Spine intervertebral disc labeling using a fully convolutional redundant counting model

Labeling intervertebral discs is relevant as it notably enables clinicians to understand the relationship between a patient's symptoms (pain, paralysis) and the exact level of spinal cord injury. However manually labeling those discs is a tedious and user-biased task which would benefit from automated methods. While some automated methods already exist for MRI and CT-scan, they are either not publicly available, or fail to generalize across various imaging contrasts. In this paper we combine a Fully Convolutional Network (FCN) with inception modules to localize and label intervertebral discs. We demonstrate a proof-of-concept application in a publicly-available multi-center and multi-contrast MRI database (n=235 subjects). The code is publicly available at https://github.com/neuropoly/vertebral-labeling-deep-learning.

Automatic segmentation of spinal multiple sclerosis lesions: How to generalize across MRI contrasts?

Despite recent improvements in medical image segmentation, the ability to generalize across imaging contrasts remains an open issue. To tackle this challenge, we implement Feature-wise Linear Modulation (FiLM) to leverage physics knowledge within the segmentation model and learn the characteristics of each contrast. Interestingly, a well-optimised U-Net reached the same performance as our FiLMed-Unet on a multi-contrast dataset (0.72 of Dice score), which suggests that there is a bottleneck in spinal MS lesion segmentation different from the generalization across varying contrasts. This bottleneck likely stems from inter-rater variability, which is estimated at 0.61 of Dice score in our dataset.

Revisiting Training Strategies and Generalization Performance in Deep Metric Learning

Deep Metric Learning (DML) is arguably one of the most influential lines of research for learning visual similarities with many proposed approaches every year. Although the field benefits from the rapid progress, the divergence in training protocols, architectures, and parameter choices make an unbiased comparison difficult. To provide a consistent reference point, we revisit the most widely used DML objective functions and conduct a study of the crucial parameter choices as well as the commonly neglected mini-batch sampling process. Based on our analysis, we uncover a correlation between the embedding space compression and the generalization performance of DML models. Exploiting these insights, we propose a simple, yet effective, training regularization to reliably boost the performance of ranking-based DML models on various standard benchmark datasets.

Quantifying the Value of Lateral Views in Deep Learning for Chest X-rays

Most deep learning models in chest X-ray prediction utilize the posteroanterior (PA) view due to the lack of other views available. PadChest is a large-scale chest X-ray dataset that has almost 200 labels and multiple views available. In this work, we use PadChest to explore multiple approaches to merging the PA and lateral views for predicting the radiological labels associated with the X-ray image. We find that different methods of merging the model utilize the lateral view differently. We also find that including the lateral view increases performance for 32 labels in the dataset, while being neutral for the others. The increase in overall performance is comparable to the one obtained by using only the PA view with twice the amount of patients in the training set.

On the limits of cross-domain generalization in automated X-ray prediction

This large scale study focuses on quantifying what X-rays diagnostic prediction tasks generalize well across multiple different datasets. We present evidence that the issue of generalization is not due to a shift in the images but instead a shift in the labels. We study the cross-domain performance, agreement between models, and model representations. We find interesting discrepancies between performance and agreement where models which both achieve good performance disagree in their predictions as well as models which agree yet achieve poor performance. We also test for concept similarity by regularizing a network to group tasks across multiple datasets together and observe variation across the tasks.

Is graph-based feature selection of genes better than random?

Gene interaction graphs aim to capture various relationships between genes and represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality by making machine learning models sparser and more consistent with biological common knowledge. In this work, we focus on assessing whether those graphs capture dependencies seen in gene expression data better than random. We formulate a condition that graphs should satisfy to provide a good prior knowledge and propose to test it using a `Single Gene Inference' (SGI) task. We compare random graphs with seven major gene interaction graphs published by different research groups, aiming to measure the true benefit of using biologically relevant graphs in this context. Our analysis finds that dependencies can be captured almost as well at random which suggests that, in terms of gene expression levels, the relevant information about the state of the cell is spread across many genes.

Deep Semantic Segmentation of Natural and Medical Images: A Review

The (medical) image semantic segmentation task consists of classifying each pixel of an image (or just several ones) into an instance, where each instance (or category) corresponding to a class. This task is a part of the concept of scene understanding or better explaining the global context of an image. In the medical image analysis domain, image segmentation can be used for image-guided interventions, radiotherapy, or improved radiological diagnostics. In this review, we categorize the main deep learning-based medical and non-medical image segmentation solutions into six main groups of deep architectural improvements, data synthesis-based, loss function-based improvements, sequenced models, weakly supervised, and multi-task methods and further for each group we analyzed each variant of these groups and discuss limitations of the current approaches and future research directions for semantic image segmentation.

Is graph biased feature selection of genes better than random?

Gene interaction graphs aim to capture various relationships between genes and can represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality by making machine learning models sparser and more biased with biological common knowledge. In this work, we focus on assessing whether those graphs capture dependencies seen in gene expression data better than random. We formulate a condition that graphs should satisfy to provide a good bias and propose to test it using a 'Single Gene Inference' (SGI) task. We compare random graphs with seven major gene interaction graphs published by different research groups, aiming to measure the true benefit of using biologically relevant graphs in this context. Our analysis finds that dependencies can be captured almost as well at random which suggests that, in terms of gene expression levels, the relevant information about the state of the cell is spread across many genes.