arXiv subjects

Chris G. Willcocks

Publications and source records attributed to Chris G. Willcocks.

21 records · Page 2Linked to original sources

arXiv2020

Segmentation of Macular Edema Datasets with Small Residual 3D U-Net Architectures

This paper investigates the application of deep convolutional neural networks with prohibitively small datasets to the problem of macular edema segmentation. In particular, we investigate several different heavily regularized architectures. We find that, contrary to popular belief, neural architectures within this application setting are able to achieve close to human-level performance on unseen test images without requiring large numbers of training examples. Annotating these 3D datasets is difficult, with multiple criteria required. It takes an experienced clinician two days to annotate a single 3D image, whereas our trained model achieves similar performance in less than a second. We found that an approach which uses targeted dataset augmentation, alongside architectural simplification with an emphasis on residual design, has acceptable generalization performance - despite relying on fewer than 15 training examples.

eess.IV↗

arXiv2020

Learning protein conformational space by enforcing physics with convolutions and latent interpolations

Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein conformational space with molecular simulation methodologies. Despite advances in computing hardware and sampling techniques, simulations always yield a discretized representation of this space, with transition states undersampled proportionally to their associated energy barrier. We present a convolutional neural network that learns a continuous conformational space representation from example structures, and loss functions that ensure intermediates between examples are physically plausible. We show that this network, trained with simulations of distinct protein states, can correctly predict a biologically relevant non-linear transition path, without any example on the path provided. We also show we can transfer features learnt from one protein to others, which results in superior performances, and requires a surprisingly small number of training examples.

physics.bio-ph↗

arXiv2019

TMIXT: A process flow for Transcribing MIXed handwritten and machine-printed Text

Handling large corpuses of documents is of significant importance in many fields, no more so than in the areas of crime investigation and defence, where an organisation may be presented with a large volume of scanned documents which need to be processed in a finite time. However, this problem is exacerbated both by the volume, in terms of scanned documents and the complexity of the pages, which need to be processed. Often containing many different elements, which each need to be processed and understood. Text recognition, which is a primary task of this process, is usually dependent upon the type of text, being either handwritten or machine-printed. Accordingly, the recognition involves prior classification of the text category, before deciding on the recognition method to be applied. This poses a more challenging task if a document contains both handwritten and machine-printed text. In this work, we present a generic process flow for text recognition in scanned documents containing mixed handwritten and machine-printed text without the need to classify text in advance. We realize the proposed process flow using several open-source image processing and text recognition packages1. The evaluation is performed using a specially developed variant, presented in this work, of the IAM handwriting database, where we achieve an average transcription accuracy of nearly 80% for pages containing both printed and handwritten text.

cs.LG↗