arXiv:2611.05400v1 Announce Type: cross Abstract: Thyroid nodules with indeterminate cytology (Bethesda III) carry an intermediate risk of malignancy, and molecular testing is widely used to decide between surgery and surveillance, but it is costly and not universally available. We investigated whether a convolutional neural network (CNN) applied to routine ultrasound images can stratify Bethesda III nodules, and how it compares and combines with molecular testing. We retrospectively identified 466 nodule records from 418 patients who underwent molecular testing (Afirma or ThyroSeq). A CNN pre-trained on determinate nodules was adapted to indeterminate nodules with soft labels and transfer learning. After removal of duplicate records, 119 nodules with surgical pathology were used for development and 47 were held out for testing. On the test set, the deep learning (DL) model achieved an AUC of 0.73 (95% CI 0.51-0.94), compared with 0.55 (0.38-0.71) for molecular testing (P = 0.15). At a cut-off inherited from the original algorithm, the DL model was more specific than molecular testing (0.95 vs 0.32; P < 0.001), with a higher positive predictive value (0.67 vs 0.21), a lower sensitivity (0.44 vs 0.78; P = 0.25) and a similar negative predictive value (0.88 vs 0.86). All six DL-positive test nodules were molecular-positive, and the DL output split the molecular-positive nodules into a high-risk (4/6 malignant) and a lower-risk group (3/27 malignant; P = 0.01). Surgical verification was strongly driven by the molecular result (99% of positive vs 19% of negative results), and molecular-test accuracy depended on the platform. A logistic regression of the DL output, nodule size and the molecular result dropped the DL term and did not improve on the DL output alone. Ultrasound DL complemented molecular testing for Bethesda III nodules, in particular by identifying molecular-positive nodules at lower risk of malignancy.