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Differences in staining and imaging procedures can cause significant color variations in histopathology images, leading to poor generalization when deploying deep-learning models trained from a different data source. Various color augmentation methods have been proposed to generate synthetic images during training to make models more robust, eliminating the need for stain normalization during test time. Many color augmentation methods leverage domain labels to generate synthetic images. This approach causes three significant challenges to scaling such a model. Firstly, incorporating data from a new domain into deep-learning models trained on existing domain labels is not straightforward. Secondly, dependency on domain labels prevents the use of pathology images without domain labels to improve model performance. Finally, implementation of these methods becomes complicated when multiple domain labels (e.g., patient identification, medical center, etc) are associated with a single image. We introduce ContriMix, a novel domain label free stain color augmentation method based on DRIT++, a style-transfer method. Contrimix leverages sample stain color variation within a training minibatch and random mixing to extract content and attribute information from pathology images. This information can be used by a trained ContriMix model to create synthetic images to improve the performance of existing classifiers. ContriMix outperforms competing methods on the Camelyon17-WILDS dataset. Its performance is consistent across different slides in the test set while being robust to the color variation from rare substances in pathology images. We make our code and trained ContriMix models available for research use. The code for ContriMix can be found at //gitlab.com/huutan86/contrimix

Multi-contrast (MC) Magnetic Resonance Imaging (MRI) reconstruction aims to incorporate a reference image of auxiliary modality to guide the reconstruction process of the target modality. Known MC reconstruction methods perform well with a fully sampled reference image, but usually exhibit inferior performance, compared to single-contrast (SC) methods, when the reference image is missing or of low quality. To address this issue, we propose DuDoUniNeXt, a unified dual-domain MRI reconstruction network that can accommodate to scenarios involving absent, low-quality, and high-quality reference images. DuDoUniNeXt adopts a hybrid backbone that combines CNN and ViT, enabling specific adjustment of image domain and k-space reconstruction. Specifically, an adaptive coarse-to-fine feature fusion module (AdaC2F) is devised to dynamically process the information from reference images of varying qualities. Besides, a partially shared shallow feature extractor (PaSS) is proposed, which uses shared and distinct parameters to handle consistent and discrepancy information among contrasts. Experimental results demonstrate that the proposed model surpasses state-of-the-art SC and MC models significantly. Ablation studies show the effectiveness of the proposed hybrid backbone, AdaC2F, PaSS, and the dual-domain unified learning scheme.

Raman spectroscopy is widely used across scientific domains to characterize the chemical composition of samples in a non-destructive, label-free manner. Many applications entail the unmixing of signals from mixtures of molecular species to identify the individual components present and their proportions, yet conventional methods for chemometrics often struggle with complex mixture scenarios encountered in practice. Here, we develop hyperspectral unmixing algorithms based on autoencoder neural networks, and we systematically validate them using both synthetic and experimental benchmark datasets created in-house. Our results demonstrate that unmixing autoencoders provide improved accuracy, robustness and efficiency compared to standard unmixing methods. We also showcase the applicability of autoencoders to complex biological settings by showing improved biochemical characterization of volumetric Raman imaging data from a monocytic cell.

Several mixed-effects models for longitudinal data have been proposed to accommodate the non-linearity of late-life cognitive trajectories and assess the putative influence of covariates on it. No prior research provides a side-by-side examination of these models to offer guidance on their proper application and interpretation. In this work, we examined five statistical approaches previously used to answer research questions related to non-linear changes in cognitive aging: the linear mixed model (LMM) with a quadratic term, LMM with splines, the functional mixed model, the piecewise linear mixed model, and the sigmoidal mixed model. We first theoretically describe the models. Next, using data from two prospective cohorts with annual cognitive testing, we compared the interpretation of the models by investigating associations of education on cognitive change before death. Lastly, we performed a simulation study to empirically evaluate the models and provide practical recommendations. Except for the LMM-quadratic, the fit of all models was generally adequate to capture non-linearity of cognitive change and models were relatively robust. Although spline-based models have no interpretable nonlinearity parameters, their convergence was easier to achieve, and they allow graphical interpretation. In contrast, piecewise and sigmoidal models, with interpretable non-linear parameters, may require more data to achieve convergence.

With the increasing availability of large scale datasets, computational power and tools like automatic differentiation and expressive neural network architectures, sequential data are now often treated in a data-driven way, with a dynamical model trained from the observation data. While neural networks are often seen as uninterpretable black-box architectures, they can still benefit from physical priors on the data and from mathematical knowledge. In this paper, we use a neural network architecture which leverages the long-known Koopman operator theory to embed dynamical systems in latent spaces where their dynamics can be described linearly, enabling a number of appealing features. We introduce methods that enable to train such a model for long-term continuous reconstruction, even in difficult contexts where the data comes in irregularly-sampled time series. The potential for self-supervised learning is also demonstrated, as we show the promising use of trained dynamical models as priors for variational data assimilation techniques, with applications to e.g. time series interpolation and forecasting.

Accurate medical image segmentation demands the integration of multi-scale information, spanning from local features to global dependencies. However, it is challenging for existing methods to model long-range global information, where convolutional neural networks (CNNs) are constrained by their local receptive fields, and vision transformers (ViTs) suffer from high quadratic complexity of their attention mechanism. Recently, Mamba-based models have gained great attention for their impressive ability in long sequence modeling. Several studies have demonstrated that these models can outperform popular vision models in various tasks, offering higher accuracy, lower memory consumption, and less computational burden. However, existing Mamba-based models are mostly trained from scratch and do not explore the power of pretraining, which has been proven to be quite effective for data-efficient medical image analysis. This paper introduces a novel Mamba-based model, Swin-UMamba, designed specifically for medical image segmentation tasks, leveraging the advantages of ImageNet-based pretraining. Our experimental results reveal the vital role of ImageNet-based training in enhancing the performance of Mamba-based models. Swin-UMamba demonstrates superior performance with a large margin compared to CNNs, ViTs, and latest Mamba-based models. Notably, on AbdomenMRI, Encoscopy, and Microscopy datasets, Swin-UMamba outperforms its closest counterpart U-Mamba_Enc by an average score of 2.72%.

Lensless illumination single-pixel imaging with a multicore fiber (MCF) is a computational imaging technique that enables potential endoscopic observations of biological samples at cellular scale. In this work, we show that this technique is tantamount to collecting multiple symmetric rank-one projections (SROP) of an interferometric matrix--a matrix encoding the spectral content of the sample image. In this model, each SROP is induced by the complex sketching vector shaping the incident light wavefront with a spatial light modulator (SLM), while the projected interferometric matrix collects up to $O(Q^2)$ image frequencies for a $Q$-core MCF. While this scheme subsumes previous sensing modalities, such as raster scanning (RS) imaging with beamformed illumination, we demonstrate that collecting the measurements of $M$ random SLM configurations--and thus acquiring $M$ SROPs--allows us to estimate an image of interest if $M$ and $Q$ scale log-linearly with the image sparsity level This demonstration is achieved both theoretically, with a specific restricted isometry analysis of the sensing scheme, and with extensive Monte Carlo experiments. On a practical side, we perform a single calibration of the sensing system robust to certain deviations to the theoretical model and independent of the sketching vectors used during the imaging phase. Experimental results made on an actual MCF system demonstrate the effectiveness of this imaging procedure on a benchmark image.

Stochastic reservoir characterization, a critical aspect of subsurface exploration for oil and gas reservoirs, relies on stochastic methods to model and understand subsurface properties using seismic data. This paper addresses the computational challenges associated with Bayesian reservoir inversion methods, focusing on two key obstacles: the demanding forward model and the high dimensionality of Gaussian random fields. Leveraging the generalized Bayesian approach, we replace the intricate forward function with a computationally efficient multivariate adaptive regression splines method, resulting in a 34 acceleration in computational efficiency. For handling high-dimensional Gaussian random fields, we employ a fast Fourier transform (FFT) technique. Additionally, we explore the preconditioned Crank-Nicolson method for sampling, providing a more efficient exploration of high-dimensional parameter spaces. The practicality and efficacy of our approach are tested extensively in simulations and its validity is demonstrated in application to the Alvheim field data.

This paper re-examines the security of three related block cipher modes of operation designed to provide authenticated encryption. These modes, known as PES-PCBC, IOBC and EPBC, were all proposed in the mid-1990s. However, analyses of security of the latter two modes were published more recently. In each case one or more papers describing security issues with the schemes were eventually published, although a flaw in one of these analyses (of EPBC) was subsequently discovered - this means that until now EPBC had no known major issues. This paper establishes that, despite this, all three schemes possess defects which should prevent their use - especially as there are a number of efficient alternative schemes possessing proofs of security.

We present ResMLP, an architecture built entirely upon multi-layer perceptrons for image classification. It is a simple residual network that alternates (i) a linear layer in which image patches interact, independently and identically across channels, and (ii) a two-layer feed-forward network in which channels interact independently per patch. When trained with a modern training strategy using heavy data-augmentation and optionally distillation, it attains surprisingly good accuracy/complexity trade-offs on ImageNet. We will share our code based on the Timm library and pre-trained models.