Publications

Background: The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson–Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task. This task demands a lot of computational resources, especially for aligning many long sequences, and it therefore requires efficient algorithms that utilize modern hardware when available. A subset of the secondary structures contains overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in available software. Results: We present the SeqAn-based software LaRA 2 that is significantly faster than comparable software for accurate pairwise and multiple alignments of structured RNA sequences. In contrast to other programs our approach can handle arbitrary pseudoknots. As an improved re-implementation of the LaRA tool for structural alignments, LaRA 2 uses multi-threading and vectorization for parallel execution and a new heuristic for computing a lower boundary of the solution. Our algorithmic improvements yield a program that is up to 130 times faster than the previous version. Conclusions: With LaRA 2 we provide a tool to analyse large sets of RNA secondary structures in relatively short time, based on structural alignment. The produced alignments can be used to derive structural motifs for the search in genomic databases.

Accurate prediction of future human positions is an essential task for modern video-surveillance systems. Current state-of-the-art models usually rely on a "history" of past tracked locations (e.g., 3 to 5 seconds) to predict a plausible sequence of future locations (e.g., up to the next 5 seconds). We feel that this common schema neglects critical traits of realistic applications: as the collection of input trajectories involves machine perception (i.e., detection and tracking), incorrect detection and fragmentation errors may accumulate in crowded scenes, leading to tracking drifts. On this account, the model would be fed with corrupted and noisy input data, thus fatally affecting its prediction performance.In this regard, we focus on delivering accurate predictions when only few input observations are used, thus potentially lowering the risks associated with automatic perception. To this end, we conceive a novel distillation strategy that allows a knowledge transfer from a teacher network to a student one, the latter fed with fewer observations (just two ones). We show that a properly defined teacher supervision allows a student network to perform comparably to state-of-the-art approaches that demand more observations. Besides, extensive experiments on common trajectory forecasting datasets highlight that our student network better generalizes to unseen scenarios.

This paper is focused on Wireless Sensor Network (WSN) leveraging on Bluetooth Low Energy (BLE) connectivity for low energy applications which is fault tolerant versus communication path failures. The topic is important to create a robust sensorized environment to be applied in industrial context or smart infrastructure to enable scheduled monitoring with low power consumption applications. Currently BLE applications are mainly thought for smart home solutions, health care and positioning systems. In those applications the BLE nodes are continuously supplied by external power suppliers. Our goal is to design a self-configuring network with a synchronized deep sleep behavior, aimed to optimize the energy consumption, with an overall active time interval constraint optimized with a data-driven method. The aim is to find a tradeoff between the on time and the ability to collect all the nodes data, pursuing a low power consumption. Our research is based on BLE protocols, interaction between edge systems for data collection and cloud system for data analysis and software agent optimization system. The paper analyses different configurations and describes the possible optimization algorithm to be used for the software agent design, in order to reach a fine-tuned control to improve the fault tolerance and fault diagnosis of the system. Finally experimental results are compared with the estimates obtained via a software simulation tool implemented for this architectural pattern.

Inferior Alveolar Nerve (IAN) canal detection has been the focus of multiple recent works in dentistry and maxillofacial imaging. Deep learning-based techniques have reached interesting results in this research field, although the small size of 3D maxillofacial datasets has strongly limited the performance of these algorithms. Researchers have been forced to build their own private datasets, thus precluding any opportunity for reproducing results and fairly comparing proposals. This work describes a novel, large, and publicly available mandibular Cone Beam Computed Tomography (CBCT) dataset, with 2D and 3D manual annotations, provided by expert clinicians. Leveraging this dataset and employing deep learning techniques, we are able to improve the state of the art on the 3D mandibular canal segmentation. The source code which allows to exactly reproduce all the reported experiments is released as an open-source project, along with this article.

Exploration of indoor environments has recently experienced a significant interest, also thanks to the introduction of deep neural agents built in a hierarchical fashion and trained with Deep Reinforcement Learning (DRL) on simulated environments. Current state-of-the-art methods employ a dense extrinsic reward that requires the complete a priori knowledge of the layout of the training environment to learn an effective exploration policy. However, such information is expensive to gather in terms of time and resources. In this work, we propose to train the model with a purely intrinsic reward signal to guide exploration, which is based on the impact of the robot’s actions on its internal representation of the environment. So far, impact-based rewards have been employed for simple tasks and in procedurally generated synthetic environments with countable states. Since the number of states observable by the agent in realistic indoor environments is non-countable, we include a neural-based density model and replace the traditional count-based regularization with an estimated pseudo-count of previously visited states. The proposed exploration approach outperforms DRL-based competitors relying on intrinsic rewards and surpasses the agents trained with a dense extrinsic reward computed with the environment layouts. We also show that a robot equipped with the proposed approach seamlessly adapts to point-goal navigation and real-world deployment.

Connected Components Labeling (CCL) represents an essential part of many Image Processing and Computer Vision pipelines. Given its relevance on the field, it has been part of most cutting-edge Computer Vision libraries. In this paper, all the algorithms included in the OpenCV during the years are reviewed, from sequential to parallel/GPU-based implementations. Our goal is to provide a better understanding of what has changed and why one algorithm should be preferred to another both in terms of memory usage and execution speed.

In this work we introduce a new self-supervised, semi-parametric approach for synthesizing novel views of a vehicle starting from a single monocular image.Differently from parametric (i.e. entirely learning-based) methods, we show how a-priori geometric knowledge about the object and the 3D world can be successfully integrated into a deep learning based image generation framework. As this geometric component is not learnt, we call our approach semi-parametric.In particular, we exploit man-made object symmetry and piece-wise planarity to integrate rich a-priori visual information into the novel viewpoint synthesis process. An Image Completion Network (ICN) is then trained to generate a realistic image starting from this geometric guidance.This blend between parametric and non-parametric components allows us to i) operate in a real-world scenario, ii) preserve high-frequency visual information such as textures, iii) handle truly arbitrary 3D roto-translations of the input and iv) perform shape transfer to completely different 3D models. Eventually, we show that our approach can be easily complemented with synthetic data and extended to other rigid objects with completely different topology, even in presence of concave structures and holes.A comprehensive experimental analysis against state-of-the-art competitors shows the efficacy of our method both from a quantitative and a perceptive point of view.

Embodied AI is a recent research area that aims at creating intelligent agents that can move and operate inside an environment. Existing approaches in this field demand the agents to act in completely new and unexplored scenes. However, this setting is far from realistic use cases that instead require executing multiple tasks in the same environment. Even if the environment changes over time, the agent could still count on its global knowledge about the scene while trying to adapt its internal representation to the current state of the environment. To make a step towards this setting, we propose Spot the Difference: a novel task for Embodied AI where the agent has access to an outdated map of the environment and needs to recover the correct layout in a fixed time budget. To this end, we collect a new dataset of occupancy maps starting from existing datasets of 3D spaces and generating a number of possible layouts for a single environment. This dataset can be employed in the popular Habitat simulator and is fully compliant with existing methods that employ reconstructed occupancy maps during navigation. Furthermore, we propose an exploration policy that can take advantage of previous knowledge of the environment and identify changes in the scene faster and more effectively than existing agents. Experimental results show that the proposed architecture outperforms existing state-of-the-art models for exploration on this new setting.