Secure and Effective Data Appraisal for Machine Learning

Essential for an unfettered data market is the ability to discreetly select and evaluate training data before finalizing a transaction between the data owner and model owner. To safeguard the privacy of both data and model, this process involves scrutinizing the target model through Multi-Party Computation (MPC). While prior research has posited that the MPC-based evaluation of Transformer models is excessively resource-intensive, this paper introduces an innovative approach that renders data selection practical. The contributions of this study encompass three pivotal elements: (1) a groundbreaking pipeline for confidential data selection using MPC, (2) replicating intricate high-dimensional operations with simplified low-dimensional MLPs trained on a limited subset of pertinent data, and (3) implementing MPC in a concurrent, multi-phase manner. The proposed method is assessed across an array of Transformer models and NLP/CV benchmarks. In comparison to the direct MPC-based evaluation of the target model, our approach substantially reduces the time required, from thousands of hours to mere tens of hours, with only a nominal 0.20% dip in accuracy when training with the selected data.

Multimarginal generative modeling with stochastic interpolants

Given a set of $K$ probability densities, we consider the multimarginal generative modeling problem of learning a joint distribution that recovers these densities as marginals. The structure of this joint distribution should identify multi-way correspondences among the prescribed marginals. We formalize an approach to this task within a generalization of the stochastic interpolant framework, leading to efficient learning algorithms built upon dynamical transport of measure. Our generative models are defined by velocity and score fields that can be characterized as the minimizers of simple quadratic objectives, and they are defined on a simplex that generalizes the time variable in the usual dynamical transport framework. The resulting transport on the simplex is influenced by all marginals, and we show that multi-way correspondences can be extracted. The identification of such correspondences has applications to style transfer, algorithmic fairness, and data decorruption. In addition, the multimarginal perspective enables an efficient algorithm for reducing the dynamical transport cost in the ordinary two-marginal setting. We demonstrate these capacities with several numerical examples.

Certification of Deep Learning Models for Medical Image Segmentation

In medical imaging, segmentation models have known a significant improvement in the past decade and are now used daily in clinical practice. However, similar to classification models, segmentation models are affected by adversarial attacks. In a safety-critical field like healthcare, certifying model predictions is of the utmost importance. Randomized smoothing has been introduced lately and provides a framework to certify models and obtain theoretical guarantees. In this paper, we present for the first time a certified segmentation baseline for medical imaging based on randomized smoothing and diffusion models. Our results show that leveraging the power of denoising diffusion probabilistic models helps us overcome the limits of randomized smoothing. We conduct extensive experiments on five public datasets of chest X-rays, skin lesions, and colonoscopies, and empirically show that we are able to maintain high certified Dice scores even for highly perturbed images. Our work represents the first attempt to certify medical image segmentation models, and we aspire for it to set a foundation for future benchmarks in this crucial and largely uncharted area.

Improved prediction of ligand-protein binding affinities by meta-modeling

The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts, as filtering potential candidates would save time and expenses for finding drugs. Such virtual screening depends in part on methods to predict the binding affinity between ligands and proteins. Given many computational models for binding affinity prediction with varying results across targets, we herein develop a meta-modeling framework by integrating published empirical structure-based docking and sequence-based deep learning models. In building this framework, we evaluate many combinations of individual models, training databases, and linear and nonlinear meta-modeling approaches. We show that many of our meta-models significantly improve affinity predictions over individual base models. Our best meta-models achieve comparable performance to state-of-the-art exclusively structure-based deep learning tools. Overall, we demonstrate that diverse modeling approaches can be ensembled together to gain substantial improvement in binding affinity prediction while allowing control over input features such as physicochemical properties or molecular descriptors.

SIMD Dataflow Co-optimization for Efficient Neural Networks Inferences on CPUs

We address the challenges associated with deploying neural networks on CPUs, with a particular focus on minimizing inference time while maintaining accuracy. Our novel approach is to use the dataflow (i.e., computation order) of a neural network to explore data reuse opportunities using heuristic-guided analysis and a code generation framework, which enables exploration of various Single Instruction, Multiple Data (SIMD) implementations to achieve optimized neural network execution. Our results demonstrate that the dataflow that keeps outputs in SIMD registers while also maximizing both input and weight reuse consistently yields the best performance for a wide variety of inference workloads, achieving up to 3x speedup for 8-bit neural networks, and up to 4.8x speedup for binary neural networks, respectively, over the optimized implementations of neural networks today.

Deciphering Diagnoses: How Large Language Models Explanations Influence Clinical Decision Making

Clinical Decision Support Systems (CDSS) utilize evidence-based knowledge and patient data to offer real-time recommendations, with Large Language Models (LLMs) emerging as a promising tool to generate plain-text explanations for medical decisions. This study explores the effectiveness and reliability of LLMs in generating explanations for diagnoses based on patient complaints. Three experienced doctors evaluated LLM-generated explanations of the connection between patient complaints and doctor and model-assigned diagnoses across several stages. Experimental results demonstrated that LLM explanations significantly increased doctors' agreement rates with given diagnoses and highlighted potential errors in LLM outputs, ranging from 5% to 30%. The study underscores the potential and challenges of LLMs in healthcare and emphasizes the need for careful integration and evaluation to ensure patient safety and optimal clinical utility.

Statistical physics, Bayesian inference and neural information processing

Lecture notes from the course given by Professor Sara A. Solla at the Les Houches summer school on "Statistical physics of Machine Learning". The notes discuss neural information processing through the lens of Statistical Physics. Contents include Bayesian inference and its connection to a Gibbs description of learning and generalization, Generalized Linear Models as a controlled alternative to backpropagation through time, and linear and non-linear techniques for dimensionality reduction.

Enhancing Representation Learning for Periodic Time Series with Floss: A Frequency Domain Regularization Approach

Time series analysis is a fundamental task in various application domains, and deep learning approaches have demonstrated remarkable performance in this area. However, many real-world time series data exhibit significant periodic or quasi-periodic dynamics that are often not adequately captured by existing deep learning-based solutions. This results in an incomplete representation of the underlying dynamic behaviors of interest. To address this gap, we propose an unsupervised method called Floss that automatically regularizes learned representations in the frequency domain. The Floss method first automatically detects major periodicities from the time series. It then employs periodic shift and spectral density similarity measures to learn meaningful representations with periodic consistency. In addition, Floss can be easily incorporated into both supervised, semi-supervised, and unsupervised learning frameworks. We conduct extensive experiments on common time series classification, forecasting, and anomaly detection tasks to demonstrate the effectiveness of Floss. We incorporate Floss into several representative deep learning solutions to justify our design choices and demonstrate that it is capable of automatically discovering periodic dynamics and improving state-of-the-art deep learning models.

Multiple Physics-Informed Neural Network for Biomedical Tube Flows

Fluid dynamics computations for tube-like geometries are important for biomedical evaluation of vascular and airway fluid dynamics. Physics-Informed Neural Networks (PINNs) have recently emerged as a good alternative to traditional computational fluid dynamics (CFD) methods. The vanilla PINN, however, requires much longer training time than the traditional CFD methods for each specific flow scenario and thus does not justify its mainstream use. Here, we explore the use of the multi-case PINN approach for calculating biomedical tube flows, where varied geometry cases are parameterized and pre-trained on the PINN, such that results for unseen geometries can be obtained in real time. Our objective is to identify network architecture, tube-specific, and regularization strategies that can optimize this, via experiments on a series of idealized 2D stenotic tube flows.

Automated CT Lung Cancer Screening Workflow using 3D Camera

Despite recent developments in CT planning that enabled automation in patient positioning, time-consuming scout scans are still needed to compute dose profile and ensure the patient is properly positioned. In this paper, we present a novel method which eliminates the need for scout scans in CT lung cancer screening by estimating patient scan range, isocenter, and Water Equivalent Diameter (WED) from 3D camera images. We achieve this task by training an implicit generative model on over 60,000 CT scans and introduce a novel approach for updating the prediction using real-time scan data. We demonstrate the effectiveness of our method on a testing set of 110 pairs of depth data and CT scan, resulting in an average error of 5mm in estimating the isocenter, 13mm in determining the scan range, 10mm and 16mm in estimating the AP and lateral WED respectively. The relative WED error of our method is 4%, which is well within the International Electrotechnical Commission (IEC) acceptance criteria of 10%.