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V. Fonseca Hernandes

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Doctoral thesis (2025) - V. Fonseca Hernandes, R. Hanson, E. Greplová
This thesis explores how artificial intelligence (AI) can be used to bridge the gap between simulation and experiment in nanoscience. As both theoretical modeling and experimental techniques in nanoscience become increasingly sophisticated, AI is emerging as a powerful tool to tackle challenges such as tuning experiments, accelerating simulations, generating synthetic data, and automating data analysis. This work presents applications of AI in three main domains: neuroscience, quantum computing, and condensed matter physics.

In neuroscience, we address the problem of efficiently simulating neuronal activity data by implementing a quantum machine learning model that uses a reduced number of trainable parameters. On the experimental side, we develop a computational package that automates the analysis of micro-electrode array data using a neural network trained to replicate human expert detection of burst patterns from spiking activity.

In spin-based quantum computing, we develop a computational package that simulates charge stability diagrams (CSDs) based on device characteristics, enabling the efficient creation of synthetic datasets. We also demonstrate how machine learning models can be used to filter high-quality CSDs for building experimental datasets, and we present the first implementation of diffusion models to complete partially measured CSDs, an approach that can be integrated into measurement routines to accelerate the process.

In condensed matter physics, we leverage neural quantum states to detect phase transitions by analyzing the evolution of neural network weights, without the need to calculate order parameters, and discuss potential directions for combining this technique with neural quantum states trained on experimental data.

These studies show that AI can accelerate simulations and data analysis, while also supporting the design and interpretation of experiments, highlighting its growing and essential role in the future of nanoscience. ...
Journal article (2025) - Vinicius Hernandes, Eliska Greplova
Understanding how biological neural networks process information is one of the biggest open scientific questions of our time. Advances in machine learning and artificial neural networks have enabled the modeling of neuronal behavior, but classical models often require a large number of parameters and highly task-specific architectures, which can complicate model design and scalability. Quantum computing offers an alternative approach through quantum machine learning, which can achieve efficient training with fewer parameters. In this work, we introduce a quantum generative model framework for generating synthetic data that captures the spatial and temporal correlations of biological neuronal activity. Our model demonstrates the ability to achieve reliable outcomes with fewer trainable parameters compared to classical methods. These findings highlight the potential of quantum generative models to provide new tools for modeling and understanding neuronal behavior, offering a promising avenue for future research in neuroscience. ...

Machine learning-based burst detection for multi-electrode array datasets

Journal article (2024) - Vinicius Hernandes, Anouk M. Heuvelmans, Valentina Gualtieri, Dimphna H. Meijer, Geeske M.van Woerden, Eliska Greplova
Neuronal activity in the highly organized networks of the central nervous system is the vital basis for various functional processes, such as perception, motor control, and cognition. Understanding interneuronal connectivity and how activity is regulated in the neuronal circuits is crucial for interpreting how the brain works. Multi-electrode arrays (MEAs) are particularly useful for studying the dynamics of neuronal network activity and their development as they allow for real-time, high-throughput measurements of neural activity. At present, the key challenge in the utilization of MEA data is the sheer complexity of the measured datasets. Available software offers semi-automated analysis for a fixed set of parameters that allow for the definition of spikes, bursts and network bursts. However, this analysis remains time-consuming, user-biased, and limited by pre-defined parameters. Here, we present autoMEA, software for machine learning-based automated burst detection in MEA datasets. We exemplify autoMEA efficacy on neuronal network activity of primary hippocampal neurons from wild-type mice monitored using 24-well multi-well MEA plates. To validate and benchmark the software, we showcase its application using wild-type neuronal networks and two different neuronal networks modeling neurodevelopmental disorders to assess network phenotype detection. Detection of network characteristics typically reported in literature, such as synchronicity and rhythmicity, could be accurately detected compared to manual analysis using the autoMEA software. Additionally, autoMEA could detect reverberations, a more complex burst dynamic present in hippocampal cultures. Furthermore, autoMEA burst detection was sufficiently sensitive to detect changes in the synchronicity and rhythmicity of networks modeling neurodevelopmental disorders as well as detecting changes in their network burst dynamics. Thus, we show that autoMEA reliably analyses neural networks measured with the multi-well MEA setup with the precision and accuracy compared to that of a human expert. ...
Journal article (2023) - Ananda Ramires das Neves Stigger, V. Fonseca Hernandes, Mateus Meneghetti Ferrer, Mario Lucio Moreira
Calcium molybdate (CMO) is a material used in several technological applications. In this work, we explored the correlation between the optical and electrical properties of CMO in solar cell photoanodes. Six samples were prepared by a microwave-assisted hydrothermal method with pH values of 4, 7, and 10 associated with temperatures of 100 °C and 140 °C. These samples were used as a replacement for titanium dioxide TiO 2 in Graetzel solar cells. A thin blocking layer (BL), a dense and translucent film, was deposited over a CMO layer using a doctor-blade method, to create a heterojunction. We show that a strict correlation between pH, temperature, processing time, and photovoltaic response exists in CMO scheelite and needs to be considered to achieve optimal photovoltaic behavior. Almost all samples achieved typical solar cell responses, except that synthesized with pH 4 at 100 °C, which shows an anomalous behavior. Among these samples, the one synthesized with pH 10 at 100 °C was identified as the most suitable candidate for down-converter materials in solar energy applications, due to its typical diode-like properties, with an upper J sc = 180 μA cm −2, V oc = 607 mV and FF = 0.45. ...
Conference paper (2023) - Vinicius Hernandes, Eliska Greplova
Understanding the information processing in neuronal networks relies on the development of computational models that accurately reproduce their activity data. Machine learning techniques have shown promising results in generating synthetic neuronal data, but interpretability remains an issue due to a large number of parameters requiring fitting. Quantum machine learning models, particularly quantum generative learning, are emerging as more compact alternatives that offer similar outcomes. This study presents an efficient framework for generating synthetic neuronal data using a Quantum Generative Adversarial Network (QGAN), with a quantum generator and a classical discriminator. We tested the proposed framework for the minimal case of two neurons, considering the case of single time-steps. Preliminary results demonstrate the QGAN's capability to achieve reliable outcomes with a reduced number of trainable parameters, scaling efficiently for increasing neuronal network sizes. The model effectively captures spiking frequencies of real data, although further refinement is required to incorporate temporal correlations for more extended time-steps. Despite certain limitations, this study lays the foundation for future advancements in using quantum adversarial generative networks to model neuronal activity. The promising potential of QGANs in this domain highlights the possibility of gaining valuable insights into the functioning of complex biological systems through quantum-inspired computational methods. ...