def generate_df_results(molid, importances, dset, feats, model, calibration, lso):
cooccurrences, molids, expids, folds = molecules_coocurrences_df(dset=dset, feats=feats, model=model, lso=lso)
df_losses, folds_df = read_losses(dset=dset,
feats=feats,
model=model,
calibration=calibration,
lso=lso,
also_folds=True)
dico_for_df = defaultdict(dict)
MRDK = ManysourcesDataset(dset).mols()
for other_molid in molids:
if other_molid == molid:
continue
dico_for_df[other_molid] = {'importance': importances[np.where(molids == other_molid)[0][0]],
'cooc_loss': average_loss(molid,
other_molid,
cooccurrences,
molids,
expids,
df_losses),
'smiles': MolToSmiles(MRDK.molid2mol(other_molid))}
df = pd.DataFrame.from_dict(dico_for_df, orient='index')
df.index.names = ['molid']
df['relabsimportance'] = df.importance.abs() / df.importance.abs().sum()
return df[['relabsimportance', 'importance', 'smiles', 'cooc_loss']]
def do_for_one_molid(calibration, dset, feats, lso, model, molid, results_dir, rm_factory, by_source=False):
print molid
MRDK = ManysourcesDataset(dset).mols() # FIXME: this is read on each job, so once per molecule ATM...
# Train and evaluate the model
y, expids = get_y(molid, dset, feats, model, calibration, lso)
if not by_source:
X = get_X(molid, expids, dset, feats, model, lso)
else:
X = get_X_source(molid, expids, dset, feats, model) # makes no sense to run by source on LSO=False
X = ~X # coocurrences in train, less sparse, but better interpretation unless we tweak well the numbers...
rsquared, feat_weights, trained_model = build_and_validate_regression_model(X, y, model_factory=rm_factory)
rsquared = float(rsquared)
# REMOVE moldir shows r2
moldir = op.join(results_dir, 'r2=%.2f__%s' % (rsquared, molid))
ensure_dir(moldir)
# Save the model
pd.to_pickle(trained_model, op.join(moldir, 'model_trained_rsquare=%.2f.pkl' % rsquared))
# Save the smiles
smiles = MolToSmiles(MRDK.molid2mol(molid))
with open(op.join(moldir, 'smiles.txt'), 'w') as writer:
writer.write(smiles)
# Save the molecule-influence table
if not by_source:
df = generate_df_results(molid, feat_weights, dset, feats, model, calibration, lso)
pd.to_pickle(df, op.join(moldir, 'results_df.pkl'))
df.loc[molid] = (1E16, rsquared, smiles, np.mean(y)) # FIXME
df['label'] = map(MRDK.molid2label, df.index)
df = df[['label', 'relabsimportance', 'importance', 'smiles', 'cooc_loss']]
df = df.sort('relabsimportance', ascending=False)
df.head(20).to_html(op.join(moldir, 'results_df.html'))
else:
df = generate_df_results_source(molid, feat_weights, dset, feats, model, calibration, lso)
pd.to_pickle(df, op.join(moldir, 'results_df_bysource.pkl'))
df = df.sort('relabsimportance', ascending=False)
df.head(20).to_html(op.join(moldir, 'results_df_bysource.html'))
# Plot the distribution of losses (y)
plt.figure()
seaborn.distplot(y, bins=40)
plt.xlim((-0.05, 1.05))
plt.title('molid=%s, r2=%.2f' % (molid, rsquared))
plt.savefig(op.join(moldir, 'y_dist.png'), bbox_inches='tight')
plt.close()
# --- WIP gridspec with chemdeco pics and things like that
if not by_source:
show_top = 4
gs = gridspec.GridSpec(show_top, 2)
fig = plt.figure(figsize=(24, 16))
# Plot the molecule itself
ax_mol = fig.add_subplot(gs[0:show_top / 2, 0])
ax_mol.grid(False)
ax_mol.get_xaxis().set_ticks([])
ax_mol.get_yaxis().set_ticks([])
mol = MRDK.molid2mol(molid)
AllChem.Compute2DCoords(mol)
ax_mol.imshow(artdeco2(rdkit2im(mol, size=(400, 400)), color='red' if df.loc[molid]['label'] == 'INHIBITOR' else 'green', chorrada=5))
# Plot the distribution of losses
ax_distr = fig.add_subplot(gs[show_top / 2:0, 0])
seaborn.distplot(y, bins=40, ax=ax_distr)
# Plot the top (we should align all to a common scaffold and maybe highlight substructures that matter)
for rank, (inf_molid, row) in enumerate(df.iloc[1:show_top + 1].iterrows()):
ax_influential_mol = fig.add_subplot(gs[rank, 1])
ax_influential_mol.grid(False)
ax_influential_mol.get_xaxis().set_ticks([])
ax_influential_mol.get_yaxis().set_ticks([])
mol_color = 'red' if row['label'] == 'INHIBITOR' else 'green'
good_or_bad_color = 'red' if row['importance'] > 0 else 'green'
# add decos
mol = MRDK.molid2mol(inf_molid)
AllChem.Compute2DCoords(mol)
image = rdkit2im(mol)
image = artdeco1(image, decos=(('black', good_or_bad_color),))
image = artdeco2(image, color=mol_color)
ax_influential_mol.imshow(image)
ax_influential_mol.set_title('%s, inf=%.4f, cooc_loss=%.4f' %
(inf_molid, row['importance'], row['cooc_loss']))
# FIXME: cooc_loss also with stddev and standard error
fig.suptitle('%s, r2=%.2f, cooc_loss=%.4f +/- %.4f' % (molid, rsquared, float(np.mean(y)), float(np.std(y))))
plt.savefig(op.join(moldir, 'verde_que_te_quiero_verde.png'), bbox_inches='tight')
plt.close()
