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  1. Free, publicly-accessible full text available July 1, 2024
  2. With the proliferation of low-cost sensors and the Internet of Things, the rate of producing data far exceeds the compute and storage capabilities of today’s infrastructure. Much of this data takes the form of time series, and in response, there has been increasing interest in the creation of time series archives in the last decade, along with the development and deployment of novel analysis methods to process the data. The general strategy has been to apply a plurality of similarity search mechanisms to various subsets and subsequences of time series data in order to identify repeated patterns and anomalies; however, the computational demands of these approaches renders them incompatible with today’s power-constrained embedded CPUs. To address this challenge, we present FA-LAMP, an FPGA-accelerated implementation of the Learned Approximate Matrix Profile (LAMP) algorithm, which predicts the correlation between streaming data sampled in real-time and a representative time series dataset used for training. FA-LAMP lends itself as a real-time solution for time series analysis problems such as classification. We present the implementation of FA-LAMP on both edge- and cloud-based prototypes. On the edge devices, FA-LAMP integrates accelerated computation as close as possible to IoT sensors, thereby eliminating the need to transmit and store data in the cloud for posterior analysis. On the cloud-based accelerators, FA-LAMP can execute multiple LAMP models on the same board, allowing simultaneous processing of incoming data from multiple data sources across a network. LAMP employs a Convolutional Neural Network (CNN) for prediction. This work investigates the challenges and limitations of deploying CNNs on FPGAs using the Xilinx Deep Learning Processor Unit (DPU) and the Vitis AI development environment. We expose several technical limitations of the DPU, while providing a mechanism to overcome them by attaching custom IP block accelerators to the architecture. We evaluate FA-LAMP using a low-cost Xilinx Ultra96-V2 FPGA as well as a cloud-based Xilinx Alveo U280 accelerator card and measure their performance against a prototypical LAMP deployment running on a Raspberry Pi 3, an Edge TPU, a GPU, a desktop CPU, and a server-class CPU. In the edge scenario, the Ultra96-V2 FPGA improved performance and energy consumption compared to the Raspberry Pi; in the cloud scenario, the server CPU and GPU outperformed the Alveo U280 accelerator card, while the desktop CPU achieved comparable performance; however, the Alveo card offered an order of magnitude lower energy consumption compared to the other four platforms. Our implementation is publicly available at https://github.com/aminiok1/lamp-alveo. 
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  3. Mattoli, Virgilio (Ed.)
    Pneumatically-actuated soft robots have advantages over traditional rigid robots in many applications. In particular, their flexible bodies and gentle air-powered movements make them more suitable for use around humans and other objects that could be injured or damaged by traditional robots. However, existing systems for controlling soft robots currently require dedicated electromechanical hardware (usually solenoid valves) to maintain the actuation state (expanded or contracted) of each independent actuator. When combined with power, computation, and sensing components, this control hardware adds considerable cost, size, and power demands to the robot, thereby limiting the feasibility of soft robots in many important application areas. In this work, we introduce a pneumatic memory that uses air (not electricity) to set and maintain the states of large numbers of soft robotic actuators without dedicated electromechanical hardware. These pneumatic logic circuits use normally-closed microfluidic valves as transistor-like elements; this enables our circuits to support more complex computational functions than those built from normally-open valves. We demonstrate an eight-bit nonvolatile random-access pneumatic memory (RAM) that can maintain the states of multiple actuators, control both individual actuators and multiple actuators simultaneously using a pneumatic version of time division multiplexing (TDM), and set actuators to any intermediate position using a pneumatic version of analog-to-digital conversion. We perform proof-of-concept experimental testing of our pneumatic RAM by using it to control soft robotic hands playing individual notes, chords, and songs on a piano keyboard. By dramatically reducing the amount of hardware required to control multiple independent actuators in pneumatic soft robots, our pneumatic RAM can accelerate the spread of soft robotic technologies to a wide range of important application areas. 
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  4. null (Ed.)
    This paper introduces BioScript , a domain-specific language (DSL) for programmable biochemistry that executes on emerging microfluidic platforms. The goal of this research is to provide a simple, intuitive, and type-safe DSL that is accessible to life science practitioners. The novel feature of the language is its syntax, which aims to optimize human readability; the technical contribution of the paper is the BioScript type system. The type system ensures that certain types of errors, specific to biochemistry, do not occur, such as the interaction of chemicals that may be unsafe. Results are obtained using a custom-built compiler that implements the BioScript language and type system. 
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  5. Microfluidic cell sorters have shown great potential to revolutionize the current technique of enriching rare cells. In the past decades, different microfluidic cell sorters have been developed by researchers for separating circulating tumor cells, T-cells, and other biological markers from blood samples. However, it typically takes months or even years to design these microfluidic cell sorters by hand. Thus, researchers tend to use computer simulation (usually finite element analysis) to verify their designs before fabrication and experimental testing. Despite this, conducting precision finite element analysis of microfluidic devices is computationally expensive and labor-intensive. To address this issue, we recently presented a microfluidic simulation method that can simulate the behavior of fluids and particles in some typical microfluidic chips instantaneously. Our method decomposes the chip into channels and intersections. The behavior of fluid in each channel is determined by leveraging analogies with electronic circuits, and the behavior of fluid and particles in each intersection is determined by querying a database containing 92,934 pre-simulated channel intersections. While this approach successfully predicts the behavior of complex microfluidic chips in a fraction of the time required by existing techniques, we nonetheless identified three major limitations with this method: (1) the library of pre-simulated channel intersections is unnecessarily large (only 2,072 of 92,934 were used); (2) the library contains only cross-shaped intersections (and no other intersection geometries); and (3) the range of fluid flow rates in the library is limited to 0 to 2 cm/s. To address these deficiencies, in this work we present an improved method for instantaneously simulating the trajectories of particles in microfluidic chips. Firstly, inspired by dynamic programming, our new method optimizes the generation of pre-simulated intersection units and avoids generating unnecessary simulations. Secondly, we constructed a cloud database (http://cloud.microfluidics.cc) to share our pre-simulated results and to let users become contributors and upload their simulation results into the cloud database as a benefit to the whole microfluidic simulation community. Lastly, we investigated the impact of different channel angles and different fluid flow rates on predicting the trajectories of particles. We found a wide range of device geometries and flow rates over which our existing simulation results can be extended without having to perform additional simulations. Our method should accelerate the simulation of particles in microfluidic chips and enable researchers to design new microfluidic cell sorter chips more efficiently. 
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  6. Programmable microfluidic laboratories-on-a-chip (LoCs) offer the benefits of automation and miniaturization to the life sciences. This paper presents an updated version of the BioCoder language and a fully static (offline) compiler that can target an emerging class of LoCs called Digital Microfluidic Biochips (DMFBs), which manipulate discrete droplets of liquid on a 2D electrode grid. The BioCoder language and runtime execution engine leverage advances in sensor integration to enable specification, compilation, and execution of assays (bio-chemical procedures) that feature online decision-making based on sensory data acquired during assay execution. The compiler features a novel hybrid intermediate representation (IR) that interleaves fluidic operations with computations performed on sensor data. The IR extends the traditional notions of liveness and interference to fluidic variables and operations, as needed to target the DMFB, which itself can be viewed as a spatially reconfigurable array. The code generator converts the IR into the following: (1) a set of electrode activation sequences for each basic block in the control flow graph (CFG); (2) a set of computations performed on sensor data, which dynamically determine the result of each control flow operation; and (3) a set of electrode activation sequences for each control flow transfer operation (CFG edge). The compiler is validated using a software simulator which produces animated videos of realistic bioassay execution on a DMFB. 
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