LinAlgError: SVD did not converge

[Li-ZhiD]

Run morpho_align_transformation after harmony:

transformation = st.align.morpho_align_transformation(
    models=adatas,
    spatial_key='spatial',
    key_added='spateo_spatial',
    device='cpu',
    verbose=False,
    rep_layer='X_pca_harmony',
    rep_field='obsm',
    dissimilarity='kl'
)

error:

---------------------------------------------------------------------------
LinAlgError                               Traceback (most recent call last)
Cell In[84], line 1
----> 1 transformation = st.align.morpho_align_transformation(
      2     models=adatas,
      3     spatial_key='spatial',
      4     key_added='spateo_spatial',
      5     device='cpu',
      6     verbose=False,
      7     rep_layer='X_pca_harmony',
      8     rep_field='obsm',
      9     dissimilarity='kl'
     10 )

File /mnt/data1/aaa/software/miniconda3/envs/spateo/lib/python3.9/site-packages/spateo/alignment/morpho_alignment.py:206, in morpho_align_transformation(models, models_path, save_transformation, transformation_path, resume, rep_layer, rep_field, genes, spatial_key, key_added, iter_key_added, vecfld_key_added, dissimilarity, max_iter, dtype, device, verbose, **kwargs)
    187     modelB = models[i + 1]
    189 morpho_model = Morpho_pairwise(
    190     sampleA=modelB,  # reverse
    191     sampleB=modelA,  # reverse
   (...)
    204     **kwargs,
    205 )
--> 206 _ = morpho_model.run()
    208 optimal_R, optimal_t = solve_RT_by_correspondence(
    209     morpho_model.optimal_RnA[:, :2], modelB.obsm[spatial_key][:, :2]
    210 )
    211 cur_transformation = {"Rotation": optimal_R, "Translation": optimal_t}

File /mnt/data1/aaa/software/miniconda3/envs/spateo/lib/python3.9/site-packages/torch/utils/_contextlib.py:116, in context_decorator.<locals>.decorate_context(*args, **kwargs)
    113 @functools.wraps(func)
    114 def decorate_context(*args, **kwargs):
    115     with ctx_factory():
--> 116         return func(*args, **kwargs)

File /mnt/data1/aaa/software/miniconda3/envs/spateo/lib/python3.9/site-packages/spateo/alignment/methods/morpho_class.py:291, in Morpho_pairwise.run(self)
    289     self.nonrigid_flag = True
    290     self._update_nonrigid()
--> 291 self._update_rigid()
    292 self.XAHat = self.VnA + self.RnA
    293 self._update_sigma2(iter=iter)

File /mnt/data1/aaa/software/miniconda3/envs/spateo/lib/python3.9/site-packages/spateo/alignment/methods/morpho_class.py:1369, in Morpho_pairwise._update_rigid(self)
   1364 if self.nn_init:
   1365     A -= (self.sigma2 * self.nn_init_weight * self.Sp / self.nx.sum(self.inlier_P)) * self.nx.dot(
   1366         (inlier_A_hat * self.inlier_P).T, -inlier_B_hat
   1367     ).T
-> 1369 svdU, svdS, svdV = _linalg(self.nx).svd(A)
   1370 self.C[-1, -1] = _linalg(self.nx).det(self.nx.dot(svdU, svdV))
   1372 R = self.nx.dot(self.nx.dot(svdU, self.C), svdV)

File /mnt/data1/aaa/software/miniconda3/envs/spateo/lib/python3.9/site-packages/numpy/linalg/linalg.py:1681, in svd(a, full_matrices, compute_uv, hermitian)
   1678         gufunc = _umath_linalg.svd_n_s
   1680 signature = 'D->DdD' if isComplexType(t) else 'd->ddd'
-> 1681 u, s, vh = gufunc(a, signature=signature, extobj=extobj)
   1682 u = u.astype(result_t, copy=False)
   1683 s = s.astype(_realType(result_t), copy=False)

File /mnt/data1/aaa/software/miniconda3/envs/spateo/lib/python3.9/site-packages/numpy/linalg/linalg.py:121, in _raise_linalgerror_svd_nonconvergence(err, flag)
    120 def _raise_linalgerror_svd_nonconvergence(err, flag):
--> 121     raise LinAlgError("SVD did not converge")

LinAlgError: SVD did not converge

[YifanLu2000]

Hi @Li-ZhiD, I suspect the issue is caused by using KL divergence, as "X_pca_harmony" contains negative values. I suggest setting dissimilarity to "cos" instead.