Multi-Site Clinical Federated Learning using Recursive and Attentive Models and NVFlare

The prodigious growth of digital health data has precipitated a mounting interest in harnessing machine learning methodologies, such as natural language processing (NLP), to scrutinize medical records, clinical notes, and other text-based health information. Although NLP techniques have exhibited substantial potential in augmenting patient care and informing clinical decision-making, data privacy and adherence to regulations persist as critical concerns. Federated learning (FL) emerges as a viable solution, empowering multiple organizations to train machine learning models collaboratively without disseminating raw data. This paper proffers a pragmatic approach to medical NLP by amalgamating FL, NLP models, and the NVFlare framework, developed by NVIDIA. We introduce two exemplary NLP models, the Long-Short Term Memory (LSTM)-based model and Bidirectional Encoder Representations from Transformers (BERT), which have demonstrated exceptional performance in comprehending context and semantics within medical data. This paper encompasses the development of an integrated framework that addresses data privacy and regulatory compliance challenges while maintaining elevated accuracy and performance, incorporating BERT pretraining, and comprehensively substantiating the efficacy of the proposed approach.

Predicting Development of Chronic Obstructive Pulmonary Disease and its Risk Factor Analysis

Chronic Obstructive Pulmonary Disease (COPD) is an irreversible airway obstruction with a high societal burden. Although smoking is known to be the biggest risk factor, additional components need to be considered. In this study, we aim to identify COPD risk factors by applying machine learning models that integrate sociodemographic, clinical, and genetic data to predict COPD development.

Predicting Students' Exam Scores Using Physiological Signals

While acute stress has been shown to have both positive and negative effects on performance, not much is known about the impacts of stress on students grades during examinations. To answer this question, we examined whether a correlation could be found between physiological stress signals and exam performance. We conducted this study using multiple physiological signals of ten undergraduate students over three different exams. The study focused on three signals, i.e., skin temperature, heart rate, and electrodermal activity. We extracted statistics as features and fed them into a variety of binary classifiers to predict relatively higher or lower grades. Experimental results showed up to 0.81 ROC-AUC with k-nearest neighbor algorithm among various machine learning algorithms.

Deep Learning and Symbolic Regression for Discovering Parametric Equations

Symbolic regression is a machine learning technique that can learn the governing formulas of data and thus has the potential to transform scientific discovery. However, symbolic regression is still limited in the complexity and dimensionality of the systems that it can analyze. Deep learning on the other hand has transformed machine learning in its ability to analyze extremely complex and high-dimensional datasets. We propose a neural network architecture to extend symbolic regression to parametric systems where some coefficient may vary but the structure of the underlying governing equation remains constant. We demonstrate our method on various analytic expressions, ODEs, and PDEs with varying coefficients and show that it extrapolates well outside of the training domain. The neural network-based architecture can also integrate with other deep learning architectures so that it can analyze high-dimensional data while being trained end-to-end. To this end we integrate our architecture with convolutional neural networks to analyze 1D images of varying spring systems.

Surrogate- and invariance-boosted contrastive learning for data-scarce applications in science

Deep learning techniques have been increasingly applied to the natural sciences, e.g., for property prediction and optimization or material discovery. A fundamental ingredient of such approaches is the vast quantity of labelled data needed to train the model; this poses severe challenges in data-scarce settings where obtaining labels requires substantial computational or labor resources. Here, we introduce surrogate- and invariance-boosted contrastive learning (SIB-CL), a deep learning framework which incorporates three ``inexpensive'' and easily obtainable auxiliary information sources to overcome data scarcity. Specifically, these are: 1)~abundant unlabeled data, 2)~prior knowledge of symmetries or invariances and 3)~surrogate data obtained at near-zero cost. We demonstrate SIB-CL's effectiveness and generality on various scientific problems, e.g., predicting the density-of-states of 2D photonic crystals and solving the 3D time-independent Schrodinger equation. SIB-CL consistently results in orders of magnitude reduction in the number of labels needed to achieve the same network accuracies.

Scalable and Flexible Deep Bayesian Optimization with Auxiliary Information for Scientific Problems

Bayesian optimization (BO) is a popular paradigm for global optimization of expensive black-box functions, but there are many domains where the function is not completely black-box. The data may have some known structure, e.g. symmetries, and the data generation process can yield useful intermediate or auxiliary information in addition to the value of the optimization objective. However, surrogate models traditionally employed in BO, such as Gaussian Processes (GPs), scale poorly with dataset size and struggle to incorporate known structure or auxiliary information. Instead, we propose performing BO on complex, structured problems by using Bayesian Neural Networks (BNNs), a class of scalable surrogate models that have the representation power and flexibility to handle structured data and exploit auxiliary information. We demonstrate BO on a number of realistic problems in physics and chemistry, including topology optimization of photonic crystal materials using convolutional neural networks, and chemical property optimization of molecules using graph neural networks. On these complex tasks, we show that BNNs often outperform GPs as surrogate models for BO in terms of both sampling efficiency and computational cost.

Interpretable Neuroevolutionary Models for Learning Non-Differentiable Functions and Programs

A key factor in the modern success of deep learning is the astonishing expressive power of neural networks. However, this comes at the cost of complex, black-boxed models that are unable to extrapolate beyond the domain of the training dataset, conflicting with goals of expressing physical laws or building human-readable programs. In this paper, we introduce OccamNet, a neural network model that can find interpretable, compact and sparse solutions for fitting data, \`{a} la Occam's razor. Our model defines a probability distribution over a non-differentiable function space, and we introduce an optimization method that samples functions and updates the weights based on cross-entropy matching in an evolutionary strategy: we train by biasing the probability mass towards better fitting solutions. We demonstrate that we can fit a variety of algorithms, ranging from simple analytic functions through recursive programs to even simple image classification. Our method takes minimal memory footprint, does not require AI accelerators for efficient training, fits complicated functions in minutes of training on a single CPU, and demonstrates significant performance gains when scaled on GPU. Our implementation, demonstrations and instructions for reproducing the experiments are available at https://github.com/AllanSCosta/occam-net.

Integration of Neural Network-Based Symbolic Regression in Deep Learning for Scientific Discovery

Symbolic regression is a powerful technique that can discover analytical equations that describe data, which can lead to explainable models and generalizability outside of the training data set. In contrast, neural networks have achieved amazing levels of accuracy on image recognition and natural language processing tasks, but are often seen as black-box models that are difficult to interpret and typically extrapolate poorly. Here we use a neural network-based architecture for symbolic regression that we call the Sequential Equation Learner (SEQL) network and integrate it with other deep learning architectures such that the whole system can be trained end-to-end through backpropagation. To demonstrate the power of such systems, we study their performance on several substantially different tasks. First, we show that the neural network can perform symbolic regression and learn the form of several functions. Next, we present an MNIST arithmetic task where a separate part of the neural network extracts the digits. Finally, we demonstrate prediction of dynamical systems where an unknown parameter is extracted through an encoder. We find that the EQL-based architecture can extrapolate quite well outside of the training data set compared to a standard neural network-based architecture, paving the way for deep learning to be applied in scientific exploration and discovery.

Toward estimating personal well-being using voice

Estimating personal well-being draws increasing attention particularly from healthcare and pharmaceutical industries. We propose an approach to estimate personal well-being in terms of various measurements such as anxiety, sleep quality and mood using voice. With clinically validated questionnaires to score those measurements in a self-assessed way, we extract salient features from voice and train regression models with deep neural networks. Experiments with the collected database of 219 subjects show promising results in predicting the well-being related measurements; concordance correlation coefficients (CCC) between self-assessed scores and predicted scores are 0.41 for anxiety, 0.44 for sleep quality and 0.38 for mood.

Extracting Interpretable Physical Parameters from Spatiotemporal Systems using Unsupervised Learning

Experimental data is often affected by uncontrolled variables that make analysis and interpretation difficult. For spatiotemporal systems, this problem is further exacerbated by their intricate dynamics. Modern machine learning methods are particularly well-suited for analyzing and modeling complex datasets, but to be effective in science, the result needs to be interpretable. We demonstrate an unsupervised learning technique for extracting interpretable physical parameters from noisy spatiotemporal data and for building a transferable model of the system. In particular, we implement a physics-informed architecture based on variational autoencoders that is designed for analyzing systems governed by partial differential equations (PDEs). The architecture is trained end-to-end and extracts latent parameters that parameterize the dynamics of a learned predictive model for the system. To test our method, we train our model on simulated data from a variety of PDEs with varying dynamical parameters that act as uncontrolled variables. Numerical experiments show that our method can accurately identify relevant parameters and extract them from raw and even noisy spatiotemporal data (tested with roughly 10% added noise). These extracted parameters correlate well (linearly with $R^2 > 0.95$) with the ground truth physical parameters used to generate the datasets. Our method for discovering interpretable latent parameters in spatiotemporal systems will allow us to better analyze and understand real-world phenomena and datasets, which often have unknown and uncontrolled variables that alter the system dynamics and cause varying behaviors that are difficult to disentangle.