The CAPRI experiment (Critical Assessment of Predicted Interactions) simulates realistic and diverse docking challenges, each case having specific properties that may be exploited by docking algorithms. Motivated by the different CAPRI challenges, we developed and implemented a comprehensive suite of docking algorithms. These were incorporated into a dynamic docking protocol, consisting of four main stages: (1) Biological and bioinformatics research aiming to predict the binding site residues, to define distance constraints between interface atoms and to analyze the flexibility of molecules; (2) Rigid or flexible docking, performed by the PatchDock or FlexDock method, which utilizes the information gathered in the previous step. Symmetric complexes are predicted by the SymmDock method; (3) Flexible refinement and re-ranking of the rigid docking solution candidates, performed by FiberDock; and finally, (4) clustering and filtering the results based on energy funnels. We analyzed the performance of our docking protocol on a large benchmark and on recent CAPRI targets. The analysis has demonstrated the importance of biological information gathering prior to docking, which significantly increased the docking success rate, and of the refinement and re-scoring stage that significantly improved the ranking of the rigid docking solutions. Our failures were mostly a result of mishandling backbone flexibility, inaccurate homology modeling, or incorrect biological assumptions. Most of the methods are available at http://bioinfo3d.cs.tau.ac.il/.

FisHiCal v1.1 is available from http://cran.r-project.org/.

Over the past few decades we have witnessed great efforts to understand the cellular function at the cytoplasm level. Nowadays there is a growing interest in understanding the relationship between function and structure at the nuclear, chromosomal and sub-chromosomal levels. Data on chromosomal interactions that are now becoming available in unprecedented resolution and scale open the way to address this challenge. Consequently, there is a growing need for new methods and tools that will transform these data into knowledge and insights. Here, we have developed all the steps required for the analysis of chromosomal interaction data (Hi-C data). The result is a methodology which combines a wavelet change point with the Bayes factor for useful correction, segmentation and comparison of Hi-C data. We further developed chromoR, an R package that implements the methods presented here. The chromoR package provides researchers with a means to analyse chromosomal interaction data using statistical bioinformatics, offering a new and comprehensive solution to this task.

Absolute camera pose regressors estimate the position and orientation of a camera given the captured image alone. Typically, a convolutional backbone with a multi-layer perceptron (MLP) head is trained using images and pose labels to embed a single reference scene at a time. Recently, this scheme was extended to learn multiple scenes by replacing the MLP head with a set of fully connected layers. In this work, we propose to learn multi-scene absolute camera pose regression with Transformers, where encoders are used to aggregate activation maps with selfattention and decoders transform latent features and scenes encoding into pose predictions. This allows our model to focus on general features that are informative for localization, while embedding multiple scenes in parallel. We extend our previous MS-Transformer approach [1] by introducing a mixed classificationregression architecture that improves the localization accuracy. Our method is evaluated on commonly benchmark indoor and outdoor datasets and has been shown to exceed both multi-scene and state-of-the-art single-scene absolute pose regressors. We make our code publicly available from here.

Visual pose regression models estimate the camera pose from a query image with a single forward pass. Current models learn pose encoding from an image using deep convolutional networks which are trained per scene. The resulting encoding is typically passed to a multi-layer perceptron in order to regress the pose. In this work, we propose that scene-specific pose encoders are not required for pose regression and that encodings trained for visual similarity can be used instead. In order to test our hypothesis, we take a shallow architecture of several fully connected layers and train it with pre-computed encodings from a generic image retrieval model. We find that these encodings are not only sufficient to regress the camera pose, but that, when provided to a branching fully connected architecture, a trained model can achieve competitive results and even surpass current state-of-the-art pose regressors in some cases. Moreover, we show that for outdoor localization, the proposed architecture is the only pose regressor, to date, consistently localizing in under 2 meters and 5 degrees.

Activity recognition problems such as human activity recognition and smartphone location recognition can improve the accuracy of different navigation or healthcare tasks, which rely solely on inertial sensors. Current learning-based approaches for activity recognition from inertial data employ convolutional neural networks or long short term memory architectures. Recently, Transformers were shown to outperform these architectures for sequence analysis tasks. This work presents an activity recognition model based on Transformers which offers an improved and general framework for learning activity recognition tasks. For evaluation purposes, several datasets, with more than 27 hours of inertial data recordings collected by 91 users, are employed. Those datasets represent different user activity scenarios with varying difficulty. The proposed approach consistently achieves better accuracy and generalizes better across all examined datasets and scenarios.

Studying the gene regulatory networks (GRNs) that govern how cells change into specific cell types with unique roles throughout development is an active area of experimental research. The fate specification process can be viewed as a biological program prescribing the system dynamics, governed by a network of genetic interactions. To investigate the possibility that GRNs are not fixed but rather change their topology, for example as cells progress through commitment, we introduce the concept of Switching Gene Regulatory Networks (SGRNs) to enable the modelling and analysis of network reconfiguration. We define the synthesis problem of constructing SGRNs that are guaranteed to satisfy a set of constraints representing experimental observations of cell behaviour. We propose a solution to this problem that employs methods based upon Satisfiability Modulo Theories (SMT) solvers, and evaluate the feasibility and scalability of our approach by considering a set of synthetic benchmarks exhibiting possible biological behaviour of cell development. We outline how our approach is applied to a more realistic biological system, by considering a simplified network involved in the processes of neuron maturation and fate specification in the mammalian cortex.

The CytoHiC plugin, source code, user manual, example files and documentation are available at: http://apps.cytoscape.org/apps/cytohicplugin