PPCA parens

src/dartsort/cluster/gaussian_mixture.py

@@ -453,10 +453,6 @@ def m_step(
 
         if self.use_proportions and likelihoods is not None:
             self.update_proportions(likelihoods)
-        if self.log_proportions is not None:
-            assert (
-                len(self.log_proportions) == unit_ids.max() + 1 + self.with_noise_unit
-            )
 
         fit_full_indices, fit_split_indices = quick_indices(
             self.rg,

src/dartsort/cluster/ppcalib.py

@@ -2,6 +2,7 @@
 from typing import Optional
 
 import linear_operator
+from linear_operator import operators
 from linear_operator.operators import CholLinearOperator
 import torch
 import torch.nn.functional as F
@@ -10,7 +11,7 @@
 
 from ..util.noise_util import EmbeddedNoise
 from .stable_features import SpikeFeatures, SpikeNeighborhoods
-from ..util import spiketorch
+from ..util import spiketorch, more_operators
 
 vecdot = torch.linalg.vecdot
 
@@ -29,7 +30,7 @@ def ppca_em(
     mean_prior_pseudocount=0.0,
     show_progress=False,
     W_initialization="svd",
-    normalize=False,
+    normalize=True,
     em_converged_atol=0.1,
     prior_var=1.0,
     cache_global_direct=True,
@@ -145,6 +146,7 @@ def ppca_em(
             break
         if show_progress:
             iters.set_description(f"PPCA[{dmu=:.2g}, {dW=:.2g}]")
+    print(i, dmu, dW)
 
     if normalize and any_missing and state["W"] is not None:
         _, _, state["W"], state["mu"] = embed(
@@ -156,6 +158,7 @@ def ppca_em(
             state["W"],
             state["mu"],
             active_channels=active_channels,
+            ess=ess,
             active_cov_chol_factor=active_cov_chol_factor,
             prior_var=prior_var,
             normalize=normalize,
@@ -216,18 +219,18 @@ def ppca_e_step(
     D = rank * nc
 
     # get normalized weights
-    y = sp.features
+    new_zeros = sp.features.new_zeros
 
     # we will build our outputs by iterating over the unique
     # neighborhoods and adding weighted sums of moments in each
-    e_y = y.new_zeros((rank, nc))
+    e_y = new_zeros((rank, nc))
     yc = e_u = e_ycu = e_uu = None
     if return_yc:
-        yc = y.new_zeros((n, rank, nc))
+        yc = new_zeros((n, rank, nc))
     if yes_pca:
-        e_u = y.new_zeros((M,))
-        e_ycu = y.new_zeros((rank, nc, M))
-        e_uu = y.new_zeros((M, M))
+        e_u = new_zeros((M,))
+        e_ycu = new_zeros((rank, nc, M))
+        e_uu = new_zeros((M, M))
 
     # helpful tensors to keep around
     if yes_pca:
@@ -257,8 +260,8 @@ def ppca_e_step(
                 W_m = active_W[:, nd.missing_subset].reshape(D - nd.D_neighb, M)
 
         if yes_pca:
-            ubar = full_ubar[nd.neighb_members]
-            uubar = full_uubar[nd.neighb_members]
+            ubar = full_ubar[nd.u_slice]
+            uubar = full_uubar[nd.u_slice]
 
         # actual data in neighborhood
         xcc = xc = nd.x - nu
@@ -312,7 +315,7 @@ def ppca_e_step(
         wx = nd.w_norm @ nd.x
         if nd.have_missing:
             wxbar_m = nd.w_norm @ xbar_m
-            ybar = y.new_zeros((rank, nc))
+            ybar = new_zeros((rank, nc))
             ybar[:, nd.active_subset] = wx.view(rank, nd.neighb_nc)
             ybar[:, nd.missing_subset] = wxbar_m.view(rank, nc - nd.neighb_nc)
         else:
@@ -324,7 +327,7 @@ def ppca_e_step(
         if nd.have_missing and yes_pca:
             wmxcu = nd.w_norm @ e_mxcu.reshape(nd.neighb_n_spikes, -1)
             wmxcu = wmxcu.view(e_mxcu.shape[1:])
-            ycubar = y.new_zeros((rank, nc, M))
+            ycubar = new_zeros((rank, nc, M))
             ycubar[:, nd.active_subset] = wxcu.view(rank, nd.neighb_nc, M)
             ycubar[:, nd.missing_subset] = wmxcu.view(rank, nc - nd.neighb_nc, M)
         elif yes_pca:
@@ -334,12 +337,12 @@ def ppca_e_step(
         if return_yc:
             if nd.have_missing:
                 xc = xc.view(nd.neighb_n_spikes, rank, nd.neighb_nc).mT
-                yc[nd.neighb_members[:, None], :, nd.active_subset[None, :]] = xc
+                yc[nd.u_slice][:, :, nd.active_subset[None, :]] = xc
                 xbar_m -= tnu
                 txc = xbar_m.view(nd.neighb_n_spikes, rank, nc - nd.neighb_nc).mT
-                yc[nd.neighb_members[:, None], :, nd.missing_subset[None, :]] = txc
+                yc[nd.u_slice][:, :, nd.missing_subset[None, :]] = txc
             else:
-                yc[nd.neighb_members] = xc.view(nd.neighb_n_spikes, rank, nd.neighb_nc)
+                yc[nd.u_slice] = xc.view(nd.neighb_n_spikes, rank, nd.neighb_nc)
 
         # accumulate results
         e_y += ybar
@@ -367,14 +370,18 @@ def embed(
     scratch=None,
 ):
     N = len(sp)
+    new_zeros = sp.features.new_zeros
+    device = sp.features.device
+    dtype = sp.features.dtype
+
     if scratch is not None:
         _ubar, _uubar = scratch
     else:
-        _ubar = sp.features.new_zeros((N, M))
+        _ubar = features.new_zeros((N, M))
         # if not normalize:
-        _uubar = sp.features.new_zeros(N, M, M)
-    # _T = sp.features.new_zeros((N, M, M))
-    eye_M = prior_var * torch.eye(M, device=sp.features.device, dtype=sp.features.dtype)
+        _uubar = features.new_zeros(N, M, M)
+    eye_M_ = torch.eye(M, device=device, dtype=dtype)
+    eye_M = prior_var * eye_M_
 
     for nd in neighb_data:
         nu = active_mean[:, nd.active_subset].reshape(nd.D_neighb)
@@ -388,14 +395,22 @@ def embed(
         # moments of embeddings
         # T_inv = eye_M + W_o.T @ nd.C_oo_chol.solve(W_o)
         T_inv = eye_M + W_o.T @ nd.C_oo_inv @ W_o
-        T = torch.linalg.inv(T_inv)
-        u_proj = nd.C_oo_inv @ W_o @ T
+        # root = operators.LowRankRootLinearOperator(W_o.T @ nd.C_oo_cholinv)
+        # print(f"{root.shape=} {I_M.shape=}")
+        # helper = root + I_M
+        # helper = operators.LowRankRootSumLinearOperator(I_M
+        # print(f"{T_inv.shape=}")
+        # T = helper.solve(eye_M_)
+        T, info = torch.linalg.inv_ex(T_inv)
+        u_proj = nd.C_oo_inv @ (W_o @ T)
         # ubar = Cooinvxc @ (W_o @ T)
-        ubar = xc @ u_proj
-        uubar = torch.baddbmm(T, ubar[:, :, None], ubar[:, None, :])
+        # ubar = xc @ u_proj
+        # uubar = torch.baddbmm(T, ubar[:, :, None], ubar[:, None, :])
 
-        _ubar[nd.neighb_members] = ubar
-        _uubar[nd.neighb_members] = uubar
+        # _ubar[nd.u_slice] = ubar
+        # _uubar[nd.u_slice] = uubar
+        torch.mm(xc, u_proj, out=_ubar[nd.u_slice])
+        torch.baddbmm(T, _ubar[nd.u_slice].unsqueeze(2), _ubar[nd.u_slice].unsqueeze(1), out=_uubar[nd.u_slice])
 
     if normalize:
         if active_cov_chol_factor is None:
@@ -412,14 +427,14 @@ def embed(
         # active_mean = active_mean + W @ um
 
         # whitening. need to do a GEVP to start...
-        S = (weights @ _uubar.view(N, M * M)).view(N, M, M)
+        S = (weights @ _uubar.view(N, M * M)).view(M, M)
         Dx, U = torch.linalg.eigh(S)
         Dx = Dx.flip(dims=(0,))
         U = U.flip(dims=(1,))
         U.mul_(sgn(U[0]))
         UDxrt = U * Dx.sqrt()
         rhs = Wflat @ UDxrt.T
-        gevp_W_right = torch.linalg.solve_triangular(active_cov_chol_factor, rhs)
+        gevp_W_right = torch.linalg.solve_triangular(active_cov_chol_factor, rhs, upper=False)
         gevp_W = gevp_W_right.T @ gevp_W_right
         # gevp_W = linear_operator.solve(lhs=rhs.T, input=active_cov, rhs=rhs)
         Dw, V = torch.linalg.eigh(gevp_W)
@@ -435,7 +450,8 @@ def embed(
         W @= W_tf
         _ubar @= u_tf
         _uubar = torch.einsum("nij,ip,jq->npq", _uubar, u_tf, u_tf)
-        active_mean.addmm_(W, um)
+        active_mean += W @ um
+        # .addmm_(W.view(-1, M), um.unsqueeze(1))
 
     return _ubar, _uubar, W, active_mean
 
@@ -449,11 +465,13 @@ class NeighborhoodPPCAData:
 
     C_oo: linear_operator.LinearOperator
     C_oo_chol: CholLinearOperator
+    C_oo_cholinv: torch.Tensor
     C_oo_inv: CholLinearOperator
     w: torch.Tensor
     w_norm: torch.Tensor
     x: torch.Tensor
     neighb_members: torch.Tensor
+    u_slice: torch.Tensor
 
     C_mo: Optional[torch.Tensor]
     active_subset: Optional[torch.Tensor]
@@ -516,14 +534,15 @@ def get_neighborhood_data(
 
     neighborhood_data = []
     ess = weights.sum()
+    n_start = 0
     for chans_tuple, chans_data in dedup_data.items():
         *info, xs, mems = chans_data
         nid, neighb_chans, active_subset, can_cache_by_neighborhood, have_missing = info
         if len(mems) > 1:
             x = torch.concatenate(xs)
             neighb_members = torch.concatenate(mems)
-            neighb_members, order = neighb_members.sort()
-            x = x[order]
+            # neighb_members, order = neighb_members.sort()
+            # x = x[order]
             nid = None
         else:
             x = xs[0]
@@ -578,16 +597,19 @@ def get_neighborhood_data(
             have_missing=have_missing,
             C_oo=C_oo,
             C_oo_chol=C_oo_chol,
+            C_oo_cholinv=Linv,
             C_oo_inv=C_oo_inv,
             w=w,
             w_norm=w / ess,
             x=x,
             neighb_members=neighb_members,
+            u_slice=slice(n_start, n_start + n_neighb),
             C_mo=C_mo,
             active_subset=active_subset,
             missing_subset=missing_subset,
         )
         neighborhood_data.append(nd)
+        n_start += n_neighb
 
     return neighborhood_data