arXiv subjects

Rossella Arcucci

Publications and source records attributed to Rossella Arcucci.

At least 55 records · Page 3Linked to original sources

arXiv2023

ETP: Learning Transferable ECG Representations via ECG-Text Pre-training

In the domain of cardiovascular healthcare, the Electrocardiogram (ECG) serves as a critical, non-invasive diagnostic tool. Although recent strides in self-supervised learning (SSL) have been promising for ECG representation learning, these techniques often require annotated samples and struggle with classes not present in the fine-tuning stages. To address these limitations, we introduce ECG-Text Pre-training (ETP), an innovative framework designed to learn cross-modal representations that link ECG signals with textual reports. For the first time, this framework leverages the zero-shot classification task in the ECG domain. ETP employs an ECG encoder along with a pre-trained language model to align ECG signals with their corresponding textual reports. The proposed framework excels in both linear evaluation and zero-shot classification tasks, as demonstrated on the PTB-XL and CPSC2018 datasets, showcasing its ability for robust and generalizable cross-modal ECG feature learning.

eess.SP↗

arXiv2023

A generative model for surrogates of spatial-temporal wildfire nowcasting

Recent increase in wildfires worldwide has led to the need for real-time fire nowcasting. Physics-driven models, such as cellular automata and computational fluid dynamics can provide high-fidelity fire spread simulations but they are computationally expensive and time-consuming. Much effort has been put into developing machine learning models for fire prediction. However, these models are often region-specific and require a substantial quantity of simulation data for training purpose. This results in a significant amount of computational effort for different ecoregions. In this work, a generative model is proposed using a three-dimensional Vector-Quantized Variational Autoencoders to generate spatial-temporal sequences of unseen wildfire burned areas in a given ecoregion. The model is tested in the ecoregion of a recent massive wildfire event in California, known as the Chimney fire. Numerical results show that the model succeed in generating coherent and structured fire scenarios, taking into account the impact from geophysical variables, such as vegetation and slope. Generated data are also used to train a surrogate model for predicting wildfire dissemination, which has been tested on both simulation data and the real Chimney fire event.

cs.LG↗

arXiv2023

M-FLAG: Medical Vision-Language Pre-training with Frozen Language Models and Latent Space Geometry Optimization

Medical vision-language models enable co-learning and integrating features from medical imaging and clinical text. However, these models are not easy to train and the latent representation space can be complex. Here we propose a novel way for pre-training and regularising medical vision-language models. The proposed method, named Medical vision-language pre-training with Frozen language models and Latent spAce Geometry optimization (M-FLAG), leverages a frozen language model for training stability and efficiency and introduces a novel orthogonality loss to harmonize the latent space geometry. We demonstrate the potential of the pre-trained model on three downstream tasks: medical image classification, segmentation, and object detection. Extensive experiments across five public datasets demonstrate that M-FLAG significantly outperforms existing medical vision-language pre-training approaches and reduces the number of parameters by 78\%. Notably, M-FLAG achieves outstanding performance on the segmentation task while using only 1\% of the RSNA dataset, even outperforming ImageNet pre-trained models that have been fine-tuned using 100\% of the data.

cs.CV↗

arXiv2023

A novel approach for predicting epidemiological forecasting parameters based on real-time signals and Data Assimilation

This paper proposes a novel approach to predict epidemiological parameters by integrating new real-time signals from various sources of information, such as novel social media-based population density maps and Air Quality data. We implement an ensemble of Convolutional Neural Networks (CNN) models using various data sources and fusion methodology to build robust predictions and simulate several dynamic parameters that could improve the decision-making process for policymakers. Additionally, we used data assimilation to estimate the state of our system from fused CNN predictions. The combination of meteorological signals and social media-based population density maps improved the performance and flexibility of our prediction of the COVID-19 outbreak in London. While the proposed approach outperforms standard models, such as compartmental models traditionally used in disease forecasting (SEIR), generating robust and consistent predictions allows us to increase the stability of our model while increasing its accuracy.

cs.LG↗

arXiv2023

Generative Text-Guided 3D Vision-Language Pretraining for Unified Medical Image Segmentation

Vision-Language Pretraining (VLP) has demonstrated remarkable capabilities in learning visual representations from textual descriptions of images without annotations. Yet, effective VLP demands large-scale image-text pairs, a resource that suffers scarcity in the medical domain. Moreover, conventional VLP is limited to 2D images while medical images encompass diverse modalities, often in 3D, making the learning process more challenging. To address these challenges, we present Generative Text-Guided 3D Vision-Language Pretraining for Unified Medical Image Segmentation (GTGM), a framework that extends of VLP to 3D medical images without relying on paired textual descriptions. Specifically, GTGM utilizes large language models (LLM) to generate medical-style text from 3D medical images. This synthetic text is then used to supervise 3D visual representation learning. Furthermore, a negative-free contrastive learning objective strategy is introduced to cultivate consistent visual representations between augmented 3D medical image patches, which effectively mitigates the biases associated with strict positive-negative sample pairings. We evaluate GTGM on three imaging modalities - Computed Tomography (CT), Magnetic Resonance Imaging (MRI), and electron microscopy (EM) over 13 datasets. GTGM's superior performance across various medical image segmentation tasks underscores its effectiveness and versatility, by enabling VLP extension into 3D medical imagery while bypassing the need for paired text.

cs.CV↗

arXiv2023

Analyzing drop coalescence in microfluidic device with a deep learning generative model

Predicting drop coalescence based on process parameters is crucial for experiment design in chemical engineering. However, predictive models can suffer from the lack of training data and more importantly, the label imbalance problem. In this study, we propose the use of deep learning generative models to tackle this bottleneck by training the predictive models using generated synthetic data. A novel generative model, named double space conditional variational autoencoder (DSCVAE) is developed for labelled tabular data. By introducing label constraints in both the latent and the original space, DSCVAE is capable of generating consistent and realistic samples compared to standard conditional variational autoencoder (CVAE). Two predictive models, namely random forest and gradient boosting classifiers, are enhanced on synthetic data and their performances are evaluated on real experimental data. Numerical results show that considerable improvement in prediction accuracy can be achieved by using synthetic data and the proposed DSCVAE clearly outperforms the standard CVAE. This research clearly brings more insight into handling imbalanced data for classification problems, especially in chemical engineering

cs.CE↗

arXiv2023

Frozen Language Model Helps ECG Zero-Shot Learning

The electrocardiogram (ECG) is one of the most commonly used non-invasive, convenient medical monitoring tools that assist in the clinical diagnosis of heart diseases. Recently, deep learning (DL) techniques, particularly self-supervised learning (SSL), have demonstrated great potential in the classification of ECG. SSL pre-training has achieved competitive performance with only a small amount of annotated data after fine-tuning. However, current SSL methods rely on the availability of annotated data and are unable to predict labels not existing in fine-tuning datasets. To address this challenge, we propose Multimodal ECG-Text Self-supervised pre-training (METS), the first work to utilize the auto-generated clinical reports to guide ECG SSL pre-training. We use a trainable ECG encoder and a frozen language model to embed paired ECG and automatically machine-generated clinical reports separately. The SSL aims to maximize the similarity between paired ECG and auto-generated report while minimize the similarity between ECG and other reports. In downstream classification tasks, METS achieves around 10% improvement in performance without using any annotated data via zero-shot classification, compared to other supervised and SSL baselines that rely on annotated data. Furthermore, METS achieves the highest recall and F1 scores on the MIT-BIH dataset, despite MIT-BIH containing different classes of ECG compared to the pre-trained dataset. The extensive experiments have demonstrated the advantages of using ECG-Text multimodal self-supervised learning in terms of generalizability, effectiveness, and efficiency.

cs.LG↗

arXiv2023

Machine learning with data assimilation and uncertainty quantification for dynamical systems: a review

Data Assimilation (DA) and Uncertainty quantification (UQ) are extensively used in analysing and reducing error propagation in high-dimensional spatial-temporal dynamics. Typical applications span from computational fluid dynamics (CFD) to geoscience and climate systems. Recently, much effort has been given in combining DA, UQ and machine learning (ML) techniques. These research efforts seek to address some critical challenges in high-dimensional dynamical systems, including but not limited to dynamical system identification, reduced order surrogate modelling, error covariance specification and model error correction. A large number of developed techniques and methodologies exhibit a broad applicability across numerous domains, resulting in the necessity for a comprehensive guide. This paper provides the first overview of the state-of-the-art researches in this interdisciplinary field, covering a wide range of applications. This review aims at ML scientists who attempt to apply DA and UQ techniques to improve the accuracy and the interpretability of their models, but also at DA and UQ experts who intend to integrate cutting-edge ML approaches to their systems. Therefore, this article has a special focus on how ML methods can overcome the existing limits of DA and UQ, and vice versa. Some exciting perspectives of this rapidly developing research field are also discussed.

cs.LG↗

arXiv2023

Optimization of microfluidic synthesis of silver nanoparticles: a generic approach using machine learning

The properties of silver nanoparticles (AgNPs) are affected by various parameters, making optimisation of their synthesis a laborious task. This optimisation is facilitated in this work by concurrent use of a T-junction microfluidic system and machine learning approach. The AgNPs are synthesized by reducing silver nitrate with tannic acid in the presence of trisodium citrate, which has a dual role in the reaction as reducing and stabilizing agent. The study uses a decision tree-guided design of experiment method for the size of AgNPs. The developed approach uses kinetic nucleation and growth constants derived from an independent set of experiments to account for chemistry of synthesis, the Reynolds number and the ratio of Dean number to Reynolds number to reveal effect of hydrodynamics and mixing within device and storage temperature to account for particle stability after collection. The obtained model was used to define a parameter space for additional experiments carried out to improve the model further. The numerical results illustrate that well-designed experiments can contribute more effectively to the development of different machine learning models (decision tree, random forest and XGBoost) as opposed to randomly added experiments.

physics.chem-ph↗

arXiv2022

Generalised Latent Assimilation in Heterogeneous Reduced Spaces with Machine Learning Surrogate Models

Reduced-order modelling and low-dimensional surrogate models generated using machine learning algorithms have been widely applied in high-dimensional dynamical systems to improve the algorithmic efficiency. In this paper, we develop a system which combines reduced-order surrogate models with a novel data assimilation (DA) technique used to incorporate real-time observations from different physical spaces. We make use of local smooth surrogate functions which link the space of encoded system variables and the one of current observations to perform variational DA with a low computational cost. The new system, named Generalised Latent Assimilation can benefit both the efficiency provided by the reduced-order modelling and the accuracy of data assimilation. A theoretical analysis of the difference between surrogate and original assimilation cost function is also provided in this paper where an upper bound, depending on the size of the local training set, is given. The new approach is tested on a high-dimensional CFD application of a two-phase liquid flow with non-linear observation operators that current Latent Assimilation methods can not handle. Numerical results demonstrate that the proposed assimilation approach can significantly improve the reconstruction and prediction accuracy of the deep learning surrogate model which is nearly 1000 times faster than the CFD simulation.

cs.LG↗

arXiv2022

Forecasting emissions through Kaya identity using Neural Ordinary Differential Equations

Starting from the Kaya identity, we used a Neural ODE model to predict the evolution of several indicators related to carbon emissions, on a country-level: population, GDP per capita, energy intensity of GDP, carbon intensity of energy. We compared the model with a baseline statistical model - VAR - and obtained good performances. We conclude that this machine-learning approach can be used to produce a wide range of results and give relevant insight to policymakers

cs.LG↗

arXiv2021

A Scalable Inference Method For Large Dynamic Economic Systems

The nature of available economic data has changed fundamentally in the last decade due to the economy's digitisation. With the prevalence of often black box data-driven machine learning methods, there is a necessity to develop interpretable machine learning methods that can conduct econometric inference, helping policymakers leverage the new nature of economic data. We therefore present a novel Variational Bayesian Inference approach to incorporate a time-varying parameter auto-regressive model which is scalable for big data. Our model is applied to a large blockchain dataset containing prices, transactions of individual actors, analyzing transactional flows and price movements on a very granular level. The model is extendable to any dataset which can be modelled as a dynamical system. We further improve the simple state-space modelling by introducing non-linearities in the forward model with the help of machine learning architectures.

econ.EM↗

arXiv2021

Real-time Updating of Dynamic Social Networks for COVID-19 Vaccination Strategies

Vaccination strategy is crucial in fighting against the COVID-19 pandemic. Since the supply is limited, contact network-based interventions can be most powerful to set an optimal strategy by identifying high-risk individuals or communities. However, due to the high dimension, only partial and noisy network information can be available in practice, especially for dynamical systems where the contact networks are highly time-variant. Furthermore, numerous mutations of SARS-CoV-2 impact considerably the current infectious probability, requiring real-time network updating algorithms. In this study, we propose a sequential network updating approach based on data assimilation techniques to combine different sources of temporal information. We then prioritise the individuals with high-degree or high-centrality, obtained from the assimilated networks, for vaccination. The assimilation-based approach is compared with the standard method (based on partially observed networks) and a random selection strategy in terms of vaccination effectiveness in a SIR model. The numerical comparison is first carried out using real-world face-to-face dynamical networks collected in a high school, following by sequential multi-layer networks, generated relying on the Barabasi-Albert model emulating the department of Computing at Imperial College London in the UK as an example.

cs.SI↗

arXiv2021

Correcting public opinion trends through Bayesian data assimilation

Measuring public opinion is a key focus during democratic elections, enabling candidates to gauge their popularity and alter their campaign strategies accordingly. Traditional survey polling remains the most popular estimation technique, despite its cost and time intensity, measurement errors, lack of real-time capabilities and lagged representation of public opinion. In recent years, Twitter opinion mining has attempted to combat these issues. Despite achieving promising results, it experiences its own set of shortcomings such as an unrepresentative sample population and a lack of long term stability. This paper aims to merge data from both these techniques using Bayesian data assimilation to arrive at a more accurate estimate of true public opinion for the Brexit referendum. This paper demonstrates the effectiveness of the proposed approach using Twitter opinion data and survey data from trusted pollsters. Firstly, the possible existence of a time gap of 16 days between the two data sets is identified. This gap is subsequently incorporated into a proposed assimilation architecture. This method was found to adequately incorporate information from both sources and measure a strong upward trend in Leave support leading up to the Brexit referendum. The proposed technique provides useful estimates of true opinion, which is essential to future opinion measurement and forecasting research.

cs.CY↗

arXiv2021

Digital twins based on bidirectional LSTM and GAN for modelling the COVID-19 pandemic

The outbreak of the coronavirus disease 2019 (COVID-19) has now spread throughout the globe infecting over 150 million people and causing the death of over 3.2 million people. Thus, there is an urgent need to study the dynamics of epidemiological models to gain a better understanding of how such diseases spread. While epidemiological models can be computationally expensive, recent advances in machine learning techniques have given rise to neural networks with the ability to learn and predict complex dynamics at reduced computational costs. Here we introduce two digital twins of a SEIRS model applied to an idealised town. The SEIRS model has been modified to take account of spatial variation and, where possible, the model parameters are based on official virus spreading data from the UK. We compare predictions from a data-corrected Bidirectional Long Short-Term Memory network and a predictive Generative Adversarial Network. The predictions given by these two frameworks are accurate when compared to the original SEIRS model data. Additionally, these frameworks are data-agnostic and could be applied to towns, idealised or real, in the UK or in other countries. Also, more compartments could be included in the SEIRS model, in order to study more realistic epidemiological behaviour.

cs.LG↗

arXiv2021

Adversarial autoencoders and adversarial LSTM for improved forecasts of urban air pollution simulations

This paper presents an approach to improve the forecast of computational fluid dynamics (CFD) simulations of urban air pollution using deep learning, and most specifically adversarial training. This adversarial approach aims to reduce the divergence of the forecasts from the underlying physical model. Our two-step method integrates a Principal Components Analysis (PCA) based adversarial autoencoder (PC-AAE) with adversarial Long short-term memory (LSTM) networks. Once the reduced-order model (ROM) of the CFD solution is obtained via PCA, an adversarial autoencoder is used on the principal components time series. Subsequentially, a Long Short-Term Memory network (LSTM) is adversarially trained on the latent space produced by the PC-AAE to make forecasts. Once trained, the adversarially trained LSTM outperforms a LSTM trained in a classical way. The study area is in South London, including three-dimensional velocity vectors in a busy traffic junction.

cs.LG↗

arXiv2021

Attention-based Convolutional Autoencoders for 3D-Variational Data Assimilation

We propose a new 'Bi-Reduced Space' approach to solving 3D Variational Data Assimilation using Convolutional Autoencoders. We prove that our approach has the same solution as previous methods but has significantly lower computational complexity; in other words, we reduce the computational cost without affecting the data assimilation accuracy. We tested the new method with data from a real-world application: a pollution model of a site in Elephant and Castle, London and found that we could reduce the size of the background covariance matrix representation by O(10^3) and, at the same time, increase our data assimilation accuracy with respect to existing reduced space methods.

cs.LG↗

arXiv2021

Adversarially trained LSTMs on reduced order models of urban air pollution simulations

This paper presents an approach to improve computational fluid dynamics simulations forecasts of air pollution using deep learning. Our method, which integrates Principal Components Analysis (PCA) and adversarial training, is a way to improve the forecast skill of reduced order models obtained from the original model solution. Once the reduced-order model (ROM) is obtained via PCA, a Long Short-Term Memory network (LSTM) is adversarially trained on the ROM to make forecasts. Once trained, the adversarially trained LSTM outperforms a LSTM trained in a classical way. The study area is in London, including velocities and a concentration tracer that replicates a busy traffic junction. This adversarially trained LSTM-based approach is used on the ROM in order to produce faster forecasts of the air pollution tracer.

cs.LG↗