Towards Intelligent Data Acquisition Systems with Embedded Deep Learning on MPSoC

Large-scale scientific experiments rely on dedicated high-performance data-acquisition systems to sample, readout, analyse, and store experimental data. However, with the rapid development in detector technology in various fields, the number of channels and the data rate are increasing. For trigger and control tasks data acquisition systems needs to satisfy real-time constraints, enable short-time latency and provide the possibility to integrate intelligent data processing. During recent years machine learning approaches have been used successfully in many applications. This dissertation will study how machine learning techniques can be integrated already in the data acquisition of large-scale experiments. A universal data acquisition platform for multiple data channels has been developed. Different machine learning implementation methods and application have been realized using this system. On the hardware side, recent FPGAs do not only provide high-performance parallel logic but more and more additional features, like ultra-fast transceivers and embedded ARM processors. TSMC\u27s 16nm FinFET Plus (16FF+) 3D transistor technology enables Xilinx in the Zynq UltraScale+ FPGA devices to increase the performance/watt ratio by 2 to 5 times compared to their previous generation. The selected main processor ZU11EG owns 32 GTH transceivers where each one could operate up to $16.3$ Gb/s and 16 GTY transceivers where each of them could operate up to $32.75$ Gb/s. These transceivers are routed to x16 lanes Gen $3$/$4$ PCIe, $12$ lanes full-duplex FireFly electrical/optical data link and VITA 57.4 FMC+ connector. The new Zynq UltraScale+ device provides at least three major advantages for advanced data acquisition systems: First, the 16nm FinFET+ programmable logic (PL) provides high-speed readout capabilities by high-speed transceivers; second, built-in quad-core 64-bit ARM Cortex-A53 processor enable host embedded Linux system. Thus, webservers, slow control and monitoring application could be realized in a embedded processor environment; third, the Zynq Multiprocessor System-on-Chip technology connects programmable logic and microprocessors. In this thesis, the benefits of such architectures for the integration of machine learning algorithms in data acquisition systems and control application are demonstrated. On the algorithm side, there have been many achievements in the field of machine learning over the last decades. Existing machine learning algorithms split into several categories depending on how the learning phase is organized: Supervised Learning, Unsupervised Learning, Semi-Supervised Learning and Reinforcement Learning. Most commonly used in scientific applications are supervised learning and reinforcement learning. Supervised learning learns from the labelled input and output, and generates a function that could predict the future different input to the appropriate output. A common application instance is a classification. They have a wide difference in basic math theory, training, inference, and their implementation. One of the natural solutions is Application Specific Integrated Circuit (ASIC) Artificial Intelligence (AI) chips. A typical example is the Google Tensor Processing Unit (TPU), it could cover the training and inference for both supervised learning and reinforcement learning. One of the major issues is that such chip could not provide high data transferring bandwidth other than high compute power. As a comparison, the Xilinx UltraScale+ FPGA could also provide raw compute power and efficiency for all different data types down to a single bit. From a deployment point of view, the training part of supervised learning is typically performed by CPU/GPU/TPU on a fixed dataset. For reinforcement learning, the training phase is more complex. The algorithm needs to periodically interact with the controlled system and execute a Markov Decision Process (MDP). There is no static training dataset, but it is obtained in real-time. The time slot between each step depends on the dynamics of the controlled system. The inference is also bound to this sampling time because the algorithm needs to interact with the environment and decide the appropriate action for a response, then a higher demand on time is proposed. This thesis gives solutions for both training and inference of reinforcement learning. At first, the requirements are analyzed, then the algorithm is deduced from scratch, and training on the PS part of Zynq device is implemented, meanwhile the inference at FPGA side is proposed which is similar solution compared with supervised learning. The results for Policy Gradient show a lot of improvement over a CPU/GPU-based machine learning framework. The Deep Deterministic Policy Gradient also has improvement regarding both training latency and stability. This implementation method provides a low-latency approach for reinforcement learning on-field training process

Performance modelling with adaptive hidden Markov models and discriminatory processor sharing queues

In modern computer systems, workload varies at different times and locations. It is important to model the performance of such systems via workload models that are both representative and efficient. For example, model-generated workloads represent realistic system behaviour, especially during peak times, when it is crucial to predict and address performance bottlenecks. In this thesis, we model performance, namely throughput and delay, using adaptive models and discrete queues. Hidden Markov models (HMMs) parsimoniously capture the correlation and burstiness of workloads with spatiotemporal characteristics. By adapting the batch training of standard HMMs to incremental learning, online HMMs act as benchmarks on workloads obtained from live systems (i.e. storage systems and financial markets) and reduce time complexity of the Baum-Welch algorithm. Similarly, by extending HMM capabilities to train on multiple traces simultaneously it follows that workloads of different types are modelled in parallel by a multi-input HMM. Typically, the HMM-generated traces verify the throughput and burstiness of the real data. Applications of adaptive HMMs include predicting user behaviour in social networks and performance-energy measurements in smartphone applications. Equally important is measuring system delay through response times. For example, workloads such as Internet traffic arriving at routers are affected by queueing delays. To meet quality of service needs, queueing delays must be minimised and, hence, it is important to model and predict such queueing delays in an efficient and cost-effective manner. Therefore, we propose a class of discrete, processor-sharing queues for approximating queueing delay as response time distributions, which represent service level agreements at specific spatiotemporal levels. We adapt discrete queues to model job arrivals with distributions given by a Markov-modulated Poisson process (MMPP) and served under discriminatory processor-sharing scheduling. Further, we propose a dynamic strategy of service allocation to minimise delays in UDP traffic flows whilst maximising a utility function.Open Acces

Leveraging EST Evidence to Automatically Predict Alternatively Spliced Genes, Master\u27s Thesis, December 2006

Current methods for high-throughput automatic annotation of newly sequenced genomes are largely limited to tools which predict only one transcript per gene locus. Evidence suggests that 20-50% of genes in higher eukariotic organisms are alternatively spliced. This leaves the remainder of the transcripts to be annotated by hand, an expensive time-consuming process. Genomes are being sequenced at a much higher rate than they can be annotated. We present three methods for using the alignments of inexpensive Expressed Sequence Tags in combination with HMM-based gene prediction with N-SCAN EST to recreate the vast majority of hand annotations in the D.melanogaster genome. In our first method, we “piece together” N-SCAN EST predictions with clustered EST alignments to increase the number of transcripts per locus predicted. This is shown to be a sensitve and accurate method, predicting the vast majority of known transcripts in the D.melanogaster genome. We present an approach of using these clusters of EST alignments to construct a Multi-Pass gene prediction phase, again, piecing it together with clusters of EST alignments. While time consuming, Multi-Pass gene prediction is very accurate and more sensitive than single-pass. Finally, we present a new Hidden Markov Model instance, which augments the current N-SCAN EST HMM, that predicts multiple splice forms in a single pass of prediction. This method is less time consuming, and performs nearly as well as the multi-pass approach

CellCognition : time-resolved phenotype annotation in high-throughput live cell imaging

Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Methods 7 (2010): 747-754, doi:10.1038/nmeth.1486.Fluorescence time-lapse imaging has become a powerful tool to investigate complex dynamic processes such as cell division or intracellular trafficking. Automated microscopes generate time-resolved imaging data at high throughput, yet tools for quantification of large-scale movie data are largely missing. Here, we present CellCognition, a computational framework to annotate complex cellular dynamics. We developed a machine learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states. The incorporation of time information into the annotation scheme was essential to suppress classification noise at state transitions, and confusion between different functional states with similar morphology. We demonstrate generic applicability in a set of different assays and perturbation conditions, including a candidate-based RNAi screen for mitotic exit regulators in human cells. CellCognition is published as open source software, enabling live imaging-based screening with assays that directly score cellular dynamics.Work in the Gerlich laboratory is supported by Swiss National Science Foundation (SNF) research grant 3100A0-114120, SNF ProDoc grant PDFMP3_124904, a European Young Investigator (EURYI) award of the European Science Foundation, an EMBO YIP fellowship, and a MBL Summer Research Fellowship to D.W.G., an ETH TH grant, a grant by the UBS foundation, a Roche Ph.D. fellowship to M.H.A.S, and a Mueller fellowship of the Molecular Life Sciences Ph.D. program Zurich to M.H. M.H. and M.H.A.S are fellows of the Zurich Ph.D. Program in Molecular Life Sciences. B.F. was supported by European Commission’s seventh framework program project Cancer Pathways. Work in the Ellenberg laboratory is supported by a European Commission grant within the Mitocheck consortium (LSHG-CT-2004-503464). Work in the Peter laboratory is supported by the ETHZ, Oncosuisse, SystemsX.ch (LiverX) and the SNF

Inductive learning of answer set programs for autonomous surgical task planning

The quality of robot-assisted surgery can be improved and the use of hospital resources can be optimized by enhancing autonomy and reliability in the robot’s operation. Logic programming is a good choice for task planning in robot-assisted surgery because it supports reliable reasoning with domain knowledge and increases transparency in the decision making. However, prior knowledge of the task and the domain is typically incomplete, and it often needs to be refined from executions of the surgical task(s) under consideration to avoid sub-optimal performance. In this paper, we investigate the applicability of inductive logic programming for learning previously unknown axioms governing domain dynamics. We do so under answer set semantics for a benchmark surgical training task, the ring transfer. We extend our previous work on learning the immediate preconditions of actions and constraints, to also learn axioms encoding arbitrary temporal delays between atoms that are effects of actions under the event calculus formalism. We propose a systematic approach for learning the specifications of a generic robotic task under the answer set semantics, allowing easy knowledge refinement with iterative learning. In the context of 1000 simulated scenarios, we demonstrate the significant improvement in performance obtained with the learned axioms compared with the hand-written ones; specifically, the learned axioms address some critical issues related to the plan computation time, which is promising for reliable real-time performance during surgery