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BayesSpace v1.11.3 #111

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6b73168
fix: bugs when reading H5
Jun 3, 2023
3c8d3a9
fix: bugs
Jun 4, 2023
5f73f19
fix: bugs
Jun 5, 2023
86de359
fix: added sinity check and core tuning
senbaikang Jul 5, 2023
3c0f502
doc: updated doc
senbaikang Jul 5, 2023
40fdaa1
fix: fixed bugs & faster code
senbaikang Sep 7, 2023
e20e5a3
feat: adaptive mcmc
senbaikang Sep 11, 2023
d6abb37
feat: adaptive mcmc
senbaikang Sep 20, 2023
7186e72
feat: adaptive MCMC
senbaikang Sep 22, 2023
94a9df0
feat: label adjustment
senbaikang Sep 25, 2023
7129c45
fix: bugs
senbaikang Oct 4, 2023
e25d9b2
feat: option for restricted adaptive MCMC
senbaikang Oct 5, 2023
a9c094e
fix: [v1.11.7] bugs in func
senbaikang Dec 8, 2023
b5bd8f2
fix: bugs
senbaikang Feb 6, 2024
f69e023
fix: [v1.11.8] bugs in processing z
senbaikang Feb 16, 2024
6d02fdf
fix: [v1.11.8] bugs in processing z
senbaikang Feb 16, 2024
483645e
fix: bug
senbaikang Feb 19, 2024
65736e4
fix: updated outdated functions
senbaikang Feb 19, 2024
98c1d15
fix: updated outdated functions
senbaikang Feb 19, 2024
8d34497
fix: updated outdated functions
senbaikang Feb 19, 2024
2190e56
feat: [v1.11.10] refactored neighbor finding for subspots
senbaikang Mar 7, 2024
554b98b
fix: bugs
senbaikang Mar 7, 2024
79e11b9
Support for VisiumHD (#1)
senbaikang Mar 7, 2024
fc0d4c7
fix: bugs
senbaikang Mar 8, 2024
4a347ce
fix: cleaned up coords assignment for subspots
senbaikang Mar 13, 2024
6140799
fix: bug in plotting clusters
senbaikang Mar 13, 2024
06b5cf6
feat: [v1.13.1] plot clusters align with the image
senbaikang Mar 14, 2024
ec91302
fix: bugs
senbaikang Mar 14, 2024
d7ad525
feat: [v1.13.2] parallelized PCA
senbaikang Mar 18, 2024
6b28b43
feat: [v1.13.2] removed unrelated probes; parallized modeling of gene…
senbaikang Mar 19, 2024
db2d58d
feat: [v1.13.4] thining in c++ code
senbaikang Mar 20, 2024
dff61c8
fix: bugs
senbaikang Mar 24, 2024
18be765
feat: [v1.13.5] customized number of subspots
senbaikang Mar 25, 2024
9a5f742
fix: bugs
senbaikang Mar 25, 2024
d3e9275
doc: updated doc
senbaikang Mar 26, 2024
1fc79ae
fix: typo
senbaikang Apr 2, 2024
b9640f9
feat: [v1.13.6] added a few helper functions
senbaikang Apr 8, 2024
df216c1
fix: bugs
senbaikang Oct 15, 2024
0d6b7ac
doc: update NEWS
senbaikang Oct 15, 2024
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fix: bugs
  • Loading branch information
senbaikang committed Oct 4, 2023
commit 7129c455120849a5fbfdc21fa22bf55e74b4325a
12 changes: 7 additions & 5 deletions src/cluster.cpp
Original file line number Diff line number Diff line change
@@ -51,13 +51,11 @@ adaptive_mcmc(
const double step_size =
std::min(1.0, samples.n_elem * std::pow(curr_iter, -2.0 / 3));

const mat sample_mtx = resize(samples, samples.n_elem, 1);

return chol(
adaptive_mtx *
(identity_mtx +
step_size * (accpetance_rate - target_acceptance_rate) * sample_mtx *
sample_mtx.t() / accu(samples % samples)) *
(identity_mtx + step_size *
(accpetance_rate - target_acceptance_rate) *
samples.t() * samples / accu(samples % samples)) *
adaptive_mtx.t(),
"lower"
);
@@ -810,6 +808,10 @@ iterate_deconv(
const mat Y_j_prev = Y.rows(j0_vector * n0 + j0);
mat error_j = error.rows(j0_vector * n0 + j0);

if (i > 10 && j0 == 0) {
std::cout << "i = " << i << ":\n" << adaptive_mtx[0] << std::endl;
}

if (jitter_scale == 0.0) {
for (int r = 0; r < subspots; r++) {
error_j.row(r) = trans(