diff --git a/compute/core/src/pdf/runLayoutModel.ts b/compute/core/src/pdf/runLayoutModel.ts
index c97dd6b..5c726e0 100644
--- a/compute/core/src/pdf/runLayoutModel.ts
+++ b/compute/core/src/pdf/runLayoutModel.ts
@@ -286,11 +286,29 @@ export async function runLayoutModel(input: RunLayoutInput): Promise<LayoutRegio
     const logits = output.logits?.data as Float32Array | undefined;
     const predBoxes = output.pred_boxes?.data as Float32Array | undefined;
     if (!logits || !predBoxes) return [];
+    if (predBoxes.length === 0 && logits.length === 0) return [];
+    if (predBoxes.length === 0 || logits.length === 0) {
+      throw new Error(
+        `layout-model-invalid-output-shape: pred_boxes length=${predBoxes.length}, logits length=${logits.length}`,
+      );
+    }
 
-    const numQueries = Math.floor(predBoxes.length / 4);
-    if (numQueries <= 0) return [];
-    const classCount = Math.floor(logits.length / numQueries);
-    if (classCount <= 0) return [];
+    if (predBoxes.length % 4 !== 0) {
+      throw new Error(`layout-model-invalid-pred-box-shape: length ${predBoxes.length} is not divisible by 4`);
+    }
+    const numQueries = predBoxes.length / 4;
+    if (numQueries <= 0) {
+      throw new Error(`layout-model-invalid-pred-box-shape: expected positive query count, got ${numQueries}`);
+    }
+    if (logits.length % numQueries !== 0) {
+      throw new Error(
+        `layout-model-invalid-logit-shape: length ${logits.length} is not divisible by query count ${numQueries}`,
+      );
+    }
+    const classCount = logits.length / numQueries;
+    if (classCount <= 0) {
+      throw new Error(`layout-model-invalid-logit-shape: expected positive class count, got ${classCount}`);
+    }
     const regions: LayoutRegion[] = [];
 
     for (let queryIdx = 0; queryIdx < numQueries; queryIdx += 1) {
diff --git a/compute/core/tests/control-plane/run-layout-model.test.ts b/compute/core/tests/control-plane/run-layout-model.test.ts
index 490d0b4..e951bf3 100644
--- a/compute/core/tests/control-plane/run-layout-model.test.ts
+++ b/compute/core/tests/control-plane/run-layout-model.test.ts
@@ -133,4 +133,43 @@ describe('runLayoutModel', () => {
       expect.closeTo(40, 5),
     ]);
   });
+
+  test('drops unlabeled query winners and keeps only labeled regions', async () => {
+    mockState.runOutput = {
+      logits: {
+        data: new Float32Array([
+          0.1,
+          0.2,
+          5,
+          4,
+          0.1,
+          0.1,
+        ]),
+      },
+      pred_boxes: {
+        data: new Float32Array([
+          0.25, 0.25, 0.3, 0.3,
+          0.75, 0.75, 0.3, 0.3,
+        ]),
+      },
+    };
+
+    const { runLayoutModel } = await import('../../src/pdf/runLayoutModel');
+    const regions = await runLayoutModel({
+      pageWidth: 100,
+      pageHeight: 100,
+      textItems: [{} as never],
+      pageImage: Buffer.from([1]),
+    });
+
+    expect(regions).toHaveLength(1);
+    expect(regions[0]?.label).toBe('text');
+    expect(regions[0]?.confidence).toBeCloseTo(0.96109135, 5);
+    expect(regions[0]?.bbox).toEqual([
+      expect.closeTo(60, 5),
+      expect.closeTo(60, 5),
+      expect.closeTo(90, 5),
+      expect.closeTo(90, 5),
+    ]);
+  });
 });