Future 6G wireless networks are expected to evolve toward AI-native systems that support intelligent, environment-aware services, including positioning and mapping. Current research has already integrated AI into several aspects of communication, particularly wireless channel estimation. However, most learning-based channel estimators focus on communication-oriented objectives rather than explicitly estimating multipath parameters such as delay, angle of arrival (AoA), and angle of departure (AoD). These parameters provide essential geometric information for downstream tasks including positioning and radio simultaneous localization and mapping (SLAM). In this work, we propose a Spectral-Convolutional Factorized Transformer (SCFT) for joint multipath component (MPC) estimation from noisy complex channel estimates and physical beam-pair descriptors. SCFT combines local spectral convolution, permutation-equivariant beam-set attention, and a query-based Transformer decoder to detect and classify line-of-sight and non-line-of-sight paths and estimate their observed delays, AoAs, and AoDs. Experiments on realistic ray-tracing data show that SCFT reduces the generalized optimal sub-pattern assignment error by 13.1% compared with ResNet, the strongest competing baseline. We further demonstrate this advantage in independent snapshot positioning and radio SLAM, where SCFT reduces position RMSE by 18.5% and 65.0%, respectively, relative to ResNet. These findings highlight the importance of explicitly recovering multipath geometry, as improvements in MPC estimation can translate into substantial gains in downstream tasks.

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