mypy issues! * Added description and made argument names consistent * Added substructure descriptorscorresponding to the instance * mypy strikes! * Removed highlights from morganfp bits * fix classic plots * Fixed selfies encoder error * renamed the notebook dirs and added LIME nbs to github actions * Fixed rdkit argument and added tikhonov reg * Changed kernel name to be consistent with Geemi's notebooks * Use a smaller frac of data * CI doesn't like me :| * Make sure frags don't show up * Silly errors * I made sure everything runs.. CI, be nice! * Update changelog and version bump * Fixed svg not showing for ECFP fps * Renamed descriptor method * Added nbs to toc and added printed note for MACCS desc * training alphabet sometimes gave an error * return beta conditionally in lime_explain * Updated doc string and instructions on accessing t-statistics * Made test cover more examples * argument is return_beta * Added ecfp example to readme * Added ecfp example to readme * Changed demo image to contain ecfp instead of MACCS * Removed Bertz Ct and fixed parity plots * Changed code for RF to include heteroatoms * Rdkit MACCS fps has a dummy key at index 0 * Grammatical corrections Co-authored-by: Heta Gandhi <hetagandhi@Hetas-MacBook-Pro.local> Co-authored-by: Andrew White <white.d.andrew@gmail.com>