Balsa wood defects can resemble natural grain, making successful detection insufficient to establish precise localization or robustness to acquisition changes. This study investigates these limitations using the previously published YOLOv11–BiFPN–DAAF framework as a reference for analyzing adaptive multiscale attention. On a 508-image industrial dataset, five training seeds support selected-IoU evaluation, geometric box-error analysis, stratification by defect size, contrast, and elongation, and controlled comparisons of within-scale attention and mixing operators. Robustness is assessed under 15 brightness, contrast, noise, blur, and compression conditions and an external production campaign. Relative to YOLOv11, the complete framework increases internal-test AP from 0.865 to 0.892 at IoU 0.50, from 0.385 to 0.442 at IoU 0.75, and from 0.082 to 0.125 at IoU 0.90, while reducing mean geometric errors among matched detections. It improves mAP@0.5:0.95 by 0.035 (paired-seed 95% CI: 0.03061–0.03939) and exhibits smaller mean degradation under every tested perturbation, while external mAP@0.5:0.95 decreases from the internal value of 0.384 to 0.358. In the within-scale ablation, learned gating exceeds fixed mixing by 0.003 in mean mAP@0.5:0.95 (0.384 versus 0.381), with additional trainable capacity. Composite spatial-attention maps yield a concentration ratio of $4.8\pm 0.7$, indicating higher mean weights inside annotation boxes without establishing a causal suppression mechanism. Paired statistical analyses distinguish training-seed variability from test-panel uncertainty. The findings identify localization gains, acquisition sensitivities, and the observed contribution of adaptive refinement within the established architecture. They support further evaluation of difficult defects and independent production domains rather than unrestricted generalization claims.

Transmembrane proteins (TMPs) constitute approximately 30% of the mammalian proteome and are critical targets in biomedical research due to their involvement in signaling, transport, and drug interactions. However, their unique structural characteristics pose significant challenges for conventional multiple sequence alignment (MSA) methods, which are typically optimized for soluble proteins. In this paper, we propose TMP-M2Align, a novel topology-aware multiobjective algorithm specifically designed for the multiple alignment of TMPs. The method simultaneously optimizes two complementary objectives: (i) a topology-aware Sum-of-Pairs (SPs) score that integrates region-specific substitution matrices and gap penalties, and (ii) an Aligned Regions (ARs) score that rewards consistent alignment of functional and topological domains. By combining these objectives, TMP-M2Align generates Pareto front approximations of alignment solutions, enabling researchers to select trade-offs that best suit their biological questions. We evaluated TMP-M2Align on BAliBASE Reference Set 7 and on complete datasets of human G protein-coupled receptors (GPCRs) from classes A, B1, and C. Experimental results demonstrate that TMP-M2Align consistently outperforms both traditional alignment tools and specialized TM-specific methods in terms of SPs and Total Column metrics. Moreover, qualitative topological analyses confirm that TMP-M2Align preserves the integrity of transmembrane helices and loop boundaries more effectively than competing approaches. These findings highlight the effectiveness of integrating topology-aware scoring with multiobjective optimization for achieving accurate and biologically meaningful alignments of TMPs.

Transmembrane proteins (TMPs) constitute approximately 30% of the mammalian proteome and are critical targets in biomedical research due to their involvement in signaling, transport, and drug interactions. However, their unique structural characteristics pose significant challenges for conventional multiple sequence alignment (MSA) methods, which are typically optimized for soluble proteins. In this paper, we propose TMP-M2Align, a novel topology-aware multiobjective algorithm specifically designed for the multiple alignment of TMPs. The method simultaneously optimizes two complementary objectives: (i) a topology-aware Sum-of-Pairs (SP) score that integrates region-specific substitution matrices and gap penalties, and (ii) an Aligned Regions (AR) score that rewards consistent alignment of functional and topological domains. By combining these objectives, TMP-M2Align generates Pareto front approximations of alignment solutions, enabling researchers to select trade-offs that best suit their biological questions. We evaluated TMP-M2Align on BAliBASE Reference Set 7 and on complete datasets of human G protein-coupled receptors (GPCRs) from classes A, B1, and C. Experimental results demonstrate that TMP-M2Align consistently outperforms both traditional alignment tools and specialized TM-specific methods in terms of SP and Total Column metrics. Moreover, qualitative topological analyses confirm that TMP-M2Align preserves the integrity of transmembrane helices and loop boundaries more effectively than competing approaches. These findings highlight the effectiveness of integrating topology-aware scoring with multiobjective optimization for achieving accurate and biologically meaningful alignments of TMPs.