Blind Biological Sequence Denoising with Self-Supervised Set Learning

Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate multiple subreads, or noisy observations of the same sequence. Denoising these subreads with alignment-based approaches often fails when too few subreads are available or error rates are too high. In this paper, we propose a novel method for blindly denoising sets of sequences without directly observing clean source sequence labels. Our method, Self-Supervised Set Learning (SSSL), gathers subreads together in an embedding space and estimates a single set embedding as the midpoint of the subreads in both the latent and sequence spaces. This set embedding represents the "average" of the subreads and can be decoded into a prediction of the clean sequence. In experiments on simulated long-read DNA data, SSSL methods denoise small reads of $\leq 6$ subreads with 17% fewer errors and large reads of $>6$ subreads with 8% fewer errors compared to the best baseline. On a real dataset of antibody sequences, SSSL improves over baselines on two self-supervised metrics, with a significant improvement on difficult small reads that comprise over 60% of the test set. By accurately denoising these reads, SSSL promises to better realize the potential of high-throughput DNA sequencing data for downstream scientific applications

Automated design of robust discriminant analysis classifier for foot pressure lesions using kinematic data

In the recent years, the use of motion tracking systems for acquisition of functional biomechanical gait data, has received increasing interest due to the richness and accuracy of the measured kinematic information. However, costs frequently restrict the number of subjects employed, and this makes the dimensionality of the collected data far higher than the available samples. This paper applies discriminant analysis algorithms to the classification of patients with different types of foot lesions, in order to establish an association between foot motion and lesion formation. With primary attention to small sample size situations, we compare different types of Bayesian classifiers and evaluate their performance with various dimensionality reduction techniques for feature extraction, as well as search methods for selection of raw kinematic variables. Finally, we propose a novel integrated method which fine-tunes the classifier parameters and selects the most relevant kinematic variables simultaneously. Performance comparisons are using robust resampling techniques such as Bootstrap$632+$and k-fold cross-validation. Results from experimentations with lesion subjects suffering from pathological plantar hyperkeratosis, show that the proposed method can lead to$sim 96$correct classification rates with less than 10% of the original features

Image Restoration Using Joint Statistical Modeling in Space-Transform Domain

This paper presents a novel strategy for high-fidelity image restoration by characterizing both local smoothness and nonlocal self-similarity of natural images in a unified statistical manner. The main contributions are three-folds. First, from the perspective of image statistics, a joint statistical modeling (JSM) in an adaptive hybrid space-transform domain is established, which offers a powerful mechanism of combining local smoothness and nonlocal self-similarity simultaneously to ensure a more reliable and robust estimation. Second, a new form of minimization functional for solving image inverse problem is formulated using JSM under regularization-based framework. Finally, in order to make JSM tractable and robust, a new Split-Bregman based algorithm is developed to efficiently solve the above severely underdetermined inverse problem associated with theoretical proof of convergence. Extensive experiments on image inpainting, image deblurring and mixed Gaussian plus salt-and-pepper noise removal applications verify the effectiveness of the proposed algorithm.Comment: 14 pages, 18 figures, 7 Tables, to be published in IEEE Transactions on Circuits System and Video Technology (TCSVT). High resolution pdf version and Code can be found at: http://idm.pku.edu.cn/staff/zhangjian/IRJSM

Inverse Analysis of Light Scattered by Soot Aggregates

The impact of soot on human health and the environment is a function of its size and morphology. Thus, it is important to have a method to quickly and accurately determine the aggregate size distribution of soot. Elastic light scattering is considered as a method to determine the aggregate size distribution in an aerosol. The relationship between the scattered light and the aggregate size distribution is derived and a robust inversion method is presented. The method is validated against artificial data. It is then applied to experimental data from a flame condition at which a distribution obtained from TEM analysis exists, and found to work quite well. Finally, optimization is applied to the experimental angles at which light is measured. The results showed that there is indeed an optimal angle setup, and that the error at that optimal setup is reduced over other angular setups

Non-local MRI upsampling.

International audienceIn Magnetic Resonance Imaging, image resolution is limited by several factors such as hardware or time constraints. In many cases, the acquired images have to be upsampled to match a specific resolution. In such cases, image interpolation techniques have been traditionally applied. However, traditional interpolation techniques are not able to recover high frequency information of the underlying high resolution data. In this paper, a new upsampling method is proposed to recover some of this high frequency information by using a data-adaptive patch-based reconstruction in combination with a subsampling coherence constraint. The proposed method has been evaluated on synthetic and real clinical cases and compared with traditional interpolation methods. The proposed method is shown to outperform classical interpolation methods compared in terms of quantitative measures and visual observation