Morris Antonello

Fast computation of entropic profiles for the detection of conservation in genomes

The information theory has been used for quite some time in the area of computational biology. In this paper we discuss and improve the function Entropic Profile, introduced by Vinga and Almeida in [23]. The Entropic Profiler is a function of the genomic location that captures the importance of that region with respect to the whole genome. We provide a linear time linear space algorithm called Fast Entropic Profile, as opposed to the original quadratic implementation. Moreover we propose an alternative normalization that can be also efficiently implemented. We show that Fast EP is suitable for large genomes and for the discovery of motifs with unbounded length.

Fast entropic profiler: an information theoretic approach for the discovery of patterns in genomes

Information theory has been used for quite some time in the area of computational biology. In this paper we present a pattern discovery method, named Fast Entropic Profiler, that is based on a local entropy function that captures the importance of a region with respect to the whole genome. The local entropy function has been introduced by Vinga and Almeida in , here we discuss and improve the original formulation. We provide a linear time and linear space algorithm called Fast Entropic Profiler ( FastEP), as opposed to the original quadratic implementation. Moreover we propose an alternative normalization that can be also efficiently implemented. We show that FastEP is suitable for large genomes and for the discovery of patterns with unbounded length. FastEP is available at http://www.dei.unipd.it/~ciompin/main/FastEP.html.

Autonomous robotic system for thermographic detection of defects in upper layers of carbon fiber reinforced polymers

Carbon Fiber Reinforced Polymers (CFRPs) are composites whose interesting properties, like high strength-to-weight ratio and rigidity, are of interest in many industrial fields. Many defects affecting their production process are due to the wrong distribution of the thermosetting polymer in the upper layers. In this work, they are effectively and efficiently detected by automatically analyzing the thermographic images obtained by Pulsed Phase Thermography (PPT) and comparing them with a defect-free reference. The flash lamp and infrared camera needed by PPT are mounted on an industrial robot so that surfaces of CFRP automotive components, car side blades in our case, can be inspected in a series of static tests. The thermographic image analysis is based on local contrast adjustment via UnSharp Masking (USM) and takes also advantage of the high level of knowledge of the entire system provided by the calibration procedures. This system could replace manual inspection leading to a substantial increase in efficiency.

On the comparison of regulatory sequences with multiple resolution Entropic Profiles

BackgroundEnhancers are stretches of DNA (100–1000 bp) that play a major role in development gene expression, evolution and disease. It has been recently shown that in high-level eukaryotes enhancers rarely work alone, instead they collaborate by forming clusters of cis-regulatory modules (CRMs). Although the binding of transcription factors is sequence-specific, the identification of functionally similar enhancers is very difficult and it cannot be carried out with traditional alignment-based techniques.ResultsThe use of fast similarity measures, like alignment-free measures, to detect related regulatory sequences is crucial to understand functional correlation between two enhancers. In this paper we study the use of alignment-free measures for the classification of CRMs. However, alignment-free measures are generally tied to a fixed resolution k. Here we propose an alignment-free statistic, called EP2∗

Efficient Measurement of Fibre Orientation for Mapping Carbon Fibre Parts with a Robotic System

EP^{*}_{2}

A fully automatic hand-eye calibration system

, that is based on multiple resolution patterns derived from the Entropic Profiles (EPs). The Entropic Profile is a function of the genomic location that captures the importance of that region with respect to the whole genome. As a byproduct we provide a formula to compute the exact variance of variable length word counts, a result that can be of general interest also in other applications.ConclusionsWe evaluate several alignment-free statistics on simulated data and real mouse ChIP-seq sequences. The new statistic, EP2∗

An Open Source Robotic Platform for Ambient Assisted Living

EP^{*}_{2}

Brain-Computer Interface Meets ROS: A Robotic Approach to Mentally Drive Telepresence Robots

, is highly successful in discriminating functionally related enhancers and, in almost all experiments, it outperforms fixed-resolution methods. We implemented the new alignment-free measures, as well as traditional ones, in a software called EP-sim that is freely available: http://www.dei.unipd.it/~ciompin/main/EP-sim.html.

Multi-View 3D Entangled Forest for Semantic Segmentation and Mapping

The strength of carbon fibre parts depends on the fibre arrangements all over them, but only manual and sparse checks are usually executed to assess their quality. Here, we present an automatic method for computing the fibre orientations in each part point and mapping them onto the 3D model of the part. This process is automated by a robot that moves the measurement sensor above the object to be scanned. Since this sensor needs to acquire multiple images of the same point with different illuminations for correctly estimating the fibre orientation, we developed algorithms for online image registration in presence of translational sensor motion. Moreover, we propose real-time methods for projection of the estimated orientation vectors to a 3D model. Experiments show that this software allows the accurate and fast mapping of carbon fibre parts by means of an industrial robot. Accuracy assessments report a measurement accuracy below 5\(^{\circ }\).

Fast and robust detection of fallen people from a mobile robot

To retrieve the 3D coordinates of an object in the robot workspace is a fundamental capability for industrial and service applications. This can be achieved by means of a camera mounted on the robot end-effector only if the hand- eye transformation is known. The standard calibration process requires to view a calibration pattern, e.g. a checkerboard, from several different perspectives. This work extends the standard approach performing calibration pattern localization and hand- eye calibration in a fully automatic way. A two phase procedure has been developed and tested in both simulated and real scenarios, demonstrating that the automatic calibration reaches the same performance level of a standard procedure, while avoiding any human intervention. As a final contribution, the source code for an automatic and robust calibration is released.