arXiv subjects

Yvan Saeys

Publications and source records attributed to Yvan Saeys.

22 records · Page 2Linked to original sources

arXiv2018

Bayesian Deconvolution of Scanning Electron Microscopy Images Using Point-spread Function Estimation and Non-local Regularization

Microscopy is one of the most essential imaging techniques in life sciences. High-quality images are required in order to solve (potentially life-saving) biomedical research problems. Many microscopy techniques do not achieve sufficient resolution for these purposes, being limited by physical diffraction and hardware deficiencies. Electron microscopy addresses optical diffraction by measuring emitted or transmitted electrons instead of photons, yielding nanometer resolution. Despite pushing back the diffraction limit, blur should still be taken into account because of practical hardware imperfections and remaining electron diffraction. Deconvolution algorithms can remove some of the blur in post-processing but they depend on knowledge of the point-spread function (PSF) and should accurately regularize noise. Any errors in the estimated PSF or noise model will reduce their effectiveness. This paper proposes a new procedure to estimate the lateral component of the point spread function of a 3D scanning electron microscope more accurately. We also propose a Bayesian maximum a posteriori deconvolution algorithm with a non-local image prior which employs this PSF estimate and previously developed noise statistics. We demonstrate visual quality improvements and show that applying our method improves the quality of subsequent segmentation steps.

cs.CV↗

arXiv2017

Interpretable Convolutional Neural Networks for Effective Translation Initiation Site Prediction

Thanks to rapidly evolving sequencing techniques, the amount of genomic data at our disposal is growing increasingly large. Determining the gene structure is a fundamental requirement to effectively interpret gene function and regulation. An important part in that determination process is the identification of translation initiation sites. In this paper, we propose a novel approach for automatic prediction of translation initiation sites, leveraging convolutional neural networks that allow for automatic feature extraction. Our experimental results demonstrate that we are able to improve the state-of-the-art approaches with a decrease of 75.2% in false positive rate and with a decrease of 24.5% in error rate on chosen datasets. Furthermore, an in-depth analysis of the decision-making process used by our predictive model shows that our neural network implicitly learns biologically relevant features from scratch, without any prior knowledge about the problem at hand, such as the Kozak consensus sequence, the influence of stop and start codons in the sequence and the presence of donor splice site patterns. In summary, our findings yield a better understanding of the internal reasoning of a convolutional neural network when applying such a neural network to genomic data.

q-bio.GN↗

arXiv2017

On the use of convolutional neural networks for robust classification of multiple fingerprint captures

Fingerprint classification is one of the most common approaches to accelerate the identification in large databases of fingerprints. Fingerprints are grouped into disjoint classes, so that an input fingerprint is compared only with those belonging to the predicted class, reducing the penetration rate of the search. The classification procedure usually starts by the extraction of features from the fingerprint image, frequently based on visual characteristics. In this work, we propose an approach to fingerprint classification using convolutional neural networks, which avoid the necessity of an explicit feature extraction process by incorporating the image processing within the training of the classifier. Furthermore, such an approach is able to predict a class even for low-quality fingerprints that are rejected by commonly used algorithms, such as FingerCode. The study gives special importance to the robustness of the classification for different impressions of the same fingerprint, aiming to minimize the penetration in the database. In our experiments, convolutional neural networks yielded better accuracy and penetration rate than state-of-the-art classifiers based on explicit feature extraction. The tested networks also improved on the runtime, as a result of the joint optimization of both feature extraction and classification.

cs.CV↗

arXiv2007

Validating module network learning algorithms using simulated data

In recent years, several authors have used probabilistic graphical models to learn expression modules and their regulatory programs from gene expression data. Here, we demonstrate the use of the synthetic data generator SynTReN for the purpose of testing and comparing module network learning algorithms. We introduce a software package for learning module networks, called LeMoNe, which incorporates a novel strategy for learning regulatory programs. Novelties include the use of a bottom-up Bayesian hierarchical clustering to construct the regulatory programs, and the use of a conditional entropy measure to assign regulators to the regulation program nodes. Using SynTReN data, we test the performance of LeMoNe in a completely controlled situation and assess the effect of the methodological changes we made with respect to an existing software package, namely Genomica. Additionally, we assess the effect of various parameters, such as the size of the data set and the amount of noise, on the inference performance. Overall, application of Genomica and LeMoNe to simulated data sets gave comparable results. However, LeMoNe offers some advantages, one of them being that the learning process is considerably faster for larger data sets. Additionally, we show that the location of the regulators in the LeMoNe regulation programs and their conditional entropy may be used to prioritize regulators for functional validation, and that the combination of the bottom-up clustering strategy with the conditional entropy-based assignment of regulators improves the handling of missing or hidden regulators.

q-bio.QM↗