Histopathology tissue samples are widely available in two states: paraffin-embedded unstained and non-paraffin-embedded stained whole slide RGB images (WSRI). Hematoxylin and eosin stain (H&E) is one of the principal stains in histology but suffers from several shortcomings related to tissue preparation, staining proto…
On-device research index
arXiv research
A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
168,695 papers · 148 categories
Trend · papers per month
48 results for “Staining Variability”
An important part of Digital Pathology is the analysis of multiple digitised whole slide images from differently stained tissue sections. It is common practice to mount consecutive sections containing corresponding microscopic structures on glass slides, and to stain them differently to highlight specific tissue compon…
Study proposes deep learning techniques to diagnose and differentiate Celiac Disease and Environmental Enteropathy from biopsy images.
problem Challenging histopathologic overlap between Celiac Disease and Environmental Enteropathy in biopsy images.
method Color balancing and Random Multimodel Deep Learning (RMDL) architecture to address staining variability.
result Proposed deep learning techniques improve diagnosis accuracy of Celiac Disease and Environmental Enteropathy.
Visualizing the details of different cellular structures is of great importance to elucidate cellular functions. However, it is challenging to obtain high quality images of different structures directly due to complex cellular environments. Fluorescence staining is a popular technique to label different structures but …
Diffusion Generative Modeling for Spatially Resolved Gene Expression Inference from Histology Imagescs.CV
Stem uses diffusion models to infer gene expression from H&E images.
problem Inference of gene expression from H&E stained images is time-consuming and expensive.
method Conditional diffusion generative model to infer gene expression.
result Stem achieves state-of-the-art performance in spatial gene expression prediction.
A novel approach for augmenting histopathological images by blending Gaussian-Laplacian pyramids.
problem Data imbalance and inter-patient variability in histopathological images.
method Image blending using Gaussian-Laplacian pyramids to distribute inter-patient variability.
result Promising gains in performance compared to existing data augmentation techniques.
Determining the localization of specific protein in human cells is important for understanding cellular functions and biological processes of underlying diseases. Among imaging techniques, high-throughput fluorescence microscopy imaging is an efficient biotechnology to stain the protein of interest in a cell. In this w…
Automatization of the diagnosis of any kind of disease is of great importance and it's gaining speed as more and more deep learning solutions are applied to different problems. One of such computer aided systems could be a decision support too able to accurately differentiate between different types of breast cancer hi…
Deep learning natural language processing models often use vector word embeddings, such as word2vec or GloVe, to represent words. A discrete sequence of words can be much more easily integrated with downstream neural layers if it is represented as a sequence of continuous vectors. Also, semantic relationships between w…
Generative Synthetic Augmentation using Label-to-Image Translation for Nuclei Image Segmentationcs.LG
This paper proposes synthetic augmentation for nuclei image segmentation in medical pathology.
problem Rare and time-consuming labeling of tumor nuclei images for semantic segmentation.
method Label-to-image translation to generate synthetic images.
result Synthetic augmentation improves segmentation accuracy.
Evaluates deep learning models in histopathology for robustness and classification strategies.
problem Lack of comprehensive evaluation of histopathology models beyond accuracy.
method Developed a new methodology to evaluate models on five histopathology datasets, including vision transformers and CNNs.
result Identified insights into cancer classification strategies and robustness against stain variations.
Recent studies have shown promising results in using Deep Learning to detect malignancy in whole slide imaging. However, they were limited to just predicting positive or negative finding for a specific neoplasm. We attempted to use Deep Learning with a convolutional neural network algorithm to build a lymphoma diagnost…
Study uses image analysis to predict MSI status in tumors.
problem Challenges in distinguishing MSI from its counterpart.
method Interpretable pathological image analysis strategies using Haematoxylin and eosin-stained images.
result Strategies achieve decent performance in MSI prediction.
Malaria is a serious infectious disease that is responsible for over half million deaths yearly worldwide. The major cause of these mortalities is late or inaccurate diagnosis. Manual microscopy is currently considered as the dominant diagnostic method for malaria. However, it is time consuming and prone to human error…
Unified framework for semi-supervised learning reduces annotation needs.
problem Sparse annotations and large amounts of unlabeled data in computational pathology.
method S5CL integrates fully-supervised, self-supervised, and semi-supervised learning through hierarchical contrastive losses.
result S5CL improves accuracy and F1-score in histopathological datasets with sparse labels.
AI enhances cancer diagnostics using spectroscopy.
problem Early and accurate cancer diagnosis.
method Combining AI with spectroscopy-based techniques.
result AI improves cancer diagnostics speed and safety.
Automated Prostate Cancer Diagnosis Based on Gleason Grading Using Convolutional Neural Networkeess.IV
CNN-based prostate cancer grading improves accuracy and efficiency.
problem Manual Gleason grading by pathologists is time-consuming and prone to errors.
method Patch-Based Image Reconstruction (PBIR), Distribution Correction (DC), Quadratic Weighted Mean Square Error (QWMSE).
result Achieved superior expert-level performance (0.8885 quadratic-weighted kappa coefficient).
Clients are increasingly looking for fast and effective means to quickly and frequently survey and communicate the condition of their buildings so that essential repairs and maintenance work can be done in a proactive and timely manner before it becomes too dangerous and expensive. Traditional methods for this type of …
Spectral decoupling improves neural network generalization in medical imaging.
problem Poor generalization of neural networks trained on medical imaging data.
method Spectral decoupling, a regularization technique that encourages learning more features.
result Spectral decoupling increases network robustness and performance on external datasets.
We propose a new deep learning approach for medical imaging that copes with the problem of a small training set, the main bottleneck of deep learning, and apply it for classification of healthy and cancer cells acquired by quantitative phase imaging. The proposed method, called transferring of pre-trained generative ad…
Manual count of mitotic figures, which is determined in the tumor region with the highest mitotic activity, is a key parameter of most tumor grading schemes. It can be, however, strongly dependent on the area selection due to uneven mitotic figure distribution in the tumor section.We aimed to assess the question, how s…
Statistical inference is considered for variables of interest, called primary variables, when auxiliary variables are observed along with the primary variables. We consider the setting of incomplete data analysis, where some primary variables are not observed. Utilizing a parametric model of joint distribution of prima…
VC-PCR improves prediction by clustering correlated variables.
problem Decreased prediction accuracy due to cluster structure in predictor variables.
method Supervised variable selection and clustering to integrate cluster information into a sparse modeling process.
result VC-PCR achieves better prediction, variable selection, and clustering performance.
Study on inequalities for multinomial variables.
problem Understanding concentration inequalities for multinomial variables.
method Investigation of Dirichlet and Multinomial random variables.
result Results on concentration inequalities for multinomial variables.
In this paper, we propose multi-variable LSTM capable of accurate forecasting and variable importance interpretation for time series with exogenous variables. Current attention mechanism in recurrent neural networks mostly focuses on the temporal aspect of data and falls short of characterizing variable importance. To …
Variable importance is central to scientific studies, including the social sciences and causal inference, healthcare, and other domains. However, current notions of variable importance are often tied to a specific predictive model. This is problematic: what if there were multiple well-performing predictive models, and …
A neural network finds causal relationships among latent variables.
problem Learning causal structure among latent variables in high-dimensional data.
method Redundant Input Neural Network (RINN) with modified architecture and regularized objective function.
result The RINN method successfully recovers latent causal structure between input and output variables.
Derives derivatives and geometric framework for functions with non-independent variables.
problem Characterizing functions with non-independent variables in probabilistic models.
method Derives actual and dependent partial derivatives, dependent Jacobian matrix, and tensor metric.
result Derives gradient, Hessian, and Taylor expansion for functions with non-independent variables.
A new distance for mixed-variable, hierarchical datasets with meta variables.
problem Heterogeneous datasets limit generalizability and performance in machine learning and optimization.
method Developed a modeling framework for mixed-variable and hierarchical domains with meta variables, and a novel distance function.
result The novel distance function allows comparison of heterogeneous datasets, improving model performance.
Unified Bayesian Optimisation for mixed variables improves performance.
problem Efficient optimisation of problems with both categorical and continuous variables.
method Derive value proposals from the Expected Improvement criterion to optimise both categorical and continuous variables under a single acquisition metric.
result Unified approach significantly outperforms existing methods across mixed-variable tasks.
In this paper, we propose an interpretable LSTM recurrent neural network, i.e., multi-variable LSTM for time series with exogenous variables. Currently, widely used attention mechanism in recurrent neural networks mostly focuses on the temporal aspect of data and falls short of characterizing variable importance. To th…
Random Forest variable importance is improved by class balancing techniques.
problem Class imbalance problem in machine learning.
method Proposed a variable selection algorithm using RF variable importance and its confidence interval.
result Our algorithm efficiently selects an optimal feature set, leading to improved prediction performance.
Variable selection for Gaussian process models is often done using automatic relevance determination, which uses the inverse length-scale parameter of each input variable as a proxy for variable relevance. This implicitly determined relevance has several drawbacks that prevent the selection of optimal input variables i…
Knoop enhances variable selection with over-parameterization and knockoffs.
problem Challenges of variable selection in high-dimensional datasets.
method Generates knockoff variables, integrates them into an over-parameterized model, and uses anomaly-based significance tests.
result Superior performance in variable selection compared to existing methods.
A serious problem in learning probabilistic models is the presence of hidden variables. These variables are not observed, yet interact with several of the observed variables. Detecting hidden variables poses two problems: determining the relations to other variables in the model and determining the number of states of …
New method for fitting graphical models with latent variables using regularized conditional likelihood.
problem Graphical modeling with latent variables and confounding dependencies.
method Regularized conditional likelihood for exponential family graphical models.
result Framework applicable to broader settings without knowing latent variables' distribution.
CIB compresses variables causally, preserving key causal interactions.
problem Constructing causal variable abstractions in complex systems.
method Causal Information Bottleneck (CIB) method, extending IB to include causal structures.
result CIB produces causally interpretable abstractions that accurately capture causal relations.
We generalize to the finite-state case the notion of the extreme effect variable that accumulates all the effect of a variant variable observed in changes of another variable . We conduct theoretical analysis and turn the problem of finding of an effect variable into a problem of a simultaneous decomposition…
Discond-VAE separates continuous and discrete factors in data.
problem Separating shared and class-specific variations in real-world data.
method Introduces private and public latent variables to represent continuous and discrete factors, respectively.
result Discond-VAE successfully disentangles class-dependent continuous factors from discrete factors.
A new method selects important variables for clustering from dependency networks.
problem Variable selection for clustering in high-cost data scenarios.
method Create dependency networks, rank variables by centrality, select top-n variables.
result Top-n variables improve clustering performance compared to existing methods.
The paper introduces methods to identify key variables discriminating between two datasets.
problem Identifying variables that distinguish between two datasets.
method Introduces a mathematical notion of discriminating variables and proposes two methods for their selection.
result Proposed methods improve upon existing techniques in two-sample variable selection.
Electronic Medical Records (EMR) are a rich source of patient information, including measurements reflecting physiologic signs and administered therapies. Identifying which variables are useful in predicting clinical outcomes can be challenging. Advanced algorithms such as deep neural networks were designed to process …
This work presents entropic constraints from DAGs with hidden variables.
problem Characterizing causal relations in systems with hidden variables.
method Entropic inequality constraints derived from -separation relations.
result These constraints can learn about true causal models from observed data.
For recurrent neural networks trained on time series with target and exogenous variables, in addition to accurate prediction, it is also desired to provide interpretable insights into the data. In this paper, we explore the structure of LSTM recurrent neural networks to learn variable-wise hidden states, with the aim t…
Proposes a two-stage method for selecting correlated predictors in high-dimensional data.
problem Selecting correlated predictors in high-dimensional data with unknown group structures.
method Two-stage approach: variable clustering followed by group selection.
result The two-stage method improves prediction accuracy and active predictor selection.
We propose a novel application of the Simultaneous Orthogonal Matching Pursuit (S-OMP) procedure for sparsistant variable selection in ultra-high dimensional multi-task regression problems. Screening of variables, as introduced in \cite{fan08sis}, is an efficient and highly scalable way to remove many irrelevant variab…
On the Effects of Irrelevant Variables in Treatment Effect Estimation with Deep Disentanglementcs.LG
New method better identifies irrelevant variables for more accurate treatment effect estimation.
problem Handling irrelevant variables in treatment effect estimation with deep disentanglement.
method Deep embedding method to disentangle pre-treatment variables, explicitly identify and represent irrelevant variables, and orthogonalize them.
result Better identification and representation of irrelevant variables lead to more precise treatment effect prediction.
The paper proposes a method to stabilize predictions by identifying causal variables using a seed variable.
problem Stable prediction across unknown test data with potential spurious correlations.
method Conditional independence test based algorithm using a seed variable to separate causal from non-causal variables.
result The algorithm precisely separates causal and non-causal variables for stable prediction across test data.