Jakub Olczak | Searcharxiv

arXiv2024

From Radiologist Report to Image Label: Assessing Latent Dirichlet Allocation in Training Neural Networks for Orthopedic Radiograph Classification

Background: Radiography (X-rays) is the dominant modality in orthopedics, and improving the interpretation of radiographs is clinically relevant. Machine learning (ML) has revolutionized data analysis and has been applied to medicine, with some success, in the form of natural language processing (NLP) and artificial neural networks (ANN). Latent Dirichlet allocation (LDA) is an NLP method that automatically categorizes documents into topics. Successfully applying ML to orthopedic radiography could enable the creation of computer-aided decision systems for use in the clinic. We studied how an automated ML pipeline could classify orthopedic trauma radiographs from radiologist reports. Methods: Wrist and ankle radiographs from Danderyd Hospital in Sweden taken between 2002 and 2015, with radiologist reports. LDA was used to create image labels for radiographs from the radiologist reports. Radiographs and labels were used to train an image recognition ANN. The ANN outcomes were manually reviewed to get an accurate estimate of the method's utility and accuracy. Results: Image Labels generated via LDA could successfully train the ANN. The ANN reached an accuracy between 91% and 60% compared to a gold standard, depending on the label. Conclusions: We found that LDA was unsuited to label orthopedic radiographs from reports with high accuracy. However, despite this, the ANN could learn to detect some features in radiographs with high accuracy. The study also illustrates how ML and ANN can be applied to medical research.

cs.CV↗

arXiv2016

Evaluating Network Inference Methods in Terms of Their Ability to Preserve the Topology and Complexity of Genetic Networks

Network inference is a rapidly advancing field, with new methods being proposed on a regular basis. Understanding the advantages and limitations of different network inference methods is key to their effective application in different circumstances. The common structural properties shared by diverse networks naturally pose a challenge when it comes to devising accurate inference methods, but surprisingly, there is a paucity of comparison and evaluation methods. Historically, every new methodology has only been tested against \textit{gold standard} (true values) purpose-designed synthetic and real-world (validated) biological networks. In this paper we aim to assess the impact of taking into consideration aspects of topological and information content in the evaluation of the final accuracy of an inference procedure. Specifically, we will compare the best inference methods, in both graph-theoretic and information-theoretic terms, for preserving topological properties and the original information content of synthetic and biological networks. New methods for performance comparison are introduced by borrowing ideas from gene set enrichment analysis and by applying concepts from algorithmic complexity. Experimental results show that no individual algorithm outperforms all others in all cases, and that the challenging and non-trivial nature of network inference is evident in the struggle of some of the algorithms to turn in a performance that is superior to random guesswork. Therefore special care should be taken to suit the method to the purpose at hand. Finally, we show that evaluations from data generated using different underlying topologies have different signatures that can be used to better choose a network reconstruction method.

q-bio.MN↗