Motivation: Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy. In particular, deep learning has proven to systematically achieve human-level performance in various recognition tasks, and thus emerges as an ideal tool to address automated identification of NMR signals. Results: We have applied a convolutional neural network for visual analysis of multidimensional NMR spectra. A comprehensive test on 31 manually annotated spectra has demonstrated top-tier average precision (AP) of 0.9596, 0.9058 and 0.8271 for backbone, side-chain and NOESY spectra, respectively. Furthermore, a combination of extracted peak lists with automated assignment routine, FLYA, outperformed other methods, including the manual one, and led to correct resonance assignment at the levels of 90.40%, 89.90% and 90.20% for three benchmark proteins. Availability and implementation: The proposed model is a part of a Dumpling software (platform for protein NMR data analysis), and is available at https://dumpling.bio/. Supplementary information: Supplementary data are available at Bioinformatics online.

The subspace restricted Boltzmann machine (subspaceRBM) is a third-order Boltzmann machine where multiplicative interactions are between one visible and two hidden units. There are two kinds of hidden units, namely, gate units and subspace units . The subspace units reflect variations of a pattern in data and the gate unit is responsible for activating the subspace units. Additionally, the gate unit can be seen as a pooling feature. We evaluate the behavior of subspaceRBM through experiments with MNIST digit recognition task and Caltech 101 Silhouettes image corpora, measuring cross-entropy reconstruction error and classification error.

In this paper, we investigate articulated human motion tracking from video sequences using Bayesian approach. We derive a generic particle-based filtering procedure with a low-dimensional manifold. The manifold can be treated as a regularizer that enforces a distribution over poses during tracking process to be concentrated around the low-dimensional embedding. We refer to our method as manifold regularized particle filter . We present a particular implementation of our method based on back-constrained gaussian process latent variable model and gaussian diffusion. The proposed approach is evaluated using the real-life benchmark dataset HumanEva . We show empirically that the presented sampling scheme outperforms sampling-importance resampling and annealed particle filter procedures.

In drug discovery field, one of the major used techniques is Nuclear Magnetic Resonance spectroscopy (NMR). To date, most of the steps in NMR analysis have been automated. The remaining step, peak picking, is still performed manually, what is extremely time-consuming and constitutes limiting factor in NMR-based drug discovery. Peak picking is a process of recognition of 2D/3D patterns in NMR image. To help automation of peak picking we have prepared a considerable benchmark, which enables testing various approaches. We also propose a baseline framework based on object detection scheme, which is well studied in the field of computer vision, and addresses automation of peak picking. Finally, we present the results of empirical studies, where a few different methods were compared, and show that peak pickers based on our framework significantly outperform the remaining methods for complex spectra and behave comparably for average ones.

MOTIVATION: A detailed analysis of multidimensional NMR spectra of macromolecules requires the identification of individual resonances (peaks). This task can be tedious and time-consuming and often requires support by experienced users. Automated peak picking algorithms were introduced more than 25 years ago, but there are still major deficiencies/flaws that often prevent complete and error free peak picking of biological macromolecule spectra. The major challenges of automated peak picking algorithms is both the distinction of artifacts from real peaks particularly from those with irregular shapes and also picking peaks in spectral regions with overlapping resonances which are very hard to resolve by existing computer algorithms. In both of these cases a visual inspection approach could be more effective than a 'blind' algorithm. RESULTS: We present a novel approach using computer vision (CV) methodology which could be better adapted to the problem of peak recognition. After suitable 'training' we successfully applied the CV algorithm to spectra of medium-sized soluble proteins up to molecular weights of 26 kDa and to a 130 kDa complex of a tetrameric membrane protein in detergent micelles. Our CV approach outperforms commonly used programs. With suitable training datasets the application of the presented method can be extended to automated peak picking in multidimensional spectra of nucleic acids or carbohydrates and adapted to solid-state NMR spectra. AVAILABILITY AND IMPLEMENTATION: CV-Peak Picker is available upon request from the authors. CONTACT: [email protected]; [email protected]; [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The knowledge extraction is an important element of the e-Health system. In this paper, we introduce a new method for decision rules extraction called Graph-based Rules Inducer to support the medical interview in the diabetes treatment. The emphasis is put on the capability of hidden context change tracking. The context is understood as a set of all factors affecting patient condition. In order to follow context changes, a forgetting mechanism with a forgetting factor is implemented in the proposed algorithm. Moreover, to aggregate data, a graph representation is used and a limitation of the search space is proposed to protect from overfitting. We demonstrate the advantages of our approach in comparison with other methods through an empirical study on the Electricity benchmark data set in the classification task. Subsequently, our method is applied in the diabetes treatment as a tool supporting medical interviews.

We propose a predictive model of structural changes in elementary sub graphs of social network based on Mixture of Markov Chains. The model is trained and verified on a dataset from a large corporate social network analyzed in short, one day-long time windows, and reveals distinctive patterns of evolution of connections on the level of local network topology. We argue that the network investigated in such short timescales is highly dynamic and therefore immune to classic methods of link prediction and structural analysis, and show that in the case of complex networks, the dynamic sub graph mining may lead to better prediction accuracy. The experiments were carried out on the logs from the Wroclaw University of Technology mail server.

In this paper a task of resources allocation in the complex system is considered. Novelty of the formulated task consists of assumption that the applications assigned with resources of one machine can be migrated to another machine during system lifetime. The formulated task has been solved using proposed heuristic optimization method. Due to non-convex set of valid solutions the optimization procedure has been decomposed into two stages and forms approach similar to the relax-and-round approach. Proposed decomposition approach facilitates fast algorithm convergence and guaranties that achieved solution satisfies assumed constraints.