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Mariano N. Cruz Bournazou

Publications and source records attributed to Mariano N. Cruz Bournazou.

2 recordsLinked to original sources

RamanBench: A Large-Scale Benchmark for Machine Learning on Raman Spectroscopy

Machine Learning (ML) has transformed many scientific fields, yet key applications still lack standardized benchmarks. Raman spectroscopy, a widely used technique for non-invasive molecular analysis, is one such field where progress is limited by fragmented datasets, inconsistent evaluation, and models that fail to capture the structure of spectral data. We introduce RamanBench, the first large-scale, fully reproducible benchmark for ML on Raman spectroscopy, consisting of streamlined data access, evaluation protocols and code, as well as a live leaderboard. It unifies 74 datasets (including 16 first released with this benchmark) across four domains, comprising 325,668 spectra and spanning classification and regression tasks under diverse experimental conditions. We benchmark 28 models under a standardized protocol, including classical methods (e.g., PLS), Raman-specific (e.g., RamanNet), Tabular Foundation Model (TFM) (e.g., TabPFN), and time-series approaches (e.g., ROCKET). TFM consistently outperform domain-specific and gradient boosting baselines, while time-series models remain competitive. However, no method generalizes across datasets, revealing a fundamental gap. Therefore, we invite the community to contribute new approaches to our living benchmark, with the potential to accelerate advances in critical applications such as medical diagnostics, biological research, and materials science.

cs.LG↗

Fitting nonlinear models to continuous oxygen data with oscillatory signal variations via a loss based on DynamicTime Warping

High throughput experimental systems play an important role in bioprocess development, as they provide an efficient way of analysing different experimental conditions and perform strain discrimination in previous phases to the industrial scale production. In the millilitre scale, these systems are combinations of parallel mini-bioreactors, liquid handling robots and automated workflows for data handling and model based operation. For successfully monitoring cultivation conditions and improving the overall process quality by model-based approaches, a proper model identification is crucial. However, the quality and amount of measurements makes this task challenging considering the complexity of the bio-processes. TheDissolved Oxygen Tension is often the only measurement which is available online, and therefore, a good understanding of the errors in this signal is important for performing a robust estimation.Some of the expected errors will provoke uncertainties in the time-domain of the measurement, and in those cases, the common Weighted Least Squares estimation procedure can fail providing good results. Moreover, these errors will have even a larger effect in the fed-batch phase where bolus feeding is applied, as this generates fast dynamic responses in the signal. In the present work, an insilico study of the performance of Weighted Least Squares estimator is analysed when the expected time-uncertainties are present in the oxygen signal. As an alternative, a loss based on the Dynamic Time Warping measure is proposed. The results show how this latter procedure outperforms the former reconstructing the oxygen signal, and in addition, returns less biased parameter estimates.

q-bio.QM↗