Search results for "Precision and recall"
showing 8 items of 8 documents
Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data
2017
AbstractThe epigenetics landscape of cells plays a key role in the establishment of cell-type specific gene expression programs characteristic of different cellular phenotypes. Different experimental procedures have been developed to obtain insights into the accessible chromatin landscape including DNase-seq, FAIRE-seq and ATAC-seq. However, current downstream computational tools fail to reliably determine regulatory region accessibility from the analysis of these experimental data. In particular, currently available peak calling algorithms are very sensitive to their parameter settings and show highly heterogeneous results, which hampers a trustworthy identification of accessible chromatin…
Automatic detection and classification of retinal vascular landmarks
2014
The main contribution of this paper is introducing a method to distinguish between different landmarks of the retina: bifurcations and crossings. The methodology may help in differentiating between arteries and veins and is useful in identifying diseases and other special pathologies, too. The method does not need any special skills, thus it can be assimilated to an automatic way for pinpointing landmarks; moreover it gives good responses for very small vessels. A skeletonized representation, taken out from the segmented binary image (obtained through a preprocessing step), is used to identify pixels with three or more neighbors. Then, the junction points are classified into bifurcations or…
Integrating genomic binding site predictions using real-valued meta classifiers
2008
Currently the best algorithms for predicting transcription factor binding sites in DNA sequences are severely limited in accuracy. There is good reason to believe that predictions from different classes of algorithms could be used in conjunction to improve the quality of predictions. In this paper, we apply single layer networks, rules sets, support vector machines and the Adaboost algorithm to predictions from 12 key real valued algorithms. Furthermore, we use a ‘window’ of consecutive results as the input vector in order to contextualise the neighbouring results. We improve the classification result with the aid of under- and over-sampling techniques. We find that support vector machines …
A novel Bayesian framework for relevance feedback in image content-based retrieval systems
2006
This paper presents a new algorithm for image retrieval in content-based image retrieval systems. The objective of these systems is to get the images which are as similar as possible to a user query from those contained in the global image database without using textual annotations attached to the images. The main problem in obtaining a robust and effective retrieval is the gap between the low level descriptors that can be automatically extracted from the images and the user intention. The algorithm proposed here to address this problem is based on the modeling of user preferences as a probability distribution on the image space. Following a Bayesian methodology, this distribution is the pr…
A Hybrid Machine Learning and Knowledge Based Approach to Limit Combinatorial Explosion in Biodegradation Prediction
2016
One of the main tasks in chemical industry regarding the sustainability of a product is the prediction of its environmental fate, i.e., its degradation products and pathways. Current methods for the prediction of biodegradation products and pathways of organic environmental pollutants either do not take into account domain knowledge or do not provide probability estimates. In this chapter, we propose a hybrid knowledge-based and machine learning-based approach to overcome these limitations in the context of the University of Minnesota Pathway Prediction System (UM-PPS). The proposed solution performs relative reasoning in a machine learning framework, and obtains one probability estimate fo…
Using the Tsetlin Machine to Learn Human-Interpretable Rules for High-Accuracy Text Categorization With Medical Applications
2019
Medical applications challenge today's text categorization techniques by demanding both high accuracy and ease-of-interpretation. Although deep learning has provided a leap ahead in accuracy, this leap comes at the sacrifice of interpretability. To address this accuracy-interpretability challenge, we here introduce, for the first time, a text categorization approach that leverages the recently introduced Tsetlin Machine. In all brevity, we represent the terms of a text as propositional variables. From these, we capture categories using simple propositional formulae, such as: if "rash" and "reaction" and "penicillin" then Allergy. The Tsetlin Machine learns these formulae from a labelled tex…
A non-parametric segmentation methodology for oral videocapillaroscopic images
2014
We aim to describe a new non-parametric methodology to support the clinician during the diagnostic process of oral videocapillaroscopy to evaluate peripheral microcirculation. Our methodology, mainly based on wavelet analysis and mathematical morphology to preprocess the images, segments them by minimizing the within-class luminosity variance of both capillaries and background. Experiments were carried out on a set of real microphotographs to validate this approach versus handmade segmentations provided by physicians. By using a leave-one-patient-out approach, we pointed out that our methodology is robust, according to precision-recall criteria (average precision and recall are equal to 0.9…
A hybrid multi-objective optimization algorithm for content based image retrieval
2013
Abstract Relevance feedback methods in CBIR (Content Based Image Retrieval) iteratively use relevance information from the user to search the space for other relevant samples. As several regions of interest may be scattered through the space, an effective search algorithm should balance the exploration of the space to find new potential regions of interest and the exploitation of areas around samples which are known relevant. However, many algorithms concentrate the search on areas which are close to the images that the user has marked as relevant, according to a distance function in the (possibly deformed) multidimensional feature space. This maximizes the number of relevant images retriev…