def compute_cell_memory_similarity_stats(sim_dict, cond_ids):
# re-organize as hierachical dict
sim_stats = {cn: {'targ': {}, 'lure': {}} for cn in cond_ids.keys()}
# for DM, RM conditions...
for cond in ['DM', 'RM']:
# compute stats for target & lure activation
for m_type in sim_stats[cond].keys():
s_ = compute_stats(np.mean(sim_dict[cond][m_type], axis=-1))
sim_stats[cond][m_type]['mu'], sim_stats[cond][m_type]['er'] = s_
# for NM trials, only compute lure activations, since there is no target
s_ = compute_stats(np.mean(sim_dict['NM']['lure'], axis=-1))
sim_stats['NM']['lure']['mu'], sim_stats['NM']['lure']['er'] = s_
return sim_stats
def sep_by_qsource(matrix_p2, q_source_info, n_se=3):
"""separate values by query source and then compute statistics
Parameters
----------
matrix_p2 : type
Description of parameter `matrix_p2`.
q_source_info : type
Description of parameter `q_source_info`.
n_se : type
Description of parameter `n_se`.
Returns
-------
type
Description of returned object.
"""
stats = {}
# loop over sources
for q_source_name, q_source_id in q_source_info.items():
T_ = np.shape(q_source_id)[1]
mu_, er_ = np.zeros(T_, ), np.zeros(T_, )
# loop over time
for t in range(T_):
# compute stats
mu_[t], er_[t] = compute_stats(matrix_p2[q_source_id[:, t], t],
n_se=n_se)
# collect stats for this source
stats[q_source_name] = [mu_, er_]
return stats
def plot_time_course_for_all_conds(
matrix,
cond_ids,
ax,
n_se=2,
axis1_start=0,
xlabel=None,
ylabel=None,
title=None,
frameon=False,
add_legend=True,
):
for i, cond_name in enumerate(TZ_COND_DICT.values()):
submatrix_ = matrix[cond_ids[cond_name], axis1_start:]
M_, T_ = np.shape(submatrix_)
mu_, er_ = compute_stats(submatrix_, axis=0, n_se=n_se)
ax.errorbar(x=range(T_), y=mu_, yerr=er_, label=cond_name)
if add_legend:
ax.legend(frameon=frameon)
ax.set_title(title)
ax.set_ylabel(ylabel)
ax.set_xlabel(xlabel)
filenames = ['./data/soc-Epinions1/soc-Epinions1.txt']
g = analysis.load_graph(filenames[0], directed=True)
print('load graph: \t', int(divmod(time.time() - start, 60)[0]), 'min:', int(divmod(time.time() - start, 60)[1]),'s')
print('=====LSCC=====')
start_lscc = time.time()
lscc = analysis.calculate_largest_strongly_connected_comp(g)
print('calculate LSCC: \t', int(divmod(time.time() - start_lscc, 60)[0]), 'min:', int(divmod(time.time() - start, 60)[1]),'s')
print('LSCC edges: \t', lscc.num_edges())
print('LSCC nodes: \t', lscc.num_vertices())
lscc_dists = analysis.calculate_distances(lscc)
print('caluclate distances LSCC: \t', int(divmod(time.time() - start_lscc, 60)[0]), 'min:', int(divmod(time.time() - start, 60)[1]),'s')
s_median, s_mean, s_diam, s_eff_diam = analysis.compute_stats(lscc_dists)
print('median distance:\t', s_median)
print('mean distance:\t', s_mean)
print('diameter:\t', s_diam)
print('effective diameter:\t', s_eff_diam)
print('LSCC done: \t', int(divmod(time.time() - start_lscc, 60)[0]), 'min:', int(divmod(time.time() - start, 60)[1]),'s')
del lscc, lscc_dists
print('=====LWCC=====')
start_lwcc = time.time()
lwcc = analysis.calculate_largest_weakly_connected_comp(g)
print('calculate LWCC: \t', int(divmod(time.time() - start_lwcc, 60)[0]), 'min:', int(divmod(time.time() - start, 60)[1]),'s')
print('LWCC edges: \t', lwcc.num_edges())
print('LWCC nodes: \t', lwcc.num_vertices())
lwcc_dists = analysis.calculate_distances(lwcc)
p_rm_ob_rcl=p_rm_ob_rcl,
)
# sample
n_samples = 256
X, Y = task.sample(n_samples, to_torch=False)
# unpack
print(f'X shape: {np.shape(X)}, n_samples x T x x_dim')
print(f'Y shape: {np.shape(Y)}, n_samples x T x y_dim')
'''show uncertainty'''
dk_wm, dk_em = batch_compute_true_dk(X, task)
print(f'np.shape(dk_wm): {np.shape(dk_wm)}')
print(f'np.shape(dk_em): {np.shape(dk_em)}')
# compute stats
dk_em_mu, dk_em_er = compute_stats(dk_em)
dk_wm_mu, dk_wm_er = compute_stats(dk_wm)
# plot
f, ax = plt.subplots(1, 1, figsize=(7, 4))
ax.errorbar(x=range(len(dk_em_mu)),
y=1 - dk_em_mu,
yerr=dk_em_er,
label='w/ EM')
ax.errorbar(x=np.arange(n_param, n_param * task.n_parts),
y=1 - dk_wm_mu,
yerr=dk_wm_er,
label='w/o EM')
ax.axvline(n_param, color='grey', linestyle='--')
ax.set_title(f'Expected performance, delay = {pad_len} / {n_param}')
ax.set_xlabel('Time, 0 = prediction onset')
'''plot spatial pattern isc '''
c_pal = sns.color_palette('colorblind', n_colors=8)
# sns.palplot(c_pal)
color_id_pick = [0, 4]
c_pal = [c_pal[color_id] for color_id in color_id_pick]
# compute stats
n_se = 1
mu_ = {rcn: {cn: [] for cn in all_conds} for rcn in all_conds}
er_ = {rcn: {cn: [] for cn in all_conds} for rcn in all_conds}
for ref_cond in cond_ids.keys():
for cond in cond_ids.keys():
d_ = np.array(bs_bc_sisc[ref_cond][cond])
if len(d_) > 0:
mu_[ref_cond][cond], er_[ref_cond][cond] = compute_stats(np.mean(
d_, axis=1),
n_se=n_se)
# plot
f, ax = plt.subplots(1, 1, figsize=(7, 5))
color_id = 0
i_rc, ref_cond = 0, 'RM'
for i_c, cond in enumerate(['RM', 'DM']):
if i_c >= i_rc:
ax.errorbar(x=range(T_part),
y=mu_[ref_cond][cond][T_part:],
yerr=er_[ref_cond][cond][T_part:],
label=f'{ref_cond}-{cond}',
color=c_pal[color_id])
color_id += 1
def_prob=def_prob)
X, Y, Misc = task.sample(n_samples, to_torch=False, return_misc=True)
# compute inter-event similarity
similarity_matrix = compute_event_similarity_matrix(Y, normalize=True)
similarity_matrix_tril = similarity_matrix[np.tril_indices(n_samples,
k=-1)]
one_matrix = np.ones((n_samples, n_samples))
tril_mask = np.tril(one_matrix, k=-1).astype(bool)
tril_k_mask = np.tril(one_matrix, k=-task.similarity_cap_lag).astype(bool)
similarity_mask_recent = np.logical_and(tril_mask, ~tril_k_mask)
event_sims[i] = similarity_matrix[similarity_mask_recent]
'''plot'''
mu, se = compute_stats(event_sims, axis=1)
cps = sns.color_palette(n_colors=len(mu))
f, ax = plt.subplots(1, 1, figsize=(9, 6))
for i in range(n_conditions):
sns.kdeplot(event_sims[i], ax=ax, label=similarity_labels[i])
ax.legend()
for j, mu_j in enumerate(mu):
ax.axvline(mu_j, color=cps[j], linestyle='--', alpha=.6)
ax.set_title('Event similarity by condition')
ax.set_xlabel('Event similarity')
sns.despine()
f.tight_layout()
# x = [0, 1]
# x.pop(0)
# x.append(2)
actual_n_subjs = len(def_path_int_g)
# get the target memory activation for each subject
tma_dmp2_g = np.array([
ma_g[i_s]['DM']['targ']['mu'][n_param:]
for i_s in range(actual_n_subjs)
])
# split the data according to whether t is schematic ...
# ... for target memory activation
tma_s = ma.masked_array(tma_dmp2_g, np.logical_not(def_tps_g))
tma_ns = ma.masked_array(tma_dmp2_g, def_tps_g)
# compute mean
tma_s_mu[pi, dpi], tma_s_se[pi,
dpi] = compute_stats(np.mean(tma_s,
axis=1))
tma_ns_mu[pi,
dpi], tma_ns_se[pi,
dpi] = compute_stats(np.mean(tma_ns, axis=1))
# ... for the em gates
inpt_s_l, inpt_ns_l = [[] for t in range(T)], [[] for t in range(T)]
ms_s_l, ms_ns_l = [[] for t in range(T)], [[] for t in range(T)]
for i_s in range(actual_n_subjs):
n_trials = np.shape(targets_dmp2_g[i_s])[0]
# compute the proto time point mask for subj i
def_path_int_i_s_rep = np.tile(def_path_int_g[i_s], (n_trials, 1))
def_tps_g_i_s_rep = np.tile(def_tps_g[i_s], (n_trials, 1))
mask_s = def_tps_g_i_s_rep
inpt_s_ = inpt_dmp2_g[i_s][:, def_tps_g[i_s]]
ma_cos_list_nonone = remove_none(ma_cos_list)
n_actual_subjs = len(ma_cos_list_nonone)
ma_cos_mu = {cond: np.zeros(n_actual_subjs, ) for cond in all_cond}
ma_cos = {cond: np.zeros((n_actual_subjs, T)) for cond in all_cond}
for i_s in range(n_actual_subjs):
for c_i, c_name in enumerate(all_cond):
# average over time
ma_cos[c_name][i_s] = ma_cos_list_nonone[i_s][c_name]['lure'][
'mu'][T:]
ma_cos_mu[c_name][i_s] = np.mean(
ma_cos_list_nonone[i_s][c_name]['lure']['mu'][T:])
# compute stats across subjects
for c_i, c_name in enumerate(all_cond):
ma_cos_mumu[p_i][c_i], ma_cos_muse[p_i][c_i] = compute_stats(
ma_cos_mu[c_name])
ma_cos_tmu[p_i][c_i], ma_cos_tse[p_i][c_i] = compute_stats(
ma_cos[c_name])
# compute memory similarity
memory_sim_mu[p_i], memory_sim_se[p_i] = compute_stats(
remove_none(memory_sim_g))
'''plot the data'''
cpal = sns.color_palette("Blues", n_colors=len(all_cond))
f, ax = plt.subplots(1, 1, figsize=(6, 5))
for p_i, penalty_test in enumerate(penalty_test_list):
ax.errorbar(x=range(len(all_cond)),
y=ma_cos_mumu[p_i],
yerr=ma_cos_muse[p_i],
color=cpal[p_i])
for lca_pid, lca_pname in lca_pnames.items():
del lca_param[ptest][lca_pid][cond]['mu'][i_ms]
del lca_param[ptest][lca_pid][cond]['er'][i_ms]
del ma_lca[ptest][i_ms]
'''compute average meory activation'''
ma_dmp2, sum_ma_dmp2 = defaultdict(), defaultdict()
ma_dmp2_mu, ma_dmp2_se = defaultdict(), defaultdict()
for p_test in penaltys_test:
ma_dmp2[p_test] = np.array([
ma_lca[p_test][s]['DM']['targ']['mu'][n_param:]
for s in range(n_subjs)
])
sum_ma_dmp2[p_test] = np.sum(ma_dmp2[p_test], axis=1)
ma_dmp2_mu[p_test], ma_dmp2_se[p_test] = compute_stats(
# ma_dmp2[p_test]
np.mean(ma_dmp2[p_test], axis=1))
ax.errorbar(x=range(len(penaltys_test)),
y=list(ma_dmp2_mu.values()),
yerr=list(ma_dmp2_se.values()),
label=exp_name,
color=cpal[ei])
ax.set_xticks(range(len(penaltys_test)))
ax.set_xticklabels(penaltys_test)
ax.set_xlabel('Penalty, test')
ax.set_ylabel('Average memory activation')
ax.legend()
sns.despine()
f.tight_layout()
# load data
data_dict = pickle_load_dict(fpath)
Yhat_all = np.array(data_dict['Yhat_all'])
Yob_all = np.array(data_dict['Yob_all'])
o_keys_p1_all = data_dict['o_keys_p1_all']
o_keys_p2_all = data_dict['o_keys_p2_all']
'''visualize the results'''
# print(f'overall acc: {np.mean(Y_match)}')
Y_match = Yhat_all == Yob_all
Y_pred_match = np.logical_and(np.logical_and(
Yhat_all != -1, Yob_all != -1), Y_match)
np.shape(Yhat_all)
# compute the decoding accuracy OVER TIME, averaged across subjects
match_ovt_mu, match_ovt_se = compute_stats(
np.mean(np.mean(Y_match, axis=1), axis=0), axis=1)
pmatch_ovt_mu, pmatch_ovt_se = compute_stats(
np.mean(np.mean(Y_pred_match, axis=1), axis=0), axis=1)
f, axes = plt.subplots(1, 2, figsize=(12, 5))
axes[0].errorbar(
x=range(n_param), y=pmatch_ovt_mu[:n_param], xerr=pmatch_ovt_se[:n_param])
axes[0].errorbar(
x=range(n_param), y=match_ovt_mu[:n_param], xerr=match_ovt_se[:n_param])
axes[1].errorbar(
x=range(n_param), y=pmatch_ovt_mu[n_param:], xerr=pmatch_ovt_se[n_param:])
axes[1].errorbar(
x=range(n_param), y=match_ovt_mu[n_param:], xerr=match_ovt_se[n_param:])
axes[0].set_xlabel('Part 1')
axes[1].set_xlabel('Part 2')
sns.heatmap(similarity_matrix,
xticklabels=n_samples // 2,
yticklabels=n_samples // 2,
cmap='viridis',
ax=ax)
ax.set_xlabel('event i')
ax.set_ylabel('event j')
ax.set_title('inter-event similarity')
one_matrix = np.ones((n_samples, n_samples))
tril_mask = np.tril(one_matrix, k=-1).astype(bool)
tril_k_mask = np.tril(one_matrix, k=-task.similarity_cap_lag).astype(bool)
similarity_mask_recent = np.logical_and(tril_mask, ~tril_k_mask)
similarity_mask_distant = tril_k_mask
mu_rc, er_rc = compute_stats(similarity_matrix[similarity_mask_recent])
mu_dt, er_dt = compute_stats(similarity_matrix[similarity_mask_distant])
bar_height = [mu_rc, mu_dt]
bar_yerr = [er_rc, er_dt]
xticks = range(len(bar_height))
xlabs = ['recent', 'distant']
f, ax = plt.subplots(1, 1, figsize=(5, 4))
ax.bar(x=xticks, height=bar_height, yerr=bar_yerr)
ax.set_title('Event similarity')
ax.set_ylabel('Param overlap')
ax.set_xticks(xticks)
ax.set_xticklabels(xlabs)
sns.despine()
f.tight_layout()
'''plot the distribution (for the lower triangular part)'''