The development of therapeutic antibodies heavily relies on accurate predictions of how antigens will interact with antibodies. Existing computational methods in antibody design often overlook crucial conformational changes that antigens undergo during the binding process, significantly impacting the reliability of the resulting antibodies. To bridge this gap, we introduce dyAb, a flexible framework that incorporates AlphaFold2-driven predictions to model pre-binding antigen structures and specifically addresses the dynamic nature of antigen conformation changes. Our dyAb model leverages a unique combination of coarse-grained interface alignment and fine-grained flow matching techniques to simulate the interaction dynamics and structural evolution of the antigen-antibody complex, providing a realistic representation of the binding process. Extensive experiments show that dyAb significantly outperforms existing models in antibody design involving changing antigen conformations. These results highlight dyAb's potential to streamline the design process for therapeutic antibodies, promising more efficient development cycles and improved outcomes in clinical applications.

Multi-spectral imaging, which simultaneously captures the spatial and spectral information of a scene, is widely used across diverse fields, including remote sensing, biomedical imaging, and agricultural monitoring. Here, we introduce a snapshot multi-spectral imaging approach employing a standard monochrome image sensor with no additional spectral filters or customized components. Our system leverages the inherent chromatic aberration of wavelength-dependent defocusing as a natural source of physical encoding of multi-spectral information; this encoded image information is rapidly decoded via a deep learning-based multi-spectral Fourier Imager Network (mFIN). We experimentally tested our method with six illumination bands and demonstrated an overall accuracy of 92.98% for predicting the illumination channels at the input and achieved a robust multi-spectral image reconstruction on various test objects. This deep learning-powered framework achieves high-quality multi-spectral image reconstruction using snapshot image acquisition with a monochrome image sensor and could be useful for applications in biomedicine, industrial quality control, and agriculture, among others.

Imaging mass spectrometry (IMS) is a powerful tool for untargeted, highly multiplexed molecular mapping of tissue in biomedical research. IMS offers a means of mapping the spatial distributions of molecular species in biological tissue with unparalleled chemical specificity and sensitivity. However, most IMS platforms are not able to achieve microscopy-level spatial resolution and lack cellular morphological contrast, necessitating subsequent histochemical staining, microscopic imaging and advanced image registration steps to enable molecular distributions to be linked to specific tissue features and cell types. Here, we present a virtual histological staining approach that enhances spatial resolution and digitally introduces cellular morphological contrast into mass spectrometry images of label-free human tissue using a diffusion model. Blind testing on human kidney tissue demonstrated that the virtually stained images of label-free samples closely match their histochemically stained counterparts (with Periodic Acid-Schiff staining), showing high concordance in identifying key renal pathology structures despite utilizing IMS data with 10-fold larger pixel size. Additionally, our approach employs an optimized noise sampling technique during the diffusion model's inference process to reduce variance in the generated images, yielding reliable and repeatable virtual staining. We believe this virtual staining method will significantly expand the applicability of IMS in life sciences and open new avenues for mass spectrometry-based biomedical research.

Virtual staining of tissue offers a powerful tool for transforming label-free microscopy images of unstained tissue into equivalents of histochemically stained samples. This study presents a diffusion model-based super-resolution virtual staining approach utilizing a Brownian bridge process to enhance both the spatial resolution and fidelity of label-free virtual tissue staining, addressing the limitations of traditional deep learning-based methods. Our approach integrates novel sampling techniques into a diffusion model-based image inference process to significantly reduce the variance in the generated virtually stained images, resulting in more stable and accurate outputs. Blindly applied to lower-resolution auto-fluorescence images of label-free human lung tissue samples, the diffusion-based super-resolution virtual staining model consistently outperformed conventional approaches in resolution, structural similarity and perceptual accuracy, successfully achieving a super-resolution factor of 4-5x, increasing the output space-bandwidth product by 16-25-fold compared to the input label-free microscopy images. Diffusion-based super-resolved virtual tissue staining not only improves resolution and image quality but also enhances the reliability of virtual staining without traditional chemical staining, offering significant potential for clinical diagnostics.

Bayesian inference provides a principled probabilistic framework for quantifying uncertainty by updating beliefs based on prior knowledge and observed data through Bayes' theorem. In Bayesian deep learning, neural network weights are treated as random variables with prior distributions, allowing for a probabilistic interpretation and quantification of predictive uncertainty. However, Bayesian methods lack theoretical generalization guarantees for unseen data. PAC-Bayesian analysis addresses this limitation by offering a frequentist framework to derive generalization bounds for randomized predictors, thereby certifying the reliability of Bayesian methods in machine learning. Temperature $T$, or inverse-temperature $\lambda = \frac{1}{T}$, originally from statistical mechanics in physics, naturally arises in various areas of statistical inference, including Bayesian inference and PAC-Bayesian analysis. In Bayesian inference, when $T < 1$ (``cold'' posteriors), the likelihood is up-weighted, resulting in a sharper posterior distribution. Conversely, when $T > 1$ (``warm'' posteriors), the likelihood is down-weighted, leading to a more diffuse posterior distribution. By balancing the influence of observed data and prior regularization, temperature adjustments can address issues of underfitting or overfitting in Bayesian models, bringing improved predictive performance.

PAC-Bayesian analysis is a frequentist framework for incorporating prior knowledge into learning. It was inspired by Bayesian learning, which allows sequential data processing and naturally turns posteriors from one processing step into priors for the next. However, despite two and a half decades of research, the ability to update priors sequentially without losing confidence information along the way remained elusive for PAC-Bayes. While PAC-Bayes allows construction of data-informed priors, the final confidence intervals depend only on the number of points that were not used for the construction of the prior, whereas confidence information in the prior, which is related to the number of points used to construct the prior, is lost. This limits the possibility and benefit of sequential prior updates, because the final bounds depend only on the size of the final batch. We present a novel and, in retrospect, surprisingly simple and powerful PAC-Bayesian procedure that allows sequential prior updates with no information loss. The procedure is based on a novel decomposition of the expected loss of randomized classifiers. The decomposition rewrites the loss of the posterior as an excess loss relative to a downscaled loss of the prior plus the downscaled loss of the prior, which is bounded recursively. As a side result, we also present a generalization of the split-kl and PAC-Bayes-split-kl inequalities to discrete random variables, which we use for bounding the excess losses, and which can be of independent interest. In empirical evaluation the new procedure significantly outperforms state-of-the-art.

Human epidermal growth factor receptor 2 (HER2) is a critical protein in cancer cell growth that signifies the aggressiveness of breast cancer (BC) and helps predict its prognosis. Accurate assessment of immunohistochemically (IHC) stained tissue slides for HER2 expression levels is essential for both treatment guidance and understanding of cancer mechanisms. Nevertheless, the traditional workflow of manual examination by board-certified pathologists encounters challenges, including inter- and intra-observer inconsistency and extended turnaround times. Here, we introduce a deep learning-based approach utilizing pyramid sampling for the automated classification of HER2 status in IHC-stained BC tissue images. Our approach analyzes morphological features at various spatial scales, efficiently managing the computational load and facilitating a detailed examination of cellular and larger-scale tissue-level details. This method addresses the tissue heterogeneity of HER2 expression by providing a comprehensive view, leading to a blind testing classification accuracy of 84.70%, on a dataset of 523 core images from tissue microarrays. Our automated system, proving reliable as an adjunct pathology tool, has the potential to enhance diagnostic precision and evaluation speed, and might significantly impact cancer treatment planning.

Systemic amyloidosis is a group of diseases characterized by the deposition of misfolded proteins in various organs and tissues, leading to progressive organ dysfunction and failure. Congo red stain is the gold standard chemical stain for the visualization of amyloid deposits in tissue sections, as it forms complexes with the misfolded proteins and shows a birefringence pattern under polarized light microscopy. However, Congo red staining is tedious and costly to perform, and prone to false diagnoses due to variations in the amount of amyloid, staining quality and expert interpretation through manual examination of tissue under a polarization microscope. Here, we report the first demonstration of virtual birefringence imaging and virtual Congo red staining of label-free human tissue to show that a single trained neural network can rapidly transform autofluorescence images of label-free tissue sections into brightfield and polarized light microscopy equivalent images, matching the histochemically stained versions of the same samples. We demonstrate the efficacy of our method with blind testing and pathologist evaluations on cardiac tissue where the virtually stained images agreed well with the histochemically stained ground truth images. Our virtually stained polarization and brightfield images 1 highlight amyloid birefringence patterns in a consistent, reproducible manner while mitigating diagnostic challenges due to variations in the quality of chemical staining and manual imaging processes as part of the clinical workflow.

Predicting protein stability changes induced by single-point mutations has been a persistent challenge over the years, attracting immense interest from numerous researchers. The ability to precisely predict protein thermostability is pivotal for various subfields and applications in biochemistry, including drug development, protein evolution analysis, and enzyme synthesis. Despite the proposition of multiple methodologies aimed at addressing this issue, few approaches have successfully achieved optimal performance coupled with high computational efficiency. Two principal hurdles contribute to the existing challenges in this domain. The first is the complexity of extracting and aggregating sufficiently representative features from proteins. The second refers to the limited availability of experimental data for protein mutation analysis, further complicating the comprehensive evaluation of model performance on unseen data samples. With the advent of Large Language Models(LLM), such as the ESM models in protein research, profound interpretation of protein features is now accessibly aided by enormous training data. Therefore, LLMs are indeed to facilitate a wide range of protein research. In our study, we introduce an ESM-assisted efficient approach that integrates protein sequence and structural features to predict the thermostability changes in protein upon single-point mutations. Furthermore, we have curated a dataset meticulously designed to preclude data leakage, corresponding to two extensively employed test datasets, to facilitate a more equitable model comparison.

Graph collaborative filtering, which learns user and item representations through message propagation over the user-item interaction graph, has been shown to effectively enhance recommendation performance. However, most current graph collaborative filtering models mainly construct the interaction graph on a single behavior domain (e.g. click), even though users exhibit various types of behaviors on real-world platforms, including actions like click, cart, and purchase. Furthermore, due to variations in user engagement, there exists an imbalance in the scale of different types of behaviors. For instance, users may click and view multiple items but only make selective purchases from a small subset of them. How to alleviate the behavior imbalance problem and utilize information from the multiple behavior graphs concurrently to improve the target behavior conversion (e.g. purchase) remains underexplored. To this end, we propose IMGCF, a simple but effective model to alleviate behavior data imbalance for multi-behavior graph collaborative filtering. Specifically, IMGCF utilizes a multi-task learning framework for collaborative filtering on multi-behavior graphs. Then, to mitigate the data imbalance issue, IMGCF improves representation learning on the sparse behavior by leveraging representations learned from the behavior domain with abundant data volumes. Experiments on two widely-used multi-behavior datasets demonstrate the effectiveness of IMGCF.