The extensive use of pesticides and synthetic dyes poses critical threats to food safety, human health, and environmental sustainability, necessitating rapid and reliable detection methods. Raman spectroscopy offers molecularly specific fingerprints but suffers from spectral noise, fluorescence background, and band overlap, limiting its real-world applicability. Here, we propose a deep learning framework based on ResNet-18 feature extraction, combined with advanced classifiers, including XGBoost, SVM, and their hybrid integration, to detect pesticides and dyes from Raman spectroscopy, called MLRaman. The MLRaman with the CNN-XGBoost model achieved a predictive accuracy of 97.4% and a perfect AUC of 1.0, while it with the CNN-SVM model provided competitive results with robust class-wise discrimination. Dimensionality reduction analyses (PCA, t-SNE, UMAP) confirmed the separability of Raman embeddings across 10 analytes, including 7 pesticides and 3 dyes. Finally, we developed a user-friendly Streamlit application for real-time prediction, which successfully identified unseen Raman spectra from our independent experiments and also literature sources, underscoring strong generalization capacity. This study establishes a scalable, practical MLRaman model for multi-residue contaminant monitoring, with significant potential for deployment in food safety and environmental surveillance.

Detecting stress in plants is crucial for both open-farm and controlled-environment agriculture. Biomolecules within plants serve as key stress indicators, offering vital markers for continuous health monitoring and early disease detection. Raman spectroscopy provides a powerful, non-invasive means to quantify these biomolecules through their molecular vibrational signatures. However, traditional Raman analysis relies on customized data-processing workflows that require fluorescence background removal and prior identification of Raman peaks of interest-introducing potential biases and inconsistencies. Here, we introduce DIVA (Deep-learning-based Investigation of Vibrational Raman spectra for plant-stress Analysis), a fully automated workflow based on a variational autoencoder. Unlike conventional approaches, DIVA processes native Raman spectra-including fluorescence backgrounds-without manual preprocessing, identifying and quantifying significant spectral features in an unbiased manner. We applied DIVA to detect a range of plant stresses, including abiotic (shading, high light intensity, high temperature) and biotic stressors (bacterial infections). By integrating deep learning with vibrational spectroscopy, DIVA paves the way for AI-driven plant health assessment, fostering more resilient and sustainable agricultural practices.

Colorectal cancer (CRC) ranks as the second leading cause of cancer-related deaths and the third most prevalent malignant tumour worldwide. Early detection of CRC remains problematic due to its non-specific and often embarrassing symptoms, which patients frequently overlook or hesitate to report to clinicians. Crucially, the stage at which CRC is diagnosed significantly impacts survivability, with a survival rate of 80-95\% for Stage I and a stark decline to 10\% for Stage IV. Unfortunately, in the UK, only 14.4\% of cases are diagnosed at the earliest stage (Stage I). In this study, we propose ColonScopeX, a machine learning framework utilizing explainable AI (XAI) methodologies to enhance the early detection of CRC and pre-cancerous lesions. Our approach employs a multimodal model that integrates signals from blood sample measurements, processed using the Savitzky-Golay algorithm for fingerprint smoothing, alongside comprehensive patient metadata, including medication history, comorbidities, age, weight, and BMI. By leveraging XAI techniques, we aim to render the model's decision-making process transparent and interpretable, thereby fostering greater trust and understanding in its predictions. The proposed framework could be utilised as a triage tool or a screening tool of the general population. This research highlights the potential of combining diverse patient data sources and explainable machine learning to tackle critical challenges in medical diagnostics.

Raman spectroscopy serves as a powerful and reliable tool for analyzing the chemical information of substances. The integration of Raman spectroscopy with deep learning methods enables rapid qualitative and quantitative analysis of materials. Most existing approaches adopt supervised learning methods. Although supervised learning has achieved satisfactory accuracy in spectral analysis, it is still constrained by costly and limited well-annotated spectral datasets for training. When spectral annotation is challenging or the amount of annotated data is insufficient, the performance of supervised learning in spectral material identification declines. In order to address the challenge of feature extraction from unannotated spectra, we propose a self-supervised learning paradigm for Raman Spectroscopy based on a Masked AutoEncoder, termed SMAE. SMAE does not require any spectral annotations during pre-training. By randomly masking and then reconstructing the spectral information, the model learns essential spectral features. The reconstructed spectra exhibit certain denoising properties, improving the signal-to-noise ratio (SNR) by more than twofold. Utilizing the network weights obtained from masked pre-training, SMAE achieves clustering accuracy of over 80% for 30 classes of isolated bacteria in a pathogenic bacterial dataset, demonstrating significant improvements compared to classical unsupervised methods and other state-of-the-art deep clustering methods. After fine-tuning the network with a limited amount of annotated data, SMAE achieves an identification accuracy of 83.90% on the test set, presenting competitive performance against the supervised ResNet (83.40%).

Exosomes are small vesicles crucial for cell signaling and disease biomarkers. Due to their complexity, an "omics" approach is preferable to individual biomarkers. While Raman spectroscopy is effective for exosome analysis, it requires high sample concentrations and has limited sensitivity to lipids and proteins. Surface-enhanced Raman spectroscopy helps overcome these challenges. In this study, we leverage Neo4j graph databases to organize 3,045 Raman spectra of exosomes, enhancing data generalization. To further refine spectral analysis, we introduce a novel spectral filtering process that integrates the PageRank Filter with optimal Dimensionality Reduction. This method improves feature selection, resulting in superior classification performance. Specifically, the Extra Trees model, using our spectral processing approach, achieves 0.76 and 0.857 accuracy in classifying hyperglycemic, hypoglycemic, and normal exosome samples based on Raman spectra and surface, respectively, with group 10-fold cross-validation. Our results show that graph-based spectral filtering combined with optimal dimensionality reduction significantly improves classification accuracy by reducing noise while preserving key biomarker signals. This novel framework enhances Raman-based exosome analysis, expanding its potential for biomedical applications, disease diagnostics, and biomarker discovery.

Raman scattering is based on molecular vibration spectroscopy and provides a powerful technology for pathogenic bacteria diagnosis using the unique molecular fingerprint information of a substance. The integration of deep learning technology has significantly improved the efficiency and accuracy of intelligent Raman spectroscopy (RS) recognition. However, the current RS recognition methods based on deep neural networks still require the annotation of a large amount of spectral data, which is labor-intensive. This paper presents a novel annotation-efficient Self-Calibrated Dual Contrasting (SCDC) method for RS recognition that operates effectively with few or no annotation. Our core motivation is to represent the spectrum from two different perspectives in two distinct subspaces: embedding and category. The embedding perspective captures instance-level information, while the category perspective reflects category-level information. Accordingly, we have implemented a dual contrastive learning approach from two perspectives to obtain discriminative representations, which are applicable for Raman spectroscopy recognition under both unsupervised and semi-supervised learning conditions. Furthermore, a self-calibration mechanism is proposed to enhance robustness. Validation of the identification task on three large-scale bacterial Raman spectroscopy datasets demonstrates that our SCDC method achieves robust recognition performance with very few (5$\%$ or 10$\%$) or no annotations, highlighting the potential of the proposed method for biospectral identification in annotation-efficient clinical scenarios.

Raman spectroscopy has attracted significant attention in various biochemical detection fields, especially in the rapid identification of pathogenic bacteria. The integration of this technology with deep learning to facilitate automated bacterial Raman spectroscopy diagnosis has emerged as a key focus in recent research. However, the diagnostic performance of existing deep learning methods largely depends on a sufficient dataset, and in scenarios where there is a limited availability of Raman spectroscopy data, it is inadequate to fully optimize the numerous parameters of deep neural networks. To address these challenges, this paper proposes a data generation method utilizing deep generative models to expand the data volume and enhance the recognition accuracy of bacterial Raman spectra. Specifically, we introduce DiffRaman, a conditional latent denoising diffusion probability model for Raman spectra generation. Experimental results demonstrate that synthetic bacterial Raman spectra generated by DiffRaman can effectively emulate real experimental spectra, thereby enhancing the performance of diagnostic models, especially under conditions of limited data. Furthermore, compared to existing generative models, the proposed DiffRaman offers improvements in both generation quality and computational efficiency. Our DiffRaman approach offers a well-suited solution for automated bacteria Raman spectroscopy diagnosis in data-scarce scenarios, offering new insights into alleviating the labor of spectroscopic measurements and enhancing rare bacteria identification.

Two-dimensional (2D) materials are poised to revolutionize current solid-state technology with their extraordinary properties. Yet, the primary challenge remains their scalable production. While there have been significant advancements, much of the scientific progress has depended on the exfoliation of materials, a method that poses severe challenges for large-scale applications. With the advent of artificial intelligence (AI) in materials science, innovative synthesis methodologies are now on the horizon. This study explores the forefront of autonomous materials synthesis using an artificial neural network (ANN) trained by evolutionary methods, focusing on the efficient production of graphene. Our approach demonstrates that a neural network can iteratively and autonomously learn a time-dependent protocol for the efficient growth of graphene, without requiring pretraining on what constitutes an effective recipe. Evaluation criteria are based on the proximity of the Raman signature to that of monolayer graphene: higher scores are granted to outcomes whose spectrum more closely resembles that of an ideal continuous monolayer structure. This feedback mechanism allows for iterative refinement of the ANN's time-dependent synthesis protocols, progressively improving sample quality. Through the advancement and application of AI methodologies, this work makes a substantial contribution to the field of materials engineering, fostering a new era of innovation and efficiency in the synthesis process.

The rapid and accurate detection of biochemical compositions in fish is a crucial real-world task that facilitates optimal utilization and extraction of high-value products in the seafood industry. Raman spectroscopy provides a promising solution for quickly and non-destructively analyzing the biochemical composition of fish by associating Raman spectra with biochemical reference data using machine learning regression models. This paper investigates different regression models to address this task and proposes a new design of Convolutional Neural Networks (CNNs) for jointly predicting water, protein, and lipids yield. To the best of our knowledge, we are the first to conduct a successful study employing CNNs to analyze the biochemical composition of fish based on a very small Raman spectroscopic dataset. Our approach combines a tailored CNN architecture with the comprehensive data preparation procedure, effectively mitigating the challenges posed by extreme data scarcity. The results demonstrate that our CNN can significantly outperform two state-of-the-art CNN models and multiple traditional machine learning models, paving the way for accurate and automated analysis of fish biochemical composition.

Prostate cancer is a disease which poses an interesting clinical question: should it be treated? A small subset of prostate cancers are aggressive and require removal and treatment to prevent metastatic spread. However, conventional diagnostics remain challenged to risk-stratify such patients, hence, new methods of approach to biomolecularly subclassify the disease are needed. Here we use an unsupervised, self-organising map approach to analyse live-cell Raman spectroscopy data obtained from prostate cell-lines; our aim is to test the feasibility of this method to differentiate, at the single-cell-level, cancer from normal using high-dimensional datasets with minimal preprocessing. The results demonstrate not only successful separation of normal prostate and cancer cells, but also a new subclustering of the prostate cancer cell-line into two groups. Initial analysis of the spectra from each of the cancer subclusters demonstrates a differential expression of lipids, which, against the normal control, may be linked to disease-related changes in cellular signalling.