RamanSeg: Interpretability-driven Deep Learning on Raman Spectra for Cancer Diagnosis

Raman spectroscopy provides label-free, chemically specific characterization of biological systems and has become an important tool for cancer diagnosis, molecular subtyping, microbiological identification, and intraoperative decision support. Biomedical Raman spectra are, however, high-dimensional, noisy, and affected by fluorescence background, acquisition variability, and biological heterogeneity, making robust computational analysis essential. This review examines the role of machine learning across the biomedical Raman spectroscopy pipeline, from preprocessing and signal correction to unsupervised structure discovery, supervised diagnosis and molecular stratification, representation and transfer learning, explainability, biomarker discovery, and multimodal integration with imaging, pathology, and molecular profiling. Emphasis is placed on the use of machine learning not only for diagnostic classification, but also for biologically interpretable and clinically actionable analysis. We also discuss the main barriers to clinical translation, including limited dataset sizes, inter-instrument variability, inconsistent preprocessing, insufficient external validation, reproducibility concerns, and limited sharing of software, data, and metadata. We argue that progress will require methodological advances together with standardization, robust validation, explainability, and deployment-ready analytical frameworks. By integrating methodological, biomedical, and translational perspectives, this review outlines key directions for developing reliable and clinically deployable Raman-AI systems.

As hematoxylin & eosin (H&E) staining constitutes the primary entry point in routine diagnostic workflows, computer-aided diagnosis from whole-slide H&E images is of particular clinical relevance. However, substantial variability in specimen preparation, staining protocols, and scanning conditions, together with inherent uncertainty in expert pixel-level annotations, makes automated analysis of H&E-stained images challenging. In this study, we propose a semantic segmentation-based framework for image-level diagnosis, grounded in the clinically motivated assumption that each histopathological image corresponds to a single cancer type. Image-level predictions are obtained by assigning the class of the dominant pixel-level label in the segmentation output. To ensure clinical relevance, we adopt the nnU-Net architecture and train it on a publicly available dataset collected in our study with pixel-level annotations for three liver cancer types: hepatocellular cacrcinoma (HCC; 55 images from 30 patients), cholangiocellular carcinoma (CCA; 55 images from 29 patients), and colorectal metastatic adenocarcinoma (CMA; 60 images from 30 patients). Annotations were independently provided by four pathologist. We hypothesize that the combination of stain normalization and semantic segmentation mitigates domain shift and reduces sensitivity to annotation noise. Five-fold cross-validation yielded balanced accuracy of 0.975 (HCC), 0.950 (CCA), and 1.000 (CMA), comparable to results obtained with immunohosthochemical staining and superior to several deep learning models trained on patch-level annotations. The proposed framework has the potential to support pathologists in prioritizing immunohistochemical marker selection, thereby reducing diagnostic costs and turnaround time. Integration with immunohistochemical findings improve overall diagnostic reliability.

Histopathology remains the gold standard for cancer diagnosis because it provides detailed cellular-level assessment of tissue morphology. However, manual histopathological examination is time-consuming, labour-intensive, and subject to inter-observer variability, creating a demand for reliable computer-assisted diagnostic tools. Recent advances in deep learning, particularly transformer-based architectures, have shown strong potential for modelling complex spatial dependencies in medical images. In this work, we propose DeepHistoViT, a transformer-based framework for automated classification of histopathological images. The model employs a customized Vision Transformer architecture with an integrated attention mechanism designed to capture fine-grained cellular structures while improving interpretability through attention-based localization of diagnostically relevant regions. The framework is evaluated on three publicly available histopathology datasets covering lung cancer, colon cancer, and acute lymphoblastic leukaemia. Experimental results demonstrate state-of-the-art performance across all datasets, with classification accuracy, precision, recall, F1-score, and ROC-AUC reaching 100 percent on the lung and colon cancer datasets, and 99.85 percent, 99.84 percent, 99.86 percent, 99.85 percent, and 99.99 percent respectively on the acute lymphoblastic leukaemia dataset. All performance metrics are reported with 95 percent confidence intervals. These results highlight the effectiveness of transformer-based architectures for histopathological image analysis and demonstrate the potential of DeepHistoViT as an interpretable computer-assisted diagnostic tool to support pathologists in clinical decision-making.