arXiv subjects

Tajana Rosing

Publications and source records attributed to Tajana Rosing.

At least 91 records · Page 5Linked to original sources

arXiv2024

RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing

Mass spectrometry (MS) is essential for protein analysis but faces significant challenges with large datasets and complex post-translational modifications, resulting in difficulties in spectral identification. Open Modification Search (OMS) improves the analysis of these modifications. We present RapidOMS, a solution leveraging the Samsung SmartSSD, which integrates SSD and FPGA in a near-storage configuration to minimize data movement and enhance the efficiency of large-scale database searching. RapidOMS employs hyperdimensional computing (HDC), a brain-inspired, high-dimensional data processing approach, exploiting the parallel processing and low-latency capabilities of FPGAs, making it well-suited for MS. Utilizing the parallelism and efficiency of bitwise operations in HDC, RapidOMS delivers up to a 60x speedup over the state-of-the-art (SOTA) CPU tool ANN-Solo and is 2.72x faster than the GPU tool HyperOMS. Furthermore, RapidOMS achieves an 11x improvement in energy efficiency compared to conventional systems, providing scalable, energy-efficient solutions for large-scale proteomics applications and advancing the efficient processing of proteomic data.

cs.DC↗

arXiv2024

FSL-HDnn: A 5.7 TOPS/W End-to-end Few-shot Learning Classifier Accelerator with Feature Extraction and Hyperdimensional Computing

This paper introduces FSL-HDnn, an energy-efficient accelerator that implements the end-to-end pipeline of feature extraction, classification, and on-chip few-shot learning (FSL) through gradient-free learning techniques in a 40 nm CMOS process. At its core, FSL-HDnn integrates two low-power modules: Weight clustering feature extractor and Hyperdimensional Computing (HDC). Feature extractor utilizes advanced weight clustering and pattern reuse strategies for optimized CNN-based feature extraction. Meanwhile, HDC emerges as a novel approach for lightweight FSL classifier, employing hyperdimensional vectors to improve training accuracy significantly compared to traditional distance-based approaches. This dual-module synergy not only simplifies the learning process by eliminating the need for complex gradients but also dramatically enhances energy efficiency and performance. Specifically, FSL-HDnn achieves an Intensity unprecedented energy efficiency of 5.7 TOPS/W for feature 1 extraction and 0.78 TOPS/W for classification and learning Training Intensity phases, achieving improvements of 2.6X and 6.6X, respectively, Storage over current state-of-the-art CNN and FSL processors.

cs.AR↗

arXiv2024

E-QUARTIC: Energy Efficient Edge Ensemble of Convolutional Neural Networks for Resource-Optimized Learning

Ensemble learning is a meta-learning approach that combines the predictions of multiple learners, demonstrating improved accuracy and robustness. Nevertheless, ensembling models like Convolutional Neural Networks (CNNs) result in high memory and computing overhead, preventing their deployment in embedded systems. These devices are usually equipped with small batteries that provide power supply and might include energy-harvesting modules that extract energy from the environment. In this work, we propose E-QUARTIC, a novel Energy Efficient Edge Ensembling framework to build ensembles of CNNs targeting Artificial Intelligence (AI)-based embedded systems. Our design outperforms single-instance CNN baselines and state-of-the-art edge AI solutions, improving accuracy and adapting to varying energy conditions while maintaining similar memory requirements. Then, we leverage the multi-CNN structure of the designed ensemble to implement an energy-aware model selection policy in energy-harvesting AI systems. We show that our solution outperforms the state-of-the-art by reducing system failure rate by up to 40% while ensuring higher average output qualities. Ultimately, we show that the proposed design enables concurrent on-device training and high-quality inference execution at the edge, limiting the performance and energy overheads to less than 0.04%.

cs.DC↗

arXiv2024

Fast-OverlaPIM: A Fast Overlap-driven Mapping Framework for Processing In-Memory Neural Network Acceleration

Processing in-memory (PIM) is promising to accelerate neural networks (NNs) because it minimizes data movement and provides large computational parallelism. Similar to machine learning accelerators, application mapping, which determines the operation scheduling and data layout, plays a critical role in the NN acceleration on PIM. The mapping optimization of previous NN accelerators focused on optimizing the latency of sequential execution. However, PIM accelerators feature a distinct design space of application mapping from conventional NN accelerators, due to the spatial execution of NN layers across different memory locations. This enables opportunities for overlapping execution of consecutive NN layers to improve the latency, where the succeeding layer can start execution before the preceding layer fully completes the computation. In this paper, we propose Fast-OverlaPIM framework that incorporates the computational overlapping optimization into the DNN mapping exploration process on PIM architectures. Fast-OverlaPIM includes analytical algorithms for fast and accurate overlap analysis. Furthermore, it proposes a novel mapping search strategy and a transformation mechanism to enable efficient design space exploration on the overlap-based mapping for the whole network. Our framework demonstrates a significant improvement in runtime performance from 3.4x to 323.1x compared to the previous state-of-the-art overlap-based framework. Our experiments show that Fast-OverlaPIM can efficiently produce mappings that are 4.6x to 18.1x faster than the state-of-the-art mapping optimization framework under the same architecture constraints.

cs.AR↗

arXiv2024

Efficient Open Modification Spectral Library Searching in High-Dimensional Space with Multi-Level-Cell Memory

Open Modification Search (OMS) is a promising algorithm for mass spectrometry analysis that enables the discovery of modified peptides. However, OMS encounters challenges as it exponentially extends the search scope. Existing OMS accelerators either have limited parallelism or struggle to scale effectively with growing data volumes. In this work, we introduce an OMS accelerator utilizing multi-level-cell (MLC) RRAM memory to enhance storage capacity by 3x. Through in-memory computing, we achieve up to 77x faster data processing with two to three orders of magnitude better energy efficiency. Testing was done on a fabricated MLC RRAM chip. We leverage hyperdimensional computing to tolerate up to 10% memory errors while delivering massive parallelism in hardware.

cs.AR↗

arXiv2024

MicroHD: An Accuracy-Driven Optimization of Hyperdimensional Computing Algorithms for TinyML systems

Hyperdimensional computing (HDC) is emerging as a promising AI approach that can effectively target TinyML applications thanks to its lightweight computing and memory requirements. Previous works on HDC showed that limiting the standard 10k dimensions of the hyperdimensional space to much lower values is possible, reducing even more HDC resource requirements. Similarly, other studies demonstrated that binary values can be used as elements of the generated hypervectors, leading to significant efficiency gains at the cost of some degree of accuracy degradation. Nevertheless, current optimization attempts do not concurrently co-optimize HDC hyper-parameters, and accuracy degradation is not directly controlled, resulting in sub-optimal HDC models providing several applications with unacceptable output qualities. In this work, we propose MicroHD, a novel accuracy-driven HDC optimization approach that iteratively tunes HDC hyper-parameters, reducing memory and computing requirements while ensuring user-defined accuracy levels. The proposed method can be applied to HDC implementations using different encoding functions, demonstrates good scalability for larger HDC workloads, and achieves compression and efficiency gains up to 200x when compared to baseline implementations for accuracy degradations lower than 1%.

cs.PF↗

arXiv2024

Lifelong Intelligence Beyond the Edge using Hyperdimensional Computing

On-device learning has emerged as a prevailing trend that avoids the slow response time and costly communication of cloud-based learning. The ability to learn continuously and indefinitely in a changing environment, and with resource constraints, is critical for real sensor deployments. However, existing designs are inadequate for practical scenarios with (i) streaming data input, (ii) lack of supervision and (iii) limited on-board resources. In this paper, we design and deploy the first on-device lifelong learning system called LifeHD for general IoT applications with limited supervision. LifeHD is designed based on a novel neurally-inspired and lightweight learning paradigm called Hyperdimensional Computing (HDC). We utilize a two-tier associative memory organization to intelligently store and manage high-dimensional, low-precision vectors, which represent the historical patterns as cluster centroids. We additionally propose two variants of LifeHD to cope with scarce labeled inputs and power constraints. We implement LifeHD on off-the-shelf edge platforms and perform extensive evaluations across three scenarios. Our measurements show that LifeHD improves the unsupervised clustering accuracy by up to 74.8% compared to the state-of-the-art NN-based unsupervised lifelong learning baselines with as much as 34.3x better energy efficiency. Our code is available at https://github.com/Orienfish/LifeHD.

cs.LG↗

arXiv2023

Federated Hyperdimensional Computing

Federated learning (FL) enables a loose set of participating clients to collaboratively learn a global model via coordination by a central server and with no need for data sharing. Existing FL approaches that rely on complex algorithms with massive models, such as deep neural networks (DNNs), suffer from computation and communication bottlenecks. In this paper, we first propose FedHDC, a federated learning framework based on hyperdimensional computing (HDC). FedHDC allows for fast and light-weight local training on clients, provides robust learning, and has smaller model communication overhead compared to learning with DNNs. However, current HDC algorithms get poor accuracy when classifying larger & more complex images, such as CIFAR10. To address this issue, we design FHDnn, which complements FedHDC with a self-supervised contrastive learning feature extractor. We avoid the transmission of the DNN and instead train only the HDC learner in a federated manner, which accelerates learning, reduces transmission cost, and utilizes the robustness of HDC to tackle network errors. We present a formal analysis of the algorithm and derive its convergence rate both theoretically, and show experimentally that FHDnn converges 3$\times$ faster vs. DNNs. The strategies we propose to improve the communication efficiency enable our design to reduce communication costs by 66$\times$ vs. DNNs, local client compute and energy consumption by ~1.5 - 6$\times$, while being highly robust to network errors. Finally, our proposed strategies for improving the communication efficiency have up to 32$\times$ lower communication costs with good accuracy.

cs.LG↗

arXiv2023

FHEmem: A Processing In-Memory Accelerator for Fully Homomorphic Encryption

Fully Homomorphic Encryption (FHE) is a technique that allows arbitrary computations to be performed on encrypted data without the need for decryption, making it ideal for securing many emerging applications. However, FHE computation is significantly slower than computation on plain data due to the increase in data size after encryption. Processing In-Memory (PIM) is a promising technology that can accelerate data-intensive workloads with extensive parallelism. However, FHE is challenging for PIM acceleration due to the long-bitwidth multiplications and complex data movements involved. We propose a PIM-based FHE accelerator, FHEmem, which exploits a novel processing in-memory architecture to achieve high-throughput and efficient acceleration for FHE. We propose an optimized end-to-end processing flow, from low-level hardware processing to high-level application mapping, that fully exploits the high throughput of FHEmem hardware. Our evaluation shows FHEmem achieves significant speedup and efficiency improvement over state-of-the-art FHE accelerators.

cs.AR↗

arXiv2023

SpecHD: Hyperdimensional Computing Framework for FPGA-based Mass Spectrometry Clustering

Mass spectrometry-based proteomics is a key enabler for personalized healthcare, providing a deep dive into the complex protein compositions of biological systems. This technology has vast applications in biotechnology and biomedicine but faces significant computational bottlenecks. Current methodologies often require multiple hours or even days to process extensive datasets, particularly in the domain of spectral clustering. To tackle these inefficiencies, we introduce SpecHD, a hyperdimensional computing (HDC) framework supplemented by an FPGA-accelerated architecture with integrated near-storage preprocessing. Utilizing streamlined binary operations in an HDC environment, SpecHD capitalizes on the low-latency and parallel capabilities of FPGAs. This approach markedly improves clustering speed and efficiency, serving as a catalyst for real-time, high-throughput data analysis in future healthcare applications. Our evaluations demonstrate that SpecHD not only maintains but often surpasses existing clustering quality metrics while drastically cutting computational time. Specifically, it can cluster a large-scale human proteome dataset-comprising 25 million MS/MS spectra and 131 GB of MS data-in just 5 minutes. With energy efficiency exceeding 31x and a speedup factor that spans a range of 6x to 54x over existing state of-the-art solutions, SpecHD emerges as a promising solution for the rapid analysis of mass spectrometry data with great implications for personalized healthcare.

q-bio.QM↗

arXiv2023

SCALE: Online Self-Supervised Lifelong Learning without Prior Knowledge

Unsupervised lifelong learning refers to the ability to learn over time while memorizing previous patterns without supervision. Although great progress has been made in this direction, existing work often assumes strong prior knowledge about the incoming data (e.g., knowing the class boundaries), which can be impossible to obtain in complex and unpredictable environments. In this paper, motivated by real-world scenarios, we propose a more practical problem setting called online self-supervised lifelong learning without prior knowledge. The proposed setting is challenging due to the non-iid and single-pass data, the absence of external supervision, and no prior knowledge. To address the challenges, we propose Self-Supervised ContrAstive Lifelong LEarning without Prior Knowledge (SCALE) which can extract and memorize representations on the fly purely from the data continuum. SCALE is designed around three major components: a pseudo-supervised contrastive loss, a self-supervised forgetting loss, and an online memory update for uniform subset selection. All three components are designed to work collaboratively to maximize learning performance. We perform comprehensive experiments of SCALE under iid and four non-iid data streams. The results show that SCALE outperforms the state-of-the-art algorithm in all settings with improvements up to 3.83%, 2.77% and 5.86% in terms of kNN accuracy on CIFAR-10, CIFAR-100, and TinyImageNet datasets.

cs.LG↗

arXiv2023

Async-HFL: Efficient and Robust Asynchronous Federated Learning in Hierarchical IoT Networks

Federated Learning (FL) has gained increasing interest in recent years as a distributed on-device learning paradigm. However, multiple challenges remain to be addressed for deploying FL in real-world Internet-of-Things (IoT) networks with hierarchies. Although existing works have proposed various approaches to account data heterogeneity, system heterogeneity, unexpected stragglers and scalibility, none of them provides a systematic solution to address all of the challenges in a hierarchical and unreliable IoT network. In this paper, we propose an asynchronous and hierarchical framework (Async-HFL) for performing FL in a common three-tier IoT network architecture. In response to the largely varied delays, Async-HFL employs asynchronous aggregations at both the gateway and the cloud levels thus avoids long waiting time. To fully unleash the potential of Async-HFL in converging speed under system heterogeneities and stragglers, we design device selection at the gateway level and device-gateway association at the cloud level. Device selection chooses edge devices to trigger local training in real-time while device-gateway association determines the network topology periodically after several cloud epochs, both satisfying bandwidth limitation. We evaluate Async-HFL's convergence speedup using large-scale simulations based on ns-3 and a network topology from NYCMesh. Our results show that Async-HFL converges 1.08-1.31x faster in wall-clock time and saves up to 21.6% total communication cost compared to state-of-the-art asynchronous FL algorithms (with client selection). We further validate Async-HFL on a physical deployment and observe robust convergence under unexpected stragglers.

cs.LG↗

arXiv2023

Streaming Encoding Algorithms for Scalable Hyperdimensional Computing

Hyperdimensional computing (HDC) is a paradigm for data representation and learning originating in computational neuroscience. HDC represents data as high-dimensional, low-precision vectors which can be used for a variety of information processing tasks like learning or recall. The mapping to high-dimensional space is a fundamental problem in HDC, and existing methods encounter scalability issues when the input data itself is high-dimensional. In this work, we explore a family of streaming encoding techniques based on hashing. We show formally that these methods enjoy comparable guarantees on performance for learning applications while being substantially more efficient than existing alternatives. We validate these results experimentally on a popular high-dimensional classification problem and show that our approach easily scales to very large data sets.

cs.LG↗

arXiv2023

RAPIDx: High-performance ReRAM Processing in-Memory Accelerator for Sequence Alignment

Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a critical bottleneck in bioinformatics analysis. The existing hardware accelerators for alignment suffer from limited on-chip memory, costly data movement, and poorly optimized alignment algorithms. They cannot afford to concurrently process the massive amount of data generated by sequencing machines. In this paper, we propose a ReRAM-based accelerator, RAPIDx, using processing in-memory (PIM) for sequence alignment. RAPIDx achieves superior efficiency and performance via software-hardware co-design. First, we propose an adaptive banded parallelism alignment algorithm suitable for PIM architecture. Compared to the original dynamic programming-based alignment, the proposed algorithm significantly reduces the required complexity, data bit width, and memory footprint at the cost of negligible accuracy degradation. Then we propose the efficient PIM architecture that implements the proposed algorithm. The data flow in RAPIDx achieves four-level parallelism and we design an in-situ alignment computation flow in ReRAM, delivering $5.5$-$9.7\times$ efficiency and throughput improvements compared to our previous PIM design, RAPID. The proposed RAPIDx is reconfigurable to serve as a co-processor integrated into existing genome analysis pipeline to boost sequence alignment or edit distance calculation. On short-read alignment, RAPIDx delivers $131.1\times$ and $46.8\times$ throughput improvements over state-of-the-art CPU and GPU libraries, respectively. As compared to ASIC accelerators for long-read alignment, the performance of RAPIDx is $1.8$-$2.9\times$ higher.

cs.AR↗

arXiv2023

DODEM: DOuble DEfense Mechanism Against Adversarial Attacks Towards Secure Industrial Internet of Things Analytics

Industrial Internet of Things (I-IoT) is a collaboration of devices, sensors, and networking equipment to monitor and collect data from industrial operations. Machine learning (ML) methods use this data to make high-level decisions with minimal human intervention. Data-driven predictive maintenance (PDM) is a crucial ML-based I-IoT application to find an optimal maintenance schedule for industrial assets. The performance of these ML methods can seriously be threatened by adversarial attacks where an adversary crafts perturbed data and sends it to the ML model to deteriorate its prediction performance. The models should be able to stay robust against these attacks where robustness is measured by how much perturbation in input data affects model performance. Hence, there is a need for effective defense mechanisms that can protect these models against adversarial attacks. In this work, we propose a double defense mechanism to detect and mitigate adversarial attacks in I-IoT environments. We first detect if there is an adversarial attack on a given sample using novelty detection algorithms. Then, based on the outcome of our algorithm, marking an instance as attack or normal, we select adversarial retraining or standard training to provide a secondary defense layer. If there is an attack, adversarial retraining provides a more robust model, while we apply standard training for regular samples. Since we may not know if an attack will take place, our adaptive mechanism allows us to consider irregular changes in data. The results show that our double defense strategy is highly efficient where we can improve model robustness by up to 64.6% and 52% compared to standard and adversarial retraining, respectively.

cs.CR↗

arXiv2022

Massively Parallel Open Modification Spectral Library Searching with Hyperdimensional Computing

Mass spectrometry, commonly used for protein identification, generates a massive number of spectra that need to be matched against a large database. In reality, most of them remain unidentified or mismatched due to unexpected post-translational modifications. Open modification search (OMS) has been proposed as a strategy to improve the identification rate by considering every possible change in spectra, but it expands the search space exponentially. In this work, we propose HyperOMS, which redesigns OMS based on hyperdimensional computing to cope with such challenges. Unlike existing algorithms that represent spectral data with floating point numbers, HyperOMS encodes them with high dimensional binary vectors and performs the efficient OMS in high-dimensional space. With the massive parallelism and simple boolean operations, HyperOMS can be efficiently handled on parallel computing platforms. Experimental results show that HyperOMS on GPU is up to $17\times$ faster and $6.4\times$ more energy efficient than the state-of-the-art GPU-based OMS tool while providing comparable search quality to competing search tools.

cs.DC↗

arXiv2022

MemFHE: End-to-End Computing with Fully Homomorphic Encryption in Memory

The increasing amount of data and the growing complexity of problems has resulted in an ever-growing reliance on cloud computing. However, many applications, most notably in healthcare, finance or defense, demand security and privacy which today's solutions cannot fully address. Fully homomorphic encryption (FHE) elevates the bar of today's solutions by adding confidentiality of data during processing. It allows computation on fully encrypted data without the need for decryption, thus fully preserving privacy. To enable processing encrypted data at usable levels of classic security, e.g., 128-bit, the encryption procedure introduces noticeable data size expansion - the ciphertext is much bigger than the native aggregate of native data types. In this paper, we present MemFHE which is the first accelerator of both client and server for the latest Ring-GSW (Gentry, Sahai, and Waters) based homomorphic encryption schemes using Processing In Memory (PIM). PIM alleviates the data movement issues with large FHE encrypted data, while providing in-situ execution and extensive parallelism needed for FHE's polynomial operations. While the client-PIM can homomorphically encrypt and decrypt data, the server-PIM can process homomorphically encrypted data without decryption. MemFHE's server-PIM is pipelined and is designed to provide flexible bootstrapping, allowing two encryption techniques and various FHE security-levels based on the application requirements. We evaluate MemFHE for various security-levels and compare it with state-of-the-art CPU implementations for Ring-GSW based FHE. MemFHE is up to 20kx (265x) faster than CPU (GPU) for FHE arithmetic operations and provides on average 2007x higher throughput than the state-of-the-art while implementing neural networks with FHE.

cs.CR↗

arXiv2022

RES-HD: Resilient Intelligent Fault Diagnosis Against Adversarial Attacks Using Hyper-Dimensional Computing

Industrial Internet of Things (I-IoT) enables fully automated production systems by continuously monitoring devices and analyzing collected data. Machine learning methods are commonly utilized for data analytics in such systems. Cyber-attacks are a grave threat to I-IoT as they can manipulate legitimate inputs, corrupting ML predictions and causing disruptions in the production systems. Hyper-dimensional computing (HDC) is a brain-inspired machine learning method that has been shown to be sufficiently accurate while being extremely robust, fast, and energy-efficient. In this work, we use HDC for intelligent fault diagnosis against different adversarial attacks. Our black-box adversarial attacks first train a substitute model and create perturbed test instances using this trained model. These examples are then transferred to the target models. The change in the classification accuracy is measured as the difference before and after the attacks. This change measures the resiliency of a learning method. Our experiments show that HDC leads to a more resilient and lightweight learning solution than the state-of-the-art deep learning methods. HDC has up to 67.5% higher resiliency compared to the state-of-the-art methods while being up to 25.1% faster to train.

cs.CR↗