Publications

Many essential cell processes, such as the conformation of embedded proteins, membrane permeability, interaction with drugs and signalling, are directly connected to the molecular dynamics of cell membranes. The importance of this biology has led to an intensifying demand for hardware and software optimized models and tools, implemented on commodity high performance low-cost hardware, in order to provide the scientific community with virtual low cost laboratories. In the light of these considerations, we implemented an accelerated version of a molecular dynamics coarse-grain lipid bilayers simulator on commodity Graphic Processing Units (GPU) architectures. The characteristics of this molecular dynamics model, such as new force fields for pair potentials that include an unconventional representation for water and charges, were particularly challenging. We introduced new algorithms and data structures required by coarse-grain models compared to atomistic ones, for the modelling of the integration timestep, neighbour list generation, and nonbonded force interactions. We characterized the impact on performance of biological systems of differing complexity in terms of size, particle type and timestep. We also compared the simulations of many particle-type systems against single particle-type systems, to evaluate the overhead of additional structures needed to model more complex molecules. Moreover, we performed a detailed analysis on the profiling of the simulation code and its execution flows due to the computation of the non-bonded forces. Finally, we characterized the acceleration and accuracy of the simulations on three GPUs having different computation capabilities and parallelism, achieving one order of magnitude faster simulation execution times.

Understanding social and collective people behaviour in open spaces is one of the frontier of modern video surveillance. Many sociological theories, and proxemics in particular, have been proved their validity as a support for classifying and interpreting human behaviour. Proxemics suggest some simple but effective behavioural rules, useful to understand what people are doing and their social involvement with other individuals. In this paper we propose to extend the proxemics analysis along the time and provide a solution for analysing sequences of proxemic states computed between trajectories of people pairs (dyads). Trajectories, computed from videosurveillance videos, are first analysed and converted to a sequence of symbols according to proxemic theory. Then an elastic measure for comparing those sequences is introduced. Finally, interactions are classified both in an off-line unsupervised way and in an on-line fashion. Results on videosurveillance data, demonstrate that sequences of proxemic states can be effective in characterizing mutual interactions and experiments in capturing the most frequent dyads interactions and on-line classifying them when a labelled training set is available are proposed.

This paper describes the design and development of a Veiling Luminance estimation system based on the use of a CMOS image sensor, fully implemented on FPGA. The system is composed of the CMOS Image sensor, FPGA, DDR SDRAM, USB controller and SPI (Serial Peripheral Interface) Flash. The FPGA is used to build a system-on-chip integrating a soft processor (Xilinx MicroBlaze) and all the hardware blocks needed to handle the external peripherals and memory. The soft processor is used to handle image acquisition and all computational tasks need to compute the Veiling Luminance value. The advantages of this single chip FPGA implementation include the reduction of the hardware requirements, power consumption, and system complexity. The problem of the high dynamic range images have been addressed with multiple acquisitions at different exposure times. Vignetting, radial distortion and angular weighting, as required by veiling luminance definition, are handled by a single integer look-up table (LUT) access. Results are compared with a state of the art certified instrument.

The interest of the research community in creating reference datasets for performance analysis is always very high. Although new datasets, collecting large amounts of video footage are spreading in surveillance and forensics, few bench-marks with annotation data are available for testing specific tasks and especially for 3D/multi-view analysis. In this paper we present 3DPeS, a new dataset for 3D/multi- view surveillance and forensic applications. This has been designed for discussing and evaluating research results in people re-identification and other related activities (people detection, people segmentation and people tracking). The new assessed version of the dataset contains hundreds of video sequences of 200 people taken from a multi-camera distributed surveillance system over several days, with different light conditions; each person is detected multiple times and from different points of view. In surveillance scenarios, the dataset can be exploited to evaluate people reacquisition, 3D body models and people activity reconstruction algorithms. In forensics it can be adopted too, by relaxing some constraints (e.g. real time) and neglecting some information (e.g. calibration). Some results on this new dataset are presented using state of the art methods for people re-identification as a benchmark for future comparisons.

A CCD-based measuring instrument aimed at the veiling luminance estimation and the relative low-cost calibration method are described. The system may allow the estimation of the optimum luminance levels in road-tunnels lighting, thus both increasing the drivers safety and avoiding energy wasting hence unjustified higher lighting-costs.

Despite the many efforts in finding effective feature sets or accurate classifiers for people detection, few works have addressed ways for reducing the computational burden introduced by the sliding window paradigm. This paper proposes a multi-stage procedure for refining the search for pedestrians using the HOG features and the monolithic SVM classifier. The multi-stage procedure is based on particle-based estimation of pdfs and exploits the margin provided by the classifier to draw more particles on the areas where the classifier's response is higher. This iterative algorithm achieves the same accuracy than sliding window using less particles (and thus being more efficient) and, conversely, is more accurate when configured to work at the same computational load. Experimental results on publicly available datasets demonstrate that this method, previously proposed for boosted classifiers only, can be successfully applied to monolithic classifiers. © 2011 IEEE.

Nowadays, a considerable amount of genetic and biomedical studies are mostly diffused on the Web and freely available. This exciting capability, if from one side opens the way to new scenarios of cooperating research, on the other side makes the knowledge retrieval and extraction an extremely time consuming operation. In this context, the development of new tools and algorithms to automatically support the scientist activity to achieve a reliable interpretation of the complex interactions among biological entities is mandatory. In this paper we present a new methodology aimed at quantifying the biological degree of correlation among biomedical terms present in literature. The proposed method overcomes the limitation of current tools based on public literature information only, by exploiting the trustworthy information provided by biological pathways databases. We demonstrate how to integrate trusted pathway information in a semantic correlation extraction chain based on UMLS Metathesaurus and relying on PubMed as literature database. The effectiveness of the obtained results remarks the importance of automatically quantifying the degree of correlation among biomedical terms in order to helpfully support the scientist research activity.

Several industrial applications do require embedded solutionsboth for compacting the hardware occupation and reducing energy consumption, and for achieving high speed performance. This paper presents a computer vision system developed for correcting image skew in applications for banknote analysis and classification. The system must be very efficient and run on a fixed-point DSP with limited computational resources. Consequently, we propose three innovative improvements to basic and general-purpose image processing techniques that can be helpful in other computer vision applications on embedded devices. In particular, we address: a) an efficient labeling with an unionfind approach for hole filling, b) a fast Hough transform implementation, and c) a very high-speed estimation of affinetransformation for skew correction. The reported results demonstrate both the accuracy and the efficiency of the system,also in presence of severe skew. In terms of efficiency, the computational time is reduced of about two orders of magnitude.