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In a longitudinal clinical registry, different measurement instruments might have been used for assessing individuals at different time points. To combine them, we investigate deep learning techniques for obtaining a joint latent representation, to which the items of different measurement instruments are mapped. This corresponds to domain adaptation, an established concept in computer science for image data. Using the proposed approach as an example, we evaluate the potential of domain adaptation in a longitudinal cohort setting with a rather small number of time points, motivated by an application with different motor function measurement instruments in a registry of spinal muscular atrophy (SMA) patients. There, we model trajectories in the latent representation by ordinary differential equations (ODEs), where person-specific ODE parameters are inferred from baseline characteristics. The goodness of fit and complexity of the ODE solutions then allows to judge the measurement instrument mappings. We subsequently explore how alignment can be improved by incorporating corresponding penalty terms into model fitting. To systematically investigate the effect of differences between measurement instruments, we consider several scenarios based on modified SMA data, including scenarios where a mapping should be feasible in principle and scenarios where no perfect mapping is available. While misalignment increases in more complex scenarios, some structure is still recovered, even if the availability of measurement instruments depends on patient state. A reasonable mapping is feasible also in the more complex real SMA dataset. These results indicate that domain adaptation might be more generally useful in statistical modeling for longitudinal registry data.

This paper elucidates the challenges and opportunities inherent in integrating data-driven methodologies into geotechnics, drawing inspiration from the success of materials informatics. Highlighting the intricacies of soil complexity, heterogeneity, and the lack of comprehensive data, the discussion underscores the pressing need for community-driven database initiatives and open science movements. By leveraging the transformative power of deep learning, particularly in feature extraction from high-dimensional data and the potential of transfer learning, we envision a paradigm shift towards a more collaborative and innovative geotechnics field. The paper concludes with a forward-looking stance, emphasizing the revolutionary potential brought about by advanced computational tools like large language models in reshaping geotechnics informatics.

Inspired by the success of WaveNet in multi-subject speech synthesis, we propose a novel neural network based on causal convolutions for multi-subject motion modeling and generation. The network can capture the intrinsic characteristics of the motion of different subjects, such as the influence of skeleton scale variation on motion style. Moreover, after fine-tuning the network using a small motion dataset for a novel skeleton that is not included in the training dataset, it is able to synthesize high-quality motions with a personalized style for the novel skeleton. The experimental results demonstrate that our network can model the intrinsic characteristics of motions well and can be applied to various motion modeling and synthesis tasks.

Learning from human feedback (LHF) -- and in particular learning from pairwise preferences -- has recently become a crucial ingredient in training large language models (LLMs), and has been the subject of much research. Most recent works frame it as a reinforcement learning problem, where a reward function is learned from pairwise preference data and the LLM is treated as a policy which is adapted to maximize the rewards, often under additional regularization constraints. We propose an alternative interpretation which centers on the generative process for pairwise preferences and treats LHF as a density estimation problem. We provide theoretical and empirical results showing that for a family of generative processes defined via preference behavior distribution equations, training a reward function on pairwise preferences effectively models an annotator's implicit preference distribution. Finally, we discuss and present findings on "annotator misspecification" -- failure cases where wrong modeling assumptions are made about annotator behavior, resulting in poorly-adapted models -- suggesting that approaches that learn from pairwise human preferences could have trouble learning from a population of annotators with diverse viewpoints.

We present compact semi-implicit finite difference schemes on structured grids for numerical solutions of the advection by an external velocity and by a speed in normal direction that are applicable in level set methods. The most involved numerical scheme is third order accurate for the linear advection with a space dependent velocity and unconditionally stable in the sense of von Neumann stability analysis. We also present a simple high-resolution scheme that gives a TVD (Total Variation Diminishing) approximation of the spatial derivative for the advected level set function. In the case of nonlinear advection, the semi-implicit discretization is proposed to linearize the problem. The compact form of implicit stencil in numerical schemes containing unknowns only in the upwind direction allows applications of efficient algebraic solvers like fast sweeping methods. Numerical tests to evolve a smooth and non-smooth interface and an example with a large variation of velocity confirm the good accuracy of the methods and fast convergence of the algebraic solver even in the case of very large Courant numbers.

Radiology reports are an instrumental part of modern medicine, informing key clinical decisions such as diagnosis and treatment. The worldwide shortage of radiologists, however, restricts access to expert care and imposes heavy workloads, contributing to avoidable errors and delays in report delivery. While recent progress in automated report generation with vision-language models offer clear potential in ameliorating the situation, the path to real-world adoption has been stymied by the challenge of evaluating the clinical quality of AI-generated reports. In this study, we build a state-of-the-art report generation system for chest radiographs, Flamingo-CXR, by fine-tuning a well-known vision-language foundation model on radiology data. To evaluate the quality of the AI-generated reports, a group of 16 certified radiologists provide detailed evaluations of AI-generated and human written reports for chest X-rays from an intensive care setting in the United States and an inpatient setting in India. At least one radiologist (out of two per case) preferred the AI report to the ground truth report in over 60$\%$ of cases for both datasets. Amongst the subset of AI-generated reports that contain errors, the most frequently cited reasons were related to the location and finding, whereas for human written reports, most mistakes were related to severity and finding. This disparity suggested potential complementarity between our AI system and human experts, prompting us to develop an assistive scenario in which Flamingo-CXR generates a first-draft report, which is subsequently revised by a clinician. This is the first demonstration of clinician-AI collaboration for report writing, and the resultant reports are assessed to be equivalent or preferred by at least one radiologist to reports written by experts alone in 80$\%$ of in-patient cases and 66$\%$ of intensive care cases.

Spatio-temporal pathogen spread is often partially observed at the metapopulation scale. Available data correspond to proxies and are incomplete, censored and heterogeneous. Moreover, representing such biological systems often leads to complex stochastic models. Such complexity together with data characteristics make the analysis of these systems a challenge. Our objective was to develop a new inference procedure to estimate key parameters of stochastic metapopulation models of animal disease spread from longitudinal and spatial datasets, while accurately accounting for characteristics of census data. We applied our procedure to provide new knowledge on the regional spread of \emph{Mycobacterium avium} subsp. \emph{paratuberculosis} (\emph{Map}), which causes bovine paratuberculosis, a worldwide endemic disease. \emph{Map} spread between herds through trade movements was modeled with a stochastic mechanistic model. Comprehensive data from 2005 to 2013 on cattle movements in 12,857 dairy herds in Brittany (western France) and partial data on animal infection status in 2,278 herds sampled from 2007 to 2013 were used. Inference was performed using a new criterion based on a Monte-Carlo approximation of a composite likelihood, coupled to a numerical optimization algorithm (Nelder-Mead Simplex-like). Our criterion showed a clear superiority to alternative ones in identifying the right parameter values, as assessed by an empirical identifiability on simulated data. Point estimates and profile likelihoods allowed us to establish the initial state of the system, identify the risk of pathogen introduction from outside the metapopulation, and confirm the assumption of the low sensitivity of the diagnostic test. Our inference procedure could easily be applied to other spatio-temporal infection dynamics, especially when ABC-like methods face challenges in defining relevant summary statistics.

We prove closed-form equations for the exact high-dimensional asymptotics of a family of first order gradient-based methods, learning an estimator (e.g. M-estimator, shallow neural network, ...) from observations on Gaussian data with empirical risk minimization. This includes widely used algorithms such as stochastic gradient descent (SGD) or Nesterov acceleration. The obtained equations match those resulting from the discretization of dynamical mean-field theory (DMFT) equations from statistical physics when applied to gradient flow. Our proof method allows us to give an explicit description of how memory kernels build up in the effective dynamics, and to include non-separable update functions, allowing datasets with non-identity covariance matrices. Finally, we provide numerical implementations of the equations for SGD with generic extensive batch-size and with constant learning rates.

Inverse imaging problems that are ill-posed can be encountered across multiple domains of science and technology, ranging from medical diagnosis to astronomical studies. To reconstruct images from incomplete and distorted data, it is necessary to create algorithms that can take into account both, the physical mechanisms responsible for generating these measurements and the intrinsic characteristics of the images being analyzed. In this work, the sparse representation of images is reviewed, which is a realistic, compact and effective generative model for natural images inspired by the visual system of mammals. It enables us to address ill-posed linear inverse problems by training the model on a vast collection of images. Moreover, we extend the application of sparse coding to solve the non-linear and ill-posed problem in microwave tomography imaging, which could lead to a significant improvement of the state-of-the-arts algorithms.

We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.