Christian Heiss

Gavrielle R. Untracht, Rolando Matos, Nikolaos Dikaios et al.

Optical coherence tomography angiography (OCTA) performs non-invasive visualization and characterization of microvasculature in research and clinical applications mainly in ophthalmology and dermatology. A wide variety of instruments, imaging protocols, processing methods and metrics have been used to describe the microvasculature, such that comparing different study outcomes is currently not feasible. With the goal of contributing to standardization of OCTA data analysis, we report a user-friendly, open-source toolbox, OCTAVA (OCTA Vascular Analyzer), to automate the pre-processing, segmentation, and quantitative analysis of en face OCTA maximum intensity projection images in a standardized workflow. We present each analysis step, including optimization of filtering and choice of segmentation algorithm, and definition of metrics. We perform quantitative analysis of OCTA images from different commercial and non-commercial instruments and samples and show OCTAVA can accurately and reproducibly determine metrics for characterization of microvasculature. Wide adoption could enable studies and aggregation of data on a scale sufficient to develop reliable microvascular biomarkers for early detection, and to guide treatment, of microvascular disease.

Mohammad Moulaeifard, Loic Coquelin, Mantas Rinkevičius et al.

Photoplethysmography (PPG) is a widely used non-invasive physiological sensing technique, suitable for various clinical applications. Such clinical applications are increasingly supported by machine learning methods, raising the question of the most appropriate input representation and model choice. Comprehensive comparisons, in particular across different input representations, are scarce. We address this gap in the research landscape by a comprehensive benchmarking study covering three kinds of input representations, interpretable features, image representations and raw waveforms, across prototypical regression and classification use cases: blood pressure and atrial fibrillation prediction. In both cases, the best results are achieved by deep neural networks operating on raw time series as input representations. Within this model class, best results are achieved by modern convolutional neural networks (CNNs). but depending on the task setup, shallow CNNs are often also very competitive. We envision that these results will be insightful for researchers to guide their choice on machine learning tasks for PPG data, even beyond the use cases presented in this work.

Yunrui Li, Hao Xu, Ambrish Kumar et al.

Nuclear Magnetic Resonance (NMR) spectroscopy is essential for revealing molecular structure, electronic environment, and dynamics. Accurate NMR shift prediction allows researchers to validate structures by comparing predicted and observed shifts. While Machine Learning (ML) has improved one-dimensional (1D) NMR shift prediction, predicting 2D NMR remains challenging due to limited annotated data. To address this, we introduce an unsupervised training framework for predicting cross-peaks in 2D NMR, specifically Heteronuclear Single Quantum Coherence (HSQC).Our approach pretrains an ML model on an annotated 1D dataset of 1H and 13C shifts, then finetunes it in an unsupervised manner using unlabeled HSQC data, which simultaneously generates cross-peak annotations. Our model also adjusts for solvent effects. Evaluation on 479 expert-annotated HSQC spectra demonstrates our model's superiority over traditional methods (ChemDraw and Mestrenova), achieving Mean Absolute Errors (MAEs) of 2.05 ppm and 0.165 ppm for 13C shifts and 1H shifts respectively. Our algorithmic annotations show a 95.21% concordance with experts' assignments, underscoring the approach's potential for structural elucidation in fields like organic chemistry, pharmaceuticals, and natural products.