geneflowdecoder 0.1.3__tar.gz → 0.1.4__tar.gz

{geneflowdecoder-0.1.3/src/geneflowdecoder.egg-info → geneflowdecoder-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: geneflowdecoder
-Version: 0.1.3
+Version: 0.1.4
 Summary: Gene Transformer + Conditional Rectified Flow decoder from cell-state z to log1p expression X.
 Author: GeneFlowDecoder Contributors
 License: MIT

{geneflowdecoder-0.1.3 → geneflowdecoder-0.1.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "geneflowdecoder"
-version = "0.1.3"
+version = "0.1.4"
 description = "Gene Transformer + Conditional Rectified Flow decoder from cell-state z to log1p expression X."
 readme = "README.md"
 requires-python = ">=3.9"

{geneflowdecoder-0.1.3 → geneflowdecoder-0.1.4}/src/geneflowdecoder/_core.py

@@ -393,11 +393,19 @@ class GeneFlowDecoder(nn.Module):
         if self.freeze_z:
             z = z.detach()
         B, G = x_t.shape
-        t_emb = self.time_mlp(self._sincos(t)).unsqueeze(1)   # [B,1,d]
-        gids = self._gene_ids[:G].unsqueeze(0).expand(B, -1)  # 明确 [B,G]
-        h = self.backbone(gids, z) + t_emb
-        v = self.vel_proj(h)                                   # [B,G,1] 或 [B,G]
-        v = v.reshape(B, G)                                    # ← 强制对齐，根治错位
+        t_emb = self.time_mlp(self._sincos(t)).unsqueeze(1)        # [B,1,d]
+        gids = self._gene_ids[:G].unsqueeze(0).expand(B, -1)       # [B,G]
+        h = self.backbone(gids, z) + t_emb                         # [B,G,d]
+
+        # ★ 关键：只对特征维 d 做线性，结果天然是 [B, G]
+        v = self.vel_proj(h.squeeze(-2) if h.ndim == 2 else h)     # [B,G,d]→[B,G]
+        if v.ndim == 3:
+            v = v.squeeze(-1)                                      # [B,G,1]→[B,G]
+        if v.ndim != 2 or v.shape != (B, G):
+            raise RuntimeError(
+                f"_velocity shape bug: got {tuple(v.shape)}, expected ({B},{G}). "
+                f"检查 vel_proj 是否为 nn.Linear(d, 1) 而非 nn.Linear(d, n_genes)"
+            )
         return v
 
     # ----------------------------------------------------------------

{geneflowdecoder-0.1.3 → geneflowdecoder-0.1.4}/src/geneflowdecoder/_version.py

@@ -1,2 +1,2 @@
 # -*- coding: utf-8 -*-
-__version__ = "0.1.3"
+__version__ = "0.1.4"

{geneflowdecoder-0.1.3 → geneflowdecoder-0.1.4/src/geneflowdecoder.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: geneflowdecoder
-Version: 0.1.3
+Version: 0.1.4
 Summary: Gene Transformer + Conditional Rectified Flow decoder from cell-state z to log1p expression X.
 Author: GeneFlowDecoder Contributors
 License: MIT