The accurate classification of lymphoma subtypes using hematoxylin and eosin (H&E)-stained tissue is complicated by the wide range of morphological features these cancers can exhibit. We present LymphoML - an interpretable machine learning method that identifies morphologic features that correlate with lymphoma subtypes. Our method applies steps to process H&E-stained tissue microarray cores, segment nuclei and cells, compute features encompassing morphology, texture, and architecture, and train gradient-boosted models to make diagnostic predictions. LymphoML's interpretable models, developed on a limited volume of H&E-stained tissue, achieve non-inferior diagnostic accuracy to pathologists using whole-slide images and outperform black box deep-learning on a dataset of 670 cases from Guatemala spanning 8 lymphoma subtypes. Using SHapley Additive exPlanation (SHAP) analysis, we assess the impact of each feature on model prediction and find that nuclear shape features are most discriminative for DLBCL (F1-score: 78.7%) and classical Hodgkin lymphoma (F1-score: 74.5%). Finally, we provide the first demonstration that a model combining features from H&E-stained tissue with features from a standardized panel of 6 immunostains results in a similar diagnostic accuracy (85.3%) to a 46-stain panel (86.1%).
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Dynamic crack branching in unsaturated porous media holds significant relevance in various fields, including geotechnical engineering, geosciences, and petroleum engineering. This article presents a numerical investigation into dynamic crack branching in unsaturated porous media using a recently developed coupled micro-periporomechanics paradigm. This paradigm extends the periporomechanics model by incorporating the micro-rotation of the solid skeleton. Within this framework, each material point is equipped with three degrees of freedom: displacement, micro-rotation, and fluid pressure. Consistent with the Cosserat continuum theory, a length scale associated with the micro-rotation of material points is inherently integrated into the model. This study encompasses several key aspects: (1) Validation of the coupled micro-periporomechanics paradigm for effectively modeling crack branching in deformable porous media, (2) Examination of the transition from a single branch to multiple branches in porous media under drained conditions, (3) Simulation of single crack branching in unsaturated porous media under dynamic loading conditions, and (4) Investigation of multiple crack branching in unsaturated porous media under dynamic loading conditions. The numerical results obtained in this study are systematically analyzed to elucidate the factors that influence dynamic crack branching in porous media subjected to dynamic loading. Furthermore, the comprehensive numerical findings underscore the efficacy and robustness of the coupled micro-periporomechanics paradigm in accurately modeling dynamic crack branching in variably saturated porous media.
We give a full classification of continuous flexible discrete axial cone-nets, which are called axial C-hedra. The obtained result can also be used to construct their semi-discrete analogs. Moreover, we identify a novel subclass within the determined class of (semi-)discrete axial cone-nets, whose members are named axial P-nets as they fulfill the proportion (P) of the intercept theorem. Known special cases of these axial P-nets are the smooth and discrete conic crease patterns with reflecting rule lines. By using a parallelism operation one can even generalize axial P-nets. The resulting general P-nets constitute a rich novel class of continuous flexible (semi-)discrete surfaces, which allow direct access to their spatial shapes by three control polylines. This intuitive method makes them suitable for transformable design tasks using interactive tools.
It is shown how mixed finite element methods for symmetric positive definite eigenvalue problems related to partial differential operators can provide guaranteed lower eigenvalue bounds. The method is based on a classical compatibility condition (inclusion of kernels) of the mixed scheme and on local constants related to compact embeddings, which are often known explicitly. Applications include scalar second-order elliptic operators, linear elasticity, and the Steklov eigenvalue problem.
Two important problems in the field of Topological Data Analysis are defining practical multifiltrations on objects and showing ability of TDA to detect the geometry. Motivated by the problems, we constuct three multifiltrations named multi-GENEO, multi-DGENEO and mix-GENEO, and prove the stability of both the interleaving distance and multiparameter persistence landscape of multi-GENEO with respect to the pseudometric of the subspace of bounded functions. We also give the estimations of upper bound for multi-DGENEO and mix-GENEO. Finally, we provide experiment results on MNIST dataset to demonstrate our bifiltrations have ability to detect geometric and topological differences of digital images.
The purpose of remote sensing image change detection (RSCD) is to detect differences between bi-temporal images taken at the same place. Deep learning has been extensively used to RSCD tasks, yielding significant results in terms of result recognition. However, due to the shooting angle of the satellite, the impacts of thin clouds, and certain lighting conditions, the problem of fuzzy edges in the change region in some remote sensing photographs cannot be properly handled using current RSCD algorithms. To solve this issue, we proposed a Body Decouple Multi-Scale by fearure Aggregation change detection (BD-MSA), a novel model that collects both global and local feature map information in the channel and space dimensions of the feature map during the training and prediction phases. This approach allows us to successfully extract the change region's boundary information while also divorcing the change region's main body from its boundary. Numerous studies have shown that the assessment metrics and evaluation effects of the model described in this paper on the publicly available datasets DSIFN-CD and S2Looking are the best when compared to other models.
We introduce a simple initialization of the Maubach bisection routine for adaptive mesh refinement which applies to any conforming initial triangulation. Using Maubach's routine with this initialization generates meshes that preserve shape regularity and satisfy the closure estimate needed for optimal convergence of adaptive schemes. Our ansatz allows for the intrinsic use of existing implementations.
The theory of generalized locally Toeplitz (GLT) sequences is a powerful apparatus for computing the asymptotic spectral distribution of matrices $A_n$ arising from numerical discretizations of differential equations. Indeed, when the mesh fineness parameter $n$ tends to infinity, these matrices $A_n$ give rise to a sequence $\{A_n\}_n$, which often turns out to be a GLT sequence. In this paper, we extend the theory of GLT sequences in several directions: we show that every GLT sequence enjoys a normal form, we identify the spectral symbol of every GLT sequence formed by normal matrices, and we prove that, for every GLT sequence $\{A_n\}_n$ formed by normal matrices and every continuous function $f:\mathbb C\to\mathbb C$, the sequence $\{f(A_n)\}_n$ is again a GLT sequence whose spectral symbol is $f(\kappa)$, where $\kappa$ is the spectral symbol of $\{A_n\}_n$. In addition, using the theory of GLT sequences, we prove a spectral distribution result for perturbed normal matrices.
In many medical image classification problems, labeled data is scarce while unlabeled data is more available. Semi-supervised learning and self-supervised learning are two different research directions that can improve accuracy by learning from extra unlabeled data. Recent methods from both directions have reported significant gains on traditional benchmarks. Yet past benchmarks do not focus on medical tasks and rarely compare self- and semi- methods together on equal footing. Furthermore, past benchmarks often handle hyperparameter tuning suboptimally. First, they may not tune hyperparameters at all, leading to underfitting. Second, when tuning does occur, it often unrealistically uses a labeled validation set much larger than the train set. Both cases make previously published rankings of methods difficult to translate to practical settings. This study contributes a systematic evaluation of self- and semi- methods with a unified experimental protocol intended to guide a practitioner with scarce overall labeled data and a limited compute budget. We answer two key questions: Can hyperparameter tuning be effective with realistic-sized validation sets? If so, when all methods are tuned well, which self- or semi-supervised methods reach the best accuracy? Our study compares 13 representative semi- and self-supervised methods to strong labeled-set-only baselines on 4 medical datasets. From 20000+ total GPU hours of computation, we provide valuable best practices to resource-constrained, results-focused practitioners.
Chiral molecule assignation is crucial for asymmetric catalysis, functional materials, and the drug industry. The conventional approach requires theoretical calculations of electronic circular dichroism (ECD) spectra, which is time-consuming and costly. To speed up this process, we have incorporated deep learning techniques for the ECD prediction. We first set up a large-scale dataset of Chiral Molecular ECD spectra (CMCDS) with calculated ECD spectra. We further develop the ECDFormer model, a Transformer-based model to learn the chiral molecular representations and predict corresponding ECD spectra with improved efficiency and accuracy. Unlike other models for spectrum prediction, our ECDFormer creatively focused on peak properties rather than the whole spectrum sequence for prediction, inspired by the scenario of chiral molecule assignation. Specifically, ECDFormer predicts the peak properties, including number, position, and symbol, then renders the ECD spectra from these peak properties, which significantly outperforms other models in ECD prediction, Our ECDFormer reduces the time of acquiring ECD spectra from 1-100 hours per molecule to 1.5s.
Background: Evidence-based medicine (EBM) is fundamental to modern clinical practice, requiring clinicians to continually update their knowledge and apply the best clinical evidence in patient care. The practice of EBM faces challenges due to rapid advancements in medical research, leading to information overload for clinicians. The integration of artificial intelligence (AI), specifically Generative Large Language Models (LLMs), offers a promising solution towards managing this complexity. Methods: This study involved the curation of real-world clinical cases across various specialties, converting them into .json files for analysis. LLMs, including proprietary models like ChatGPT 3.5 and 4, Gemini Pro, and open-source models like LLaMA v2 and Mixtral-8x7B, were employed. These models were equipped with tools to retrieve information from case files and make clinical decisions similar to how clinicians must operate in the real world. Model performance was evaluated based on correctness of final answer, judicious use of tools, conformity to guidelines, and resistance to hallucinations. Results: GPT-4 was most capable of autonomous operation in a clinical setting, being generally more effective in ordering relevant investigations and conforming to clinical guidelines. Limitations were observed in terms of model ability to handle complex guidelines and diagnostic nuances. Retrieval Augmented Generation made recommendations more tailored to patients and healthcare systems. Conclusions: LLMs can be made to function as autonomous practitioners of evidence-based medicine. Their ability to utilize tooling can be harnessed to interact with the infrastructure of a real-world healthcare system and perform the tasks of patient management in a guideline directed manner. Prompt engineering may help to further enhance this potential and transform healthcare for the clinician and the patient.
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