arXiv research

This study investigates how much knowledge from natural images can be transferred to pathology images.

Localization of chest pathologies in chest X-ray images is a challenging task because of their varying sizes and appearances. We propose a novel weakly supervised method to localize chest pathologies using class aware deep multiscale feature learning. Our method leverages intermediate feature maps from CNN layers at di…

This paper proposes synthetic augmentation for nuclei image segmentation in medical pathology.

Pseudo healthy synthesis, i.e. the creation of a subject-specific `healthy' image from a pathological one, could be helpful in tasks such as anomaly detection, understanding changes induced by pathology and disease or even as data augmentation. We treat this task as a factor decomposition problem: we aim to separate wh…

Study uses image analysis to predict MSI status in tumors.

We propose a method to classify cardiac pathology based on a novel approach to extract image derived features to characterize the shape and motion of the heart. An original semi-supervised learning procedure, which makes efficient use of a large amount of non-segmented images and a small amount of images segmented manu…

Chronic Pulmonary Aspergillosis (CPA) is a complex lung disease caused by infection with Aspergillus. Computed tomography (CT) images are frequently requested in patients with suspected and established disease, but the radiological signs on CT are difficult to quantify making accurate follow-up challenging. We propose …

In this paper we present algorithms to diagnosis Pathological Myopia (PM) and detection of retinal structures and lesions such asOptic Disc (OD), Fovea, Atrophy and Detachment. All these tasks were performed in fundus imaging from PM patients and they are requirements to participate in the Pathologic Myopia Challenge (…

Novel fusion network combines polarization and radiomics features for liver cancer classification.

A crucial challenge in image-based modeling of biomedical data is to identify trends and features that separate normality and pathology. In many cases, the morphology of the imaged object exhibits continuous change as it deviates from normality, and thus a generative model can be trained to model this morphological con…

Model learns cancer tissue images onto a low-dimensional space revealing tissue characteristics.

Data diversity is critical to success when training deep learning models. Medical imaging data sets are often imbalanced as pathologic findings are generally rare, which introduces significant challenges when training deep learning models. In this work, we propose a method to generate synthetic abnormal MRI images with…

Semi-supervised learning chain boosts histology image accuracy with minimal labeled data.

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…

Decision support tools that rely on supervised learning require large amounts of expert annotations. Using past radiological reports obtained from hospital archiving systems has many advantages as training data above manual single-class labels: they are expert annotations available in large quantities, covering a popul…

Insufficient training data and severe class imbalance are often limiting factors when developing machine learning models for the classification of rare diseases. In this work, we address the problem of classifying bone lesions from X-ray images by increasing the small number of positive samples in the training set. We …

Here we present DIVE: Data-driven Inference of Vertexwise Evolution. DIVE is an image-based disease progression model with single-vertex resolution, designed to reconstruct long-term patterns of brain pathology from short-term longitudinal data sets. DIVE clusters vertex-wise biomarker measurements on the cortical surf…

Pathology reports contain useful information such as the main involved organ, diagnosis, etc. These information can be identified from the free text reports and used for large-scale statistical analysis or serve as annotation for other modalities such as pathology slides images. However, manual classification for a hug…

We construct a large class of pathological $n$-dimensional topological spheres in ${\mathbb R}^{n+1}$ by showing that for any Cantor set $C\subset {\mathbb R}^{n+1}$ there is a topological embedding $f:{\mathbb S}^n\to{\mathbb R}^{n+1}$ of the Sobolev class $W^{1,n}$ whose image contains the Cantor set $C$.

Planning the optimal time of intervention for pulmonary valve replacement surgery in patients with the congenital heart disease Tetralogy of Fallot (TOF) is mainly based on ventricular volume and function according to current guidelines. Both of these two biomarkers are most reliably assessed by segmentation of 3D card…

We propose a new model for digital pathology segmentation, based on the observation that histopathology images are inherently symmetric under rotation and reflection. Utilizing recent findings on rotation equivariant CNNs, the proposed model leverages these symmetries in a principled manner. We present a visual analysi…

CNNs overinterpret inputs, leading to high accuracy without meaningful features.

Unified framework for semi-supervised learning reduces annotation needs.

Deep neural networks have introduced significant advancements in the field of machine learning-based analysis of digital pathology images including prostate tissue images. With the help of transfer learning, classification and segmentation performance of neural network models have been further increased. However, due t…

Histopathological images of tumors contain abundant information about how tumors grow and how they interact with their micro-environment. Better understanding of tissue phenotypes in these images could reveal novel determinants of pathological processes underlying cancer, and in turn improve diagnosis and treatment opt…

To alleviate the burden of gathering detailed expert annotations when training deep neural networks, we propose a weakly supervised learning approach to recognize metastases in microscopic images of breast lymph nodes. We describe an alternative training loss which clusters weakly labeled bags in latent space to inform…

This paper characterizes VAE training pathologies and their effects on tasks.

Vision impairment due to pathological damage of the retina can largely be prevented through periodic screening using fundus color imaging. However the challenge with large scale screening is the inability to exhaustively detect fine blood vessels crucial to disease diagnosis. In this work we present a computational ima…

A DenseNet model classifies metastatic cancer in medical images.

A Pathology report is arguably one of the most important documents in medicine containing interpretive information about the visual findings from the patient's biopsy sample. Each pathology report has a retention period of up to 20 years after the treatment of a patient. Cancer registries process and encode high volume…

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…

The paper identifies conditions for trend reversal in classification tasks.

Bayesian layer improves image segmentation and out-of-distribution detection.

KL-regularized RL from expert demos can lead to slow, unstable learning.

This work examines robust MCMC for pathological distributions.

Normalization methods play an important role in enhancing the performance of deep learning while their theoretical understandings have been limited. To theoretically elucidate the effectiveness of normalization, we quantify the geometry of the parameter space determined by the Fisher information matrix (FIM), which als…

Digital pathology is not only one of the most promising fields of diagnostic medicine, but at the same time a hot topic for fundamental research. Digital pathology is not just the transfer of histopathological slides into digital representations. The combination of different data sources (images, patient records, and *…

We introduce a novel approach, requiring only mild assumptions, for the characterization of deep neural networks at initialization. Our approach applies both to fully-connected and convolutional networks and easily incorporates batch normalization and skip-connections. Our key insight is to consider the evolution with …

Segmentation of anatomical structures and pathologies is inherently ambiguous. For instance, structure borders may not be clearly visible or different experts may have different styles of annotating. The majority of current state-of-the-art methods do not account for such ambiguities but rather learn a single mapping f…

Breast cancer has the highest mortality among cancers in women. Computer-aided pathology to analyze microscopic histopathology images for diagnosis with an increasing number of breast cancer patients can bring the cost and delays of diagnosis down. Deep learning in histopathology has attracted attention over the last d…

New analysis explains pathology of deep Gaussian processes.

Imaging-based early diagnosis of Alzheimer Disease (AD) has become an effective approach, especially by using nuclear medicine imaging techniques such as Positron Emission Topography (PET). In various literature it has been found that PET images can be better modeled as signals (e.g. uptake of florbetapir) defined on a…

Neural networks promise to bring robust, quantitative analysis to medical fields, but adoption is limited by the technicalities of training these networks. To address this translation gap between medical researchers and neural networks in the field of pathology, we have created an intuitive interface which utilizes the…

Novel approach combines local and global brain changes for AD prediction.

In this paper, we propose a classification based glottal closure instants (GCI) detection from pathological acoustic speech signal, which finds many applications in vocal disorder analysis. Till date, GCI for pathological disorder is extracted from laryngeal (glottal source) signal recorded from Electroglottograph, a d…

Causal methods for GRN inference from single-cell data often fail in real-world benchmarks.

Regularized Stein thinning improves MCMC output approximations.

A Convolutional Neural Network was used to predict kidney function in patients with chronic kidney disease from high-resolution digital pathology scans of their kidney biopsies. Kidney biopsies were taken from participants of the NEPTUNE study, a longitudinal cohort study whose goal is to set up infrastructure for obse…