As dedicated hardware is becoming more prevalent in accelerating complex applications, methods are needed to enable easy integration of multiple hardware components into a single accelerator system. However, this vision of composable hardware is hindered by the lack of standards for interfaces that allow such components to communicate. To address this challenge, the Tydi standard was proposed to facilitate the representation of streaming data in digital circuits, notably providing interface specifications of composite and variable-length data structures. At the same time, constructing hardware in a Scala embedded language (Chisel) provides a suitable environment for deploying Tydi-centric components due to its abstraction level and customizability. This article introduces Tydi-Chisel, a library that integrates the Tydi standard within Chisel, along with a toolchain and methodology for designing data-streaming accelerators. This toolchain reduces the effort needed to design streaming hardware accelerators by raising the abstraction level for streams and module interfaces, hereby avoiding writing boilerplate code, and allows for easy integration of accelerator components from different designers. This is demonstrated through an example project incorporating various scenarios where the interface-related declaration is reduced by 6-14 times. Tydi-Chisel project repository is available at https://github.com/abs-tudelft/Tydi-Chisel.

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This paper introduces TINA, a novel framework for implementing non Neural Network (NN) signal processing algorithms on NN accelerators such as GPUs, TPUs or FPGAs. The key to this approach is the concept of mapping mathematical and logic functions as a series of convolutional and fully connected layers. By mapping functions into such a small sub stack ofNN layers, it becomes possible to execute non-NN algorithms on NN hardware (HW) accelerators efficiently, as well as to ensure the portability of TINA implementations to any platform that supports such NN accelerators. Results show that TINA is highly competitive vs alternative frame-works, specifically for complex functions with iterations. For a Polyphase Filter Bank use case TINA shows GPU speedups of up to 80x vs a CPU baseline with NumPy compared to 8x speedup achieved by alternative frameworks. The frame-work is open source and publicly available at httPs://github.com/ChristiaanBoe/TINA.@en

This paper proposes an optimized quantum block-ZXZ decomposition method that results in more optimal quantum circuits than the quantum Shannon decomposition, which was presented in 2005 by M. Möttönen, and J. J. Vartiainen [in Trends in quantum computing research, edited by S. Shannon (Nova Science Publishers, 2006) Chap. 7, p. 149, arXiv:quant-ph/0504100]. The decomposition is applied recursively to generic quantum gates, and can take advantage of existing and future small-circuit optimizations. Because our method uses only single-qubit gates and uniformly controlled rotation-Z gates, it can easily be adapted to use other types of multi-qubit gates. With the proposed decomposition, a general three-qubit gate can be decomposed using 19 cnot gates (rather than 20). For general n-qubit gates, the proposed decomposition generates circuits that have 22484n-322n+53 cnot gates, which is less than the best-known exact decomposition algorithm by (4n-2-1)/3 cnot gates.

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High accuracy nanopore basecalling uses large deep neural networks, requiring powerful GPUs, which is undesirable for sequencing experiments outside the lab. Research has shown that this can be circumvented by using smaller models to increase efficiency as well as basecalling speed. However, this comes at the cost of reduced accuracy, going against the trend of increasingly more complex models to extract the highest possible accuracy out of the source data. We propose learning structured sparsity during model training to find an improved trade-off between accuracy and model size, and thus basecalling speed. Our work introduces an improved pruning method with a delayed masking scheduler and removes redundant masks, saving compute, and is optimized for the basecaller training process. We find that the model size can be reduced by up to 21× with a reduction in match rate of 0.1% to 1.3% compared to Bonito-HAC, using a standardized benchmarking method. Our results indicate that the size of basecalling models can be reduced drastically without affecting accuracy, as long as researchers use appropriate training methods. Furthermore, our work helps democratize nanopore DNA sequencing, broadening the reach and impact of this technology. The code with the masking mechanism to reproduce our results is available at https://github.com/meesfrensel/efficient-basecallers.

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In this paper, we present a fully pipelined and semi-parallel channel convolutional neural network hardware accelerator structure. This structure can trade off the compute time and the hardware utilization, allowing the accelerator to be layer pipelined without the need for fully parallelizing the input and output channels. A parallel strategy is applied to reduce the time gap in transferring the output results between different layers. The parallelism can be decided based on the hardware resources on the target FPGA. We use this structure to implement a binary ResNet18 based on the neural architecture search strategy, which can increase the accuracy of manually designed binary convolutional neural networks. Our optimized binary ResNet18 can achieve a Top-1 accuracy of 60.5% on the ImageNet dataset. We deploy this ResNet18 hardware implementation on an Alphadata 9H7 FPGA, connected with an OpenCAPI interface, to demonstrate the hardware capabilities. Depending on the amount of parallelism used, the latency can range from 1.12 to 6.33ms, with a corresponding throughput of 4.56 to 0.71 TOPS for different hardware utilization, with a 200MHz clock frequency. Our best latency is 8× lower and our best throughput is 1.9× higher compared to the best previous works. The code for our implementation is open-source and publicly available on GitHub at https://github.com/MFJI/NASBRESNET.

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In this paper, we present SENSIM, which is an open-source simulator designed specifically for the SENECA neuromorphic processor. This simulator is unique in that it combines features from both hardware-specific and hardware-agnostic spiking neural network simulators, resulting in a hybrid event-driven and time-step-driven simulation approach. This allows for flexibility between accuracy and speed during different stages of simulation. Our work highlights the open-source SENSIM platform, which enables the mapping of large-scale SNN/DNN models to the SENECA cores, as well as the benchmarking of crucial KPIs such as power and latency estimations.@en

Convolutional neural networks (CNNs) are to be effective in many application domains, especially in the computer vision area. In order to achieve lower latency CNN processing, and reduce power consumption, developers are experimenting with using FPGAs to accelerate CNN processing in several applications. Current FPGA CNN accelerators usually use the same acceleration approaches as GPUs, where operations from different network layers are mapped to the same hardware units working in a multiplexed manner. This will result in high flexibility in implementing different types of CNNs; however, this will degrade the latency that accelerators can achieve. Alternatively, we can reduce the latency of the accelerator by pipelining the processing of consecutive layers, at the expense of more FPGA resources. The continued increase in hardware resources available in FPGAs makes such implementations feasible for latency-critical application domains. In this paper, we present FPQNet, a fully pipelined and quantized CNN FPGA implementation that is channel-parallel, layer-pipelined, and network-parallel, to decrease latency and increase throughput, combined with quantization methods to optimize hardware utilization. In addition, we optimize this hardware architecture for the HDMI timing standard to avoid extra hardware utilization. This makes it possible for the accelerator to handle video datasets. We present prototypes of the FPQNet CNN network implementations on an Alpha Data 9H7 FPGA, connected with an OpenCAPI interface, to demonstrate architecture capabilities. Results show that with a 250 MHz clock frequency, an optimized LeNet-5 design is able to achieve latencies as low as 9.32 µs with an accuracy of 98.8% on the MNIST dataset, making it feasible for utilization in high frame rate video processing applications. With 10 hardware kernels working concurrently, the throughput is as high as 1108 GOPs. The methods in this paper are suitable for many other CNNs. Our analysis shows that the latency of AlexNet, ZFNet, OverFeat-Fast, and OverFeat-Accurate can be as low as 69.27, 66.95, 182.98, and 132.6 µs, using the architecture introduced in this paper, respectively. @en

Tydi is an open specification for streaming dataflow designs in digital circuits, allowing designers to express how composite and variable-length data structures are transferred over streams using clear, data-centric types. These data types are extensively used in a many application domains, such as big data and SQL applications. This way, Tydi provides a higher-level method for defining interfaces between components as opposed to existing bit- and byte-based interface specifications. In this paper, we introduce an open-source intermediate representation (IR) which allows for the declaration of Tydi's types. The IR enables creating and connecting components with Tydi Streams as interfaces, called Streamlets. It also lets backends for synthesis and simulation retain high-level information, such as documentation. Types and Streamlets can be easily reused between multiple projects, and Tydi's streams and type hierarchy can be used to define interface contracts, which aid collaboration when designing a larger system. The IR codifies the rules and properties established in the Tydi specification and serves to complement computation-oriented hardware design tools with a data-centric view on interfaces. To support different backends and targets, the IR is focused on expressing interfaces, and complements behavior described by hardware description languages and other IRs. Additionally, a testing syntax for the verification of inputs and outputs against abstract streams of data, and for substituting interdependent components, is presented which allows for the specification of behavior. To demonstrate this IR, we have created a grammar, parser, and query system, and paired these with a backend targeting VHDL.

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Background

Non-Invasive Prenatal Testing is often performed by utilizing read coverage-based profiles obtained from shallow whole genome sequencing to detect fetal copy number variations. Such screening typically operates on a discretized binned representation of the genome, where (ab)normality of bins of a set size is judged relative to a reference panel of healthy samples. In practice such approaches are too costly given that for each tested sample they require the resequencing of the reference panel to avoid technical bias. Within-sample testing methods utilize the observation that bins on one chromosome can be judged relative to the behavior of similarly behaving bins on other chromosomes, allowing the bins of a sample to be compared among themselves, avoiding technical bias.
Results

We present a comprehensive performance analysis of the within-sample testing method Wisecondor and its variants, using both experimental and simulated data. We introduced alterations to Wisecondor to explicitly address and exploit paired-end sequencing data. Wisecondor was found to yield the most stable results across different bin size scales while producing more robust calls by assigning higher Z-scores at all fetal fraction ranges.
Conclusions

Our findings show that the most recent available version of Wisecondor performs best.
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This paper offers a systematic method for creating medical knowledge-grounded patient records for use in activities involving differential diagnosis. Additionally, an assessment of machine learning models that can differentiate between various conditions based on given symptoms is also provided. We use a public disease-symptom data source called SymCat in combination with Synthea to construct the patients records. In order to increase the expressive nature of the synthetic data, we use a medically-standardized symptom modeling method called NLICE to augment the synthetic data with additional contextual information for each condition. In addition, Naive Bayes and Random Forest models are evaluated and compared on the synthetic data. The paper shows how to successfully construct SymCat-based and NLICE-based datasets. We also show results for the effectiveness of using the datasets to train predictive disease models. The SymCat-based dataset is able to train a Naive Bayes and Random Forest model yielding a 58.8% and 57.1% Top-1 accuracy score, respectively. In contrast, the NLICE-based dataset improves the results, with a Top-1 accuracy of 82.0% and Top-5 accuracy values of more than 90% for both models. Our proposed data generation approach solves a major barrier to the application of artificial intelligence methods in the healthcare domain. Our novel NLICE symptom modeling approach addresses the incomplete and insufficient information problem in the current binary symptom representation approach.@en

In this research, we extend the universal reinforcement learning agent models of artificial general intelligence to quantum environments. The utility function of a classical exploratory stochastic Knowledge Seeking Agent, KL-KSA, is generalized to distance measures from quantum information theory on density matrices. Quantum process tomography (QPT) algorithms form a tractable subset of programs for modeling environmental dynamics. The optimal QPT policy is selected based on a mutable cost function based on algorithmic complexity as well as computational resource complexity. The entire agent design is encapsulated in a self-replicating quine which mutates the cost function based on the predictive value of the optimal policy choosing scheme. Thus, multiple agents with pareto-optimal QPT policies evolve using genetic programming, mimicking the development of physical theories each with different resource trade-offs. This formal framework, termed Quantum Knowledge Seeking Agent (QKSA), is a resource-bounded participatory observer modification to the recently proposed algorithmic information-based reconstruction of quantum mechanics. A proof-of-concept is implemented and available as open-sourced software.

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Motion prediction is a key factor towards the full deployment of autonomous vehicles. It is fundamental in order to assure safety while navigating through highly interactive complex scenarios. In this work, the framework IAMP (Interaction-Aware Motion Prediction), producing multi-modal probabilistic outputs from the integration of a Dynamic Bayesian Network and Markov Chains, is extended with a learning-based approach. The integration of a machine learning model tackles the limitations of the ruled-based mechanism since it can better adapt to different driving styles and driving situations. The method here introduced generates context-dependent acceleration distributions used in a Markov-chain-based motion prediction. This hybrid approach results in better evaluation metrics when compared with the baseline in the four highly-interactive scenarios obtained from publicly available datasets.

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In spite of progress on hardware design languages, the design of high-performance hardware accelerators forces many design decisions specializing the interfaces of these accelerators in ways that complicate the understanding of the design and hinder modularity and collaboration. In response to this challenge, Tydi is presented as an open specification for streaming dataflow designs in digital circuits, allowing designers to express how composite and variable-length data structures are transferred over streams using clear, data-centric types. In contrast, Chisel, with its high level of abstraction and customizability offers a suitable platform to implement Tydi-based components. In this paper, Tydi-Chisel is presented along with an A-to-Z design-process description. Tydi-Chisel aims to simplify the design of data-streaming accelerators through the integration of the Tydi interface standard in Chisel, along with helper components and syntax sugar. In combination Chisel and Tydi help bridge the hardware-software divide, making solo-design and collaboration between designers easier.Project repository: https://github.com/ccromjongh/Tydi-Chisel@en

Many researchers have proposed replacing the aggregation server in federated learning with a blockchain system to improve privacy, robustness, and scalability. In this approach, clients would upload their updated models to the blockchain ledger and use a smart contract to perform model averaging. However, the significant delay and limited computational capabilities of blockchain systems make it inefficient to support machine learning applications on the blockchain.In this article, we propose a new public blockchain architecture called DFL, which is specially optimized for distributed federated machine learning. Our architecture inherits the merits of traditional blockchain systems while achieving low latency and low resource consumption by waiving global consensus. To evaluate the performance and robustness of our architecture, we implemented a prototype and tested it on a physical four-node network, and also developed a simulator to simulate larger networks and more complex situations. Our experiments show that the DFL architecture can reach over 90% accuracy for non-I.I.D. datasets, even in the presence of model poisoning attacks, while ensuring that the blockchain part consumes less than 5% of hardware resources.@en

Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulation platforms do not always take full advantage of modern hardware and often have a field-specific software design. Results: We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo features a modular and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, oncology and epidemiology. For each use case, we validate our findings with experimental data or an analytical solution. Our performance results show that BioDynaMo performs up to three orders of magnitude faster than the state-of-the-art baselines. This improvement makes it feasible to simulate each use case with one billion agents on a single server, showcasing the potential BioDynaMo has for computational biology research.

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In prenatal diagnostics, NIPT screening utilizing read coverage-based profiles obtained from shallow WGS data is routinely used to detect fetal CNVs. From this same data, fragment size distributions of fetal and maternal DNA fragments can be derived, which are known to be different, and often used to infer fetal fractions. We argue that the fragment size has the potential to aid in the detection of CNVs. By integrating, in parallel, fragment size and read coverage in a within-sample normalization approach, it is possible to construct a reference set encompassing both data types. This reference then allows the detection of CNVs within queried samples, utilizing both data sources. We present a new methodology, WisecondorFF, which improves sensitivity, while maintaining specificity, relative to existing approaches. WisecondorFF increases robustness of detected CNVs, and can reliably detect even at lower fetal fractions (<2%).

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Mice and rats can rapidly move their whiskers when exploring the environment. Accurate description of these movements is important for behavioral studies in neuroscience. Whisker tracking is, however, a notoriously difficult task due to the fast movements and frequent crossings and juxtapositionings among whiskers. We have recently developed WhiskEras, a computer-vision-based algorithm for whisker tracking in untrimmed, head-restrained mice. Although WhiskEras excels in tracking the movements of individual unmarked whiskers over time based on high-speed videos, the initial version of WhiskEras still had two issues preventing its widespread use: it involved tuning a great number of parameters manually to adjust for different experimental setups, and it was slow, processing less than 1 frame per second. To overcome these problems, we present here WhiskEras 2.0, in which the unwieldy stages of the initial algorithm were improved. The enhanced algorithm is more robust, not requiring intense parameter tuning. Furthermore, it was accelerated by first porting the code from MATLAB to C++ and then using advanced parallelization techniques with CUDA and OpenMP to achieve a speedup of at least 75x when processing a challenging whisker video. The improved WhiskEras 2.0 is made publicly available and is ready for processing high-speed videos, thus propelling behavioral research in neuroscience, in particular on sensorimotor integration.

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The concept of memory disaggregation has recently been gaining traction in research. With memory disaggregation, data center compute nodes can directly access memory on adjacent nodes and are therefore able to overcome local memory restrictions, introducing a new data management paradigm for distributed computing. This paper proposes and demonstrates a memory disaggregated in-memory object store framework for big data applications by leveraging the newly introduced Thymes-isFlow memory disaggregation system. The framework extends the functionality of the pre-existing Apache Arrow Plasma object store framework to distributed systems by enabling clients to easily and efficiently produce and consume data objects across multiple compute nodes. This allows big data applications to increasingly leverage parallel processing at reduced development costs. In addition, the paper includes latency and throughput measurements that indicate only a modest performance penalty is incurred for remote disaggregated memory access as opposed to local (~6.5 vs ~5.75 GiB/s). The results can be used to guide the design of future systems that leverage memory disaggregation as well as the newly presented framework. This work is open-source and publicly accessible at https://doi.org/10.5281/zenodo.6368998.@en

Current cluster scaled genomics data processing solutions rely on big data frameworks like Apache Spark, Hadoop and HDFS for data scheduling, processing and storage. These frameworks come with additional computation and memory overheads by default. It has been observed that scaling genomics dataset processing beyond 32 nodes is not efficient on such frameworks.To overcome the inefficiencies of big data frameworks for processing genomics data on clusters, we introduce a low-overhead and highly scalable solution on a SLURM based HPC batch system. This solution uses Apache Arrow as in-memory columnar data format to store genomics data efficiently and Arrow Flight as a network protocol to move and schedule this data across the HPC nodes with low communication overhead.As a use case, we use NGS short reads DNA sequencing data for pre-processing and variant calling applications. This solution outperforms existing Apache Spark based big data solutions in term of both computation time (2x) and lower communication overhead (more than 20-60% depending on cluster size). Our solution has similar performance to MPI-based HPC solutions, with the added advantage of easy programmability and transparent big data scalability. The whole solution is Python and shell script based, which makes it flexible to update and integrate alternative variant callers. Our solution is publicly available on GitHub at https://github.com/abs-tudelft/time-to-fly-high/tree/main/genomics@en