Multiple instance learning for sequence data with across bag dependencies

In Multiple Instance Learning (MIL) problem for sequence data, the instances inside the bags are sequences. In some real world applications such as bioinformatics, comparing a random couple of sequences makes no sense. In fact, each instance may have structural and/or functional relations with instances of other bags. Thus, the classification task should take into account this across bag relation. In this work, we present two novel MIL approaches for sequence data classification named ABClass and ABSim. ABClass extracts motifs from related instances and use them to encode sequences. A discriminative classifier is then applied to compute a partial classification result for each set of related sequences. ABSim uses a similarity measure to discriminate the related instances and to compute a scores matrix. For both approaches, an aggregation method is applied in order to generate the final classification result. We applied both approaches to solve the problem of bacterial Ionizing Radiation Resistance prediction. The experimental results of the presented approaches are satisfactory

Adaptive Multicore Scheduling for the LTE Uplink

International audienceThe next generation cellular system of 3GPP is named Long Term Evolution (LTE). Each millisecond, a LTE base station receives information from up to one hundred users. Multicore heterogeneous embedded systems with Digital Signal Processors (DSP) and coprocessors are power efficient solutions to decode the LTE uplink signals in base stations. The LTE uplink is a highly variable algorithm. Its multicore scheduling must be adapted every millisecond to the number of connected users and to the data rate they require. To solve the issue of the dynamic deployment while maintaining low latency, one approach would be to find efficient on-the-fly solutions using techniques such as graph generation and scheduling. This approach is opposed to a static scheduling of predefined cases. We show that the static approach is not suitable for the LTE uplink and that present DSP cores are powerful enough to recompute an efficient adaptive schedule for the LTE uplink most complex cases in real-time

A novel MapReduce-based approach for distributed frequent subgraph mining

National audienceRecently, graph mining approaches have become very popular, especially in certain domains such as bioinformatics, chemoinformatics and social networks. One of the most challenging tasks is frequent subgraph discovery. This task has been highly motivated by the tremendously increasing size of existing graph databases. Due to this fact, there is an urgent need of efficient and scaling approaches for frequent subgraph discovery. In this paper, we propose a novel approach to approximate large-scale subgraph mining by means of a density-based partitioning technique, using the MapReduce framework. Our partitioning aims to balance computational load on a collection of machines. We experimentally show that our approach decreases significantly the execution time and scales the subgraph discovery process to large graph databases

Pre- and post-scheduling memory allocation strategies on MPSoCs

6 pagesInternational audienceThis paper introduces and assesses a new method to allocate memory for applications implemented on a shared memory Multiprocessor System-on-Chip (MPSoC). This method first consists of deriving, from a Synchronous Dataflow (SDF) algorithm description, a Memory Exclusion Graph (MEG) that models all the memory objects of the application and their allocation constraints. Based on the MEG, memory allocation can be performed at three different stages of the implementation process: prior to the scheduling process, after an untimed multicore schedule is decided, or after a timed multicore schedule is decided. Each of these three alternatives offers a distinct trade-off between the amount of allocated memory and the flexibility of the application multicore execution. Tested use cases are based on descriptions of real applications and a set of random SDF graphs generated with the SDF For Free (SDF3) tool. Experimental results compare several allocation heuristics at the three implementation stages. They show that allocating memory after an untimed schedule of the application has been decided offers a reduced memory footprint as well as a flexible multicore execution

Memory Bounds for the Distributed Execution of a Hierarchical Synchronous Data-Flow Graph

International audienceThis paper presents an application analysis technique to define the boundary of shared memory requirements of Multiprocessor System-on-Chip (MPSoC) in early stages of development. This technique is part of a rapid prototyping process and is based on the analysis of a hierarchical Synchronous Data-Flow (SDF) graph description of the system application. The analysis does not require any knowledge of the system architecture, the mapping or the scheduling of the system application tasks. The initial step of the method consists of applying a set of transformations to the SDF graph so as to reveal its memory characteristics. These transformations produce a weighted graph that represents the different memory objects of the application as well as the memory allocation constraints due to their relationships. The memory boundaries are then derived from this weighted graph using analogous graph theory problems, in particular the Maximum-Weight Clique (MWC) problem. Stateof-the-art algorithms to solve these problems are presented and a heuristic approach is proposed to provide a near-optimal solution of the MWC problem. A performance evaluation of the heuristic approach is presented, and is based on hierarchical SDF graphs of realistic applications. This evaluation shows the efficiency of proposed heuristic approach in finding near optimal solutions

Novel metrics for feature extraction stability in protein sequence classication

Feature extraction is an unavoidable task, especially in the critical step of preprocessing biological sequences. This step consists for example in transforming the biological sequences into vectors of motifs where each motif is a subsequence that can be seen as a property (or attribute) characterizing the sequence. Hence, we obtain an object-property table where objects are sequences and properties are motif extracted from sequences. This output can be used to apply standard machine learning tools to perform data mining tasks such as classification. Several previous works have described feature extraction methods for bio-sequence classification, but none of them discussed the robustness of these methods when perturbing the input data. In this work, we introduce the notion of stability of the generated motifs in order to study the robustness of motif extraction methods. We express this robustness in terms of the ability of the method to reveal any change occurring in the input data and also its ability to target the interesting motifs. We use these criteria to evaluate and experimentally compare four existing extraction methods for biological sequences

Memory Bounds for the Distributed Execution of a Hierarchical Synchronous Data-Flow Graph

International audienceThis paper presents an application analysis technique to define the boundary of shared memory requirements of Multiprocessor System-on-Chip (MPSoC) in early stages of development. This technique is part of a rapid prototyping process and is based on the analysis of a hierarchical Synchronous Data-Flow (SDF) graph description of the system application. The analysis does not require any knowledge of the system architecture, the mapping or the scheduling of the system application tasks. The initial step of the method consists of applying a set of transformations to the SDF graph so as to reveal its memory characteristics. These transformations produce a weighted graph that represents the different memory objects of the application as well as the memory allocation constraints due to their relationships. The memory boundaries are then derived from this weighted graph using analogous graph theory problems, in particular the Maximum-Weight Clique (MWC) problem. Stateof-the-art algorithms to solve these problems are presented and a heuristic approach is proposed to provide a near-optimal solution of the MWC problem. A performance evaluation of the heuristic approach is presented, and is based on hierarchical SDF graphs of realistic applications. This evaluation shows the efficiency of proposed heuristic approach in finding near optimal solutions

Building a RTOS for MPSoC Dataflow Programming

International audienceMultiprocessor Systems-on-Chip (MPSoC) are becoming the standard high performance Digital Signal Processing (DSP) systems. Hardware complexity abstraction is needed to enable efficient MPSoC programming. A major challenge of MPSoC programming is efficiently handling the combination of new features necessary in a MPSoC operating system: load balancing and efficient use of the parallel resources, with the more traditional features of Real-Time Operating Systems (RTOS): resource sharing between applications, task priorities and reactivity to events. This paper presents a method to combine dataflow methods and RTOS features. The resulting system prototypes an RTOS for symmetric multiprocessing MPSoCs whose inputs are dataflow graphs of applications. The prototype is built on the uC/OS-II RTOS. Experimental results are given on a 3GPP Long Term Evolution algorithm executed on a 4-core MPSoC

PREESM: A Dataflow-Based Rapid Prototyping Framework for Simplifying Multicore DSP Programming

International audienceThe high performance Digital Signal Processors (DSP) currently manufactured by Texas Instruments are heterogeneous multiprocessor architectures. Programming these architectures is a complex task often reserved to specialized engineers because the bottlenecks of both the algorithm and the architecture need to be deeply understood in order to obtain a fairly parallel execution. The PREESM framework objective is to simplify the programming of multicore DSP systems by building on dataflow programming methods. The current functionalities of this scalable framework cover memory and time analysis, as well as automatic deadlock-free code generation. Several tutorials are provided with the tool for fast initiation of C programmers to multicore DSP programming. This paper demonstrates PREESM capabilities by comparing simulation and execution performances on a stereo matching algorithm prototyped on the TMS320C6678 8-core DSP device

FPGA based co-design of a speed fuzzy logic controller applied to an autonomous car

This paper invests in FPGA technology to control the speed of an autonomous car using fuzzy logic. For that purpose, we propose a co-design based on a novel fuzzy controller IP. It was developed using the hardware language VHDL and driven by the Zynq processor through an SDK software design written in C. The proposed IP acts according to the ambient temperature and the presence or absence of an obstacle and its distance from the car. The partitioning of the co-design tasks divides them into hardware and software parts. The simulation results of the fuzzy IP and those of the complete co-design implementation on a Xilinx Zynq board showed the effectiveness of the proposed controller to meet the target constraints and generate suitable PWM signals. The proposed hardware architecture based on 6-LUT blocks uses 11 times fewer logic resources than other previous similar designs. Also, it can be easily updated when new constraints on the system are to be considered, which makes it suitable for many related applications. Fuzzy computing was accelerated thanks to the use of digital signal processing blocks that ensure parallel processing. Indeed, a complete execution cycle takes only 7 us