Acquisition of interpretable domain information during brain MR image harmonization for content-based image retrieval

Medical images like MR scans often show domain shifts across imaging sites due to scanner and protocol differences, which degrade machine learning performance in tasks such as disease classification. Domain harmonization is thus a critical research focus. Recent approaches encode brain images $\boldsymbol{x}$ into a low-dimensional latent space $\boldsymbol{z}$, then disentangle it into $\boldsymbol{z_u}$ (domain-invariant) and $\boldsymbol{z_d}$ (domain-specific), achieving strong results. However, these methods often lack interpretability$-$an essential requirement in medical applications$-$leaving practical issues unresolved. We propose Pseudo-Linear-Style Encoder Adversarial Domain Adaptation (PL-SE-ADA), a general framework for domain harmonization and interpretable representation learning that preserves disease-relevant information in brain MR images. PL-SE-ADA includes two encoders $f_E$ and $f_{SE}$ to extract $\boldsymbol{z_u}$ and $\boldsymbol{z_d}$, a decoder to reconstruct the image $f_D$, and a domain predictor $g_D$. Beyond adversarial training between the encoder and domain predictor, the model learns to reconstruct the input image $\boldsymbol{x}$ by summing reconstructions from $\boldsymbol{z_u}$ and $\boldsymbol{z_d}$, ensuring both harmonization and informativeness. Compared to prior methods, PL-SE-ADA achieves equal or better performance in image reconstruction, disease classification, and domain recognition. It also enables visualization of both domain-independent brain features and domain-specific components, offering high interpretability across the entire framework.

iCBIR-Sli: Interpretable Content-Based Image Retrieval with 2D Slice Embeddings

Current methods for searching brain MR images rely on text-based approaches, highlighting a significant need for content-based image retrieval (CBIR) systems. Directly applying 3D brain MR images to machine learning models offers the benefit of effectively learning the brain's structure; however, building the generalized model necessitates a large amount of training data. While models that consider depth direction and utilize continuous 2D slices have demonstrated success in segmentation and classification tasks involving 3D data, concerns remain. Specifically, using general 2D slices may lead to the oversight of pathological features and discontinuities in depth direction information. Furthermore, to the best of the authors' knowledge, there have been no attempts to develop a practical CBIR system that preserves the entire brain's structural information. In this study, we propose an interpretable CBIR method for brain MR images, named iCBIR-Sli (Interpretable CBIR with 2D Slice Embedding), which, for the first time globally, utilizes a series of 2D slices. iCBIR-Sli addresses the challenges associated with using 2D slices by effectively aggregating slice information, thereby achieving low-dimensional representations with high completeness, usability, robustness, and interoperability, which are qualities essential for effective CBIR. In retrieval evaluation experiments utilizing five publicly available brain MR datasets (ADNI2/3, OASIS3/4, AIBL) for Alzheimer's disease and cognitively normal, iCBIR-Sli demonstrated top-1 retrieval performance (macro F1 = 0.859), comparable to existing deep learning models explicitly designed for classification, without the need for an external classifier. Additionally, the method provided high interpretability by clearly identifying the brain regions indicative of the searched-for disease.

Domain-invariant feature learning in brain MR imaging for content-based image retrieval

When conducting large-scale studies that collect brain MR images from multiple facilities, the impact of differences in imaging equipment and protocols at each site cannot be ignored, and this domain gap has become a significant issue in recent years. In this study, we propose a new low-dimensional representation (LDR) acquisition method called style encoder adversarial domain adaptation (SE-ADA) to realize content-based image retrieval (CBIR) of brain MR images. SE-ADA reduces domain differences while preserving pathological features by separating domain-specific information from LDR and minimizing domain differences using adversarial learning. In evaluation experiments comparing SE-ADA with recent domain harmonization methods on eight public brain MR datasets (ADNI1/2/3, OASIS1/2/3/4, PPMI), SE-ADA effectively removed domain information while preserving key aspects of the original brain structure and demonstrated the highest disease search accuracy.