Real-time data analysis for medical diagnosis using FPGA-accelerated neural networks
Real-time analysis of patient data during medical procedures can provide vital diagnostic feedback that significantly improves chances of success. With sensors becoming increasingly fast, frameworks such as Deep Neural Networks are required to perform calculations within the strict timing constraints for real-time operation. However, traditional computing platforms responsible for running these algorithms incur a large overhead due to communication protocols, memory accesses, and static (often generic) architectures. In this work, we implement a low-latency Multi-Layer Perceptron (MLP) processor using Field Programmable Gate Arrays (FPGAs). Unlike CPUs and Graphics Processing Units (GPUs), our FPGA-based design can directly interface sensors, storage devices, display devices and even actuators, thus reducing the delays of data movement between ports and compute pipelines. Moreover, the compute pipelines themselves are tailored specifically to the application, improving resource utilization and reducing idle cycles. We demonstrate the effectiveness of our approach using mass-spectrometry data sets for real-time cancer detection.
We demonstrate that correct parameter sizing, based on the application, can reduce latency by 20% on average. Furthermore, we show that in an application with tightly coupled data-path and latency constraints, having a large amount of computing resources can actually reduce performance. Using mass-spectrometry benchmarks, we show that our proposed FPGA design outperforms both CPU and GPU implementations, with an average speedup of 144x and 21x, respectively.
In our work, we demonstrate the importance of application-specific optimizations in order to minimize latency and maximize resource utilization for MLP inference. By directly interfacing and processing sensor data with ultra-low latency, FPGAs can perform real-time analysis during procedures and provide diagnostic feedback that can be critical to achieving higher percentages of successful patient outcomes.
KeywordsFPGA Machine learning Multi-layer perceptrons Real-time Inference Cancer Mass-spectrometry
Adaptive logic module
Arithmetic logic unit
Deep neural network
Digital signal processor
Field programmable gate arrays
Gated recurrent unit
General purpose input/output
Graphics processing unit
High bandwidth memory
Long short-term memory
Matrix vector multiplication
Most significant bit
Persistent critical path
Support vector machine recursive feature elimination
Surface-enhanced laser desorption and ionization
Variable critical path
Machine learning (ML) plays an integral part in solving many key scientific problems. It has been applied to such varied domains as finding cancer treatments , weather simulations , and design of new nanocatalysts . Machine learning methods have been used in medical applications for many years . First of all, machine learning can be used in monitoring patients’ vital signs. Muller, et al. introduced a Brain-Computer Interface (BCI)  based technique that can extract appropriate features from continuous EEG signal . The proposed system collects a number of trials from patients while they are asked to perform fixed tasks. Using the collected datasets as training data, the system infers the typical EEG patterns in real-time. In , Shoeb and Guttag presented a machine learning algorithm to recognize epileptic seizure from the scaled EEG signal. Machine learning is also widely used in medical image retrieval, enhancement, processing and mapping as introduced in [8, 9, 10, 11, 12]. Zacharaki, et al. performed a study on distinguishing different types of brain tumors based on Support Vector Machine Recursive Feature Elimination (SVM-RFE) algorithm . Pereira et al. introduced an approach to use machine learning algorithms to decode variables of interest from fMRI data . Apart from that, machine learning is also an effective supplement in diagnosing diseases [15, 16]. Ozcift, et al. constructed Rotation Forest (RF) ensemble classifiers for multiple machine learning algorithms in a computer-aided diagnosis (CADx) system that is used for diagnosing diseases like diabetes and Parkinson . Li and Zhou proposed a semi-supervised learning algorithm, Co-Forest, that uses undiagnosed samples along with only a small amount of diagnosed ones as training datasets for CAD systems targeting breast cancer diagnosis .
Multi-Layer Perceptrons (MLPs) are an important subset of ML that not only optimize existing applications and practices but also widen that pool by enabling designs to meet more stringent requirements of reliability, performance, complexity, and portability that are not possible from traditional approaches. MLPs consist of multiple layers of firing neurons, with each layer using responses of previous neurons as stimulus. Use of MLPs is divided into two stages: training and inference. Training is an iterative process that determines neuron connection strengths in a given MLP. We assign initial values to connection strengths and then apply training cases as inputs to the model. The correct results of training cases are known beforehand, which we refer to as expected values. Corresponding measured outputs of the model are compared with these expected values, and connection strengths are then updated by a (static or dynamic) factor in order to minimize the error between the two sets of results. This process is repeated until measured results converge to values that reduce errors to within acceptable bounds. Training is typically an offline operation and thus does not impact analysis timeframes. Inference, on the other hand, is performed in real-time and refers to the process of performing classification (or regression) on a set of test input cases using the trained model. In our work, we focus on improving inference latency in order to achieve small analysis timeframes.
Traditional processors running inference algorithms cannot meet the required timing constraints in most cases due to the large overhead of communication protocols, memory accesses, and static (often generic) architectures. Data must first be moved from sensors to CPU buffers, typically by using serial ports, thus limiting the bandwidth. For CPU-based implementations, processing individual test cases results in a large number of cache misses. This is because MLPs have virtually no data reuse for the same test case, and batch processing is not possible due to latency bounds. Moreover, meaningful model sizes tend to be larger than the higher cache levels (closer to the CPU) and hence entire models cannot fit in the L1 or L2 cache. For GPU implementations, further memory transactions are required to move data to and from the device memory over the PCIe bus, which increases the overhead. Low data reuse and batch-less processing also hurt GPU performance since the computations may not be sufficiently parallel to fully utilize the thousands of available cores. For cores that are assigned work, a significant number of cycles are likely to be idle as threads wait for off-chip data to be accessed. ASIC based designs have typically managed to fill this gap by providing massive amounts of resources and specialized pipelines that are tailored for Deep Neural Networks (DNNs); one example is the Google TPU . However, as the number of diverse applications and their associated models grows, these ASICs effectively address a domain, rather than a particular application, and hence are unable utilize application-specific optimizations at the level needed.
Reconfigurable architectures, such as FPGAs, are becoming increasingly popular since their logic can be configured to construct application-specific architectures [20, 21, 22, 23, 24, 25]. For MLPs in particular, arbitrary sized models can be easily implemented, scaled, and even transferred to newer generation technologies by recompiling the design. Like GPUs, FPGAs are Commercial-Off-The-Shelf (COTS), which means users can buy the device, generate logic for their desired model, and ensure that the resulting compute pipelines are optimal not only for MLPs, but also for their specific MLP application. Moreover, since the underlying computation structure does not change, complex HDL codes do not have to be written. Instead, simple scripts can be used to create the required architecture. As FPGA on-chip memory grows, reaching several megabytes in the current generation, users can move all model parameters to the on-chip SRAM and remove idle cycles caused by fetching weights from off-chip DRAM. Moreover, FPGAs offer support for most common serial and parallel protocols and can thus further minimize the latency of memory and I/O transactions by supplying data directly (from sensors) to compute pipelines. All these features result in a transition of the computation from memory bound to compute bound.
Improving latency (and hence performance) of compute-bound MLP inference requires all pipelines to operate both stall free and at high bandwidth. The former is achieved by ensuring modules in the design source/sink data at rates that are constrained by the latter. Since modules in MLP architectures are tightly coupled and operate within the same clock domain, constraints can occur even for indirect connectivity. Therefore, by selecting higher interface bandwidths for particular ports, the complexity (and hence latency) of potentially multiple modules can become significantly large. This increase in complexity can outweigh the benefits of higher module throughput and thus increase the overall latency of the computation.
FPGA-based MLP implementations have received significantly less attention than other DNNs such as Convolutional Neural Networks. The most prominent design is Microsoft’s FPGA-based inference architecture, Brainwave , targeting low compute-to-data ratio DNN applications such as MLPs, Long Short-Term Memories (LSTMs), and Gated Recurrent Units (GRUs). The memory bandwidth bound is alleviated by using on-chip block RAM for weight matrix storage. For an 8-bit integer implementation on Stratix V FPGAs, Brainwave achieves 2.0 TOps/s, while on Stratix 10 FPGAs, they claim to have 31 TOps/s performance running at 500 MHz. In [27, 28], the authors proposed FPGA-based MLP architectures, but their work serves as a proof-of-concept and is also constrained by off-chip memory bandwidth. Sharma et al. presented an automated DNN design generation framework, DNNWeaver , which also depends on DRAM access speed for performance. Moreover, the DNNWeaver compute units are constrained to Digital Signal Processor (DSP)-only implementations and logic cells are not used for ALUs. Gomperts et al. introduce a general purpose architecture for MLP based on FPGAs . Their design generates individual processing elements for each layer, which is not feasible for large neural networks where resources on a single FPGA may not even be sufficient to compute a single layer in parallel.
With regard to stand-alone operation with a direct interface to sensors, FPGAs have shown support for various forms of connectivity without host support. Apart from General Purpose I/O pins [31, 32] that can implement virtually any communication protocol, they also offer direct chip-chip connectivity through Multi-Gigabit Transceivers (MGTs) and network connectivity through dedicated Ethernet controllers. MGTs are serial links that provide low-latency, high-bandwidth, and low-energy interfaces [33, 34, 35, 36, 37, 38] and enable communication at rates of 100 Gbps per MGT. Current high-end FPGAs can have close to 100 MGTs. These MGTs can be used to connect multiple FPGAs together and perform computations for models that are too large for a single device. Large multi-FPGA clusters have long been a staple of computational finance and certain other industries. George et al.  presented an academic example of a 64 FPGA cluster with direct FPGA-to-FPGA links in a 3D torus network. Similarly, Microsoft’s original Catapult System [40, 41] consists of 1632 nodes with FPGAs directly interconnected via MGTs in a series of 6×8 tori.
In our work, we explore the application-aware optimization space for compute-bound MLP inference processors using our proposed FPGA-based architecture. By identifying modules in the critical path and their interconnectivity, we determine and optimize parameters for a given application in order to minimize the latency of the entire model evaluation and meet real-time constraints. This strategy enables our design to be feasible for applications such as real-time medical diagnosis.
In this study, we have designed and implemented a real-time Multi-Layer Perceptron inference processor for medical diagnosis using FPGAs. Our focus is on achieving ultra-low analysis latency to meet real-time constraints. The proposed system consists of a modular approach with standardized interfaces that enables hardware of individual functions to be easily modified based on changes to the inference model, design practices, or resource availability. We demonstrate that the ability to be application specific enables FPGA-based designs to choose architecture parameters that minimize latency and maximize utilization of computing resources. Using mass spectrometry benchmarks for cancer detection, we show that FPGAs can outperform traditional computing technologies such as CPUs and GPUs for real-time MLP applications.
We have tested our designs on the Intel Arria 10 FPGA (AX115H3F34E2SGE3), which has 427,200 Adaptive Logic Modules (ALMs), 1518 DSP blocks, 53 megabits of on-chip memory, and a maximum of 624 user General Purpose Inputs/Outputs (GPIOs) . The GPU used is a Tesla P100 which has 3594 CUDA cores and a 12 gigabyte High Bandwidth Memory (HBM2) with a peak bandwidth of 549 GB/s. For the baseline, we use an eight-core 2.6 GHz Intel Xeon E5-2650v2 CPU.
FPGA designs are implemented by using Altera OpenCL 16.0.2  to ensure that standard optimizations are applied and the impact of varying design parameters on latency can be fairly determined. Resource usage is measured by using the Quartus Prime Pro 16.0 compiler. GPU reference designs are compiled by using TensorFlow  r1.4, python 3.6.2, cuDNN 6.0 and CUDA 8.0. CPU code is also compiled by using TensorFlow r1.4. Both GPU and CPU designs use single-precision floating point, while the FPGA implementation uses fixed-point arithmetic, with arbitrary variable sizes that are optimized for each computation stage.
Proposed MLP models for mass spectrometry benchmarks
15154 × 512 × 512 ×2
15154 × 64 × 512 ×2
Multi layer perceptrons
Inputs to the hidden and output layer neurons are scaled and accumulated by using weights (connection strengths) that are determined during training. A non-linear function, called the activation function, is applied to the result, which then becomes the neuron output. Figure 1b shows this operation represented as a Matrix Vector Multiplication (MVM). Each layer has a unique weight matrix, which contains connection strengths, and a bias vector. Layer inputs are the result vector from the previous layer, or the input vector if it is the first hidden layer. A given row from the X×Y weight matrix for a given layer represents the connection strengths of Y neurons in the previous layer assigned to one of the X neurons in the current layer. The activation function is applied to individual elements of the output vector. During the training process, all data are floating point. Classification can be performed by using integer arithmetic without loss of accuracy.
MLP Inference architecture
If the size of a Scalar Product module is smaller than the input vector, multiple iterations are required to accumulate partial sums and obtain a final value. Moreover, a bias value must be added to the sum. The Accumulate module performs all of these functions by using dedicated Accumulate Registers. It receives triggers from the control plane on whether to accumulate or to re-initialize the registers for a new operation cycle.
Activation & requantization
The Activation & Quantization module reads data from the buffer, performs 32-bit ReLU activation (RELU(x)=max(x,0)), and then quantizes data back to 8 bits for the next layer. Quantization is performed by using truncation because of the high costs of division hardware. Because of the nature of the operation (compression), the difference in results is small in this particular context. Moreover, ReLU activation ensures that the Most Significant Bit (MSB) of our 8-bit result is always 0. Therefore the effective compression target is 7 bits, which further reduces the difference between division and truncation results.
Being able to perform quantization requires knowledge of the upper and lower data limits. Because of the ReLU activation, we are guaranteed a lower limit of 0. Searching for the upper limit must be done without stalling the data stream. Consequently, we use the Max Search module to perform local maxima searches on data as it becomes available and update an associated register if a local maximum exceeds the current global maximum. This approach ensures that latency is based on the dimensions of the accumulator outputs and not the full input vector. Employing a tree-based search further reduces the delay.
Once the maximum value for a given output has been determined, we use the Leading 1 module to find the most significant non-zero bit and use this position to perform truncations for quantization. The output is constrained to be between 6 and 30 (on a scale of 0-31) since the former means all values are already within 8 bits while the latter represents the largest possible positive numbers. As with Scalar Product and Max Search, the evaluation is performed with logarithmic complexity.
Of the compute plane modules discussed above, all but the Buffer lie in the critical path. We divide these modules into two categories; the Variable Critical Path (VCP) and the Persistent Critical Path (PCP). The Variable Critical Path is entirely the Scalar Product module. It is equal to the number of calls needed for the Scalar Product module to perform all multiplication operations. Since it is based on the relative dimensions of the weight matrix and Scalar Product module, it will vary for each layer. Once the last set of results has been produced, modules that need to evaluate this last result before a new layer can be processed are referred to as the Persistent Critical Path. It corresponds to a fixed number of cycles independent of layer dimensions. Applicable modules include Accumulator (with register), Max Search (with register), Leading 1, and Activation & Quantize.
Because of the tight coupling of our system design and the latency requirement, certain modules should be able to sink stall-free the entire throughput of their preceding component, as well as source the required throughput to their subsequent one. A chain of such modules where this throughput cannot be modified specifies a design parameter. In the proposed architecture, two such chains exist.
The first chain connects the Buffer and Scalar Product modules. It constrains i) the output size of the Buffer, ii) the size of the Activation & Quantize module, and iii) the length of a vector input to the Scalar Product module. We refer to this parameter as M. The value of M determines the number of columns being processed in the weight matrix. The second chain connects the Scalar Product to the Max Search module. It constrains i) the number of Scalar Product units, ii) the number of parallel accumulators needed to add partial sums, and iii) the number of elements over which to perform a maximum value search. We refer to this parameter as N. The value of N determines the number of rows being processed in the weight matrix. A third chain, between Max Search and Leading 1 modules, always has a throughput of one 32-bit element per cycle and hence does not have a variable design parameter. In our work, we explore the impact of varying M and N on performance.
Latency tags for defining trigger ranges
L_QA(M) + L_MM(M,N) + BLOCKS[i] + L_AC(N) + 1 + L_MX(N) + 1 + L_LO
L_QA(M) + L_MM(M,N)
L_QA(M) + L_MM(M,N) + L_AC(N) + 1 + L_MX(N)
L_QA(M) + L_MM(M,N) + BLOCKS[i] + L_AC(N) + 1 + L_MX(N)
L_QA(M) + L_MM(M,N) + BLOCKS[i] + L_AC(N) + 1 + L_MX(N) + 1 + L_LO -1
L_QA(M) + L_MM(M,N) + L_AC(N) + 1
L_QA(M) + L_MM(M,N) + BLOCKS[i] + L_AC(N) + 1
L_QA(M) + L_MM(M,N) + BLOCKS[i] + L_AC(N) + 1
FPGA implementation details
The hurdle to performing real-time analysis on patient data is meeting timing constraints. This is difficult to do on traditional, fixed-logic platforms because of a large number of sources of overhead. Meeting timing constraints with fixed-logic platforms may continue to become less feasible. With technological advancements and greater integration of sensors into medical procedures, both the data throughput of individual sensors and their overall number can be expected to increase. Our results highlight the importance of application-specific optimizations for minimizing the latency of MLP inference and meeting significantly stricter performance requirements.
When constructing modules, several factors must be considered when determining parameter sizing, such as the impact on VCP and PCP. For PCP, when standard optimizations were applied using OpenCL-based architecture generation, the size and complexity of basic components, along with the nature of the overall computation, had a significant impact on the module latency. This is nearly invariant of the application itself and depends more on the design strategies for implementing individual modules. The VCP, on the other hand, is significantly more application-specific since it depends on the ratio of parameter values to nearly every layer size in the model. Thus, while there is an initial bias toward increasing the size of M over N, all latency contributions must be considered on a per-application basis to determine the optimal architecture.
An important observed trend in the performance results emphasizes the impact of batch-less execution on traditional accelerators. As the size of the model decreases, from Ovarian to JNCI, the FPGA execution time is also reduced since fewer computations are required for the smaller first hidden layer in JNCI. However, the GPU performance for the same transition shows a decrease. The reason is that GPUs depend heavily on batch processing of multiple test vectors in order to get good utilization of the thousands of computing cores. As a result, the lower number of test vectors for JNCI results in worse GPU performance despite there being fewer overall computations. Overall, we expect the CPU and GPU performance values to be even lower if batch-less test sets are run (as opposed to computing the average).
We show the importance of application-specific optimizations in order to minimize latency and maximize resource utilization for MLP inference. By directly interfacing with and processing sensor data during procedures, FPGAs can perform real-time analysis and provide diagnostic feedback that can be critical to achieving higher percentages of successful patient outcomes. We propose a modular architecture that enables modifications to be easily performed based on the application model, design updates, and resource availability as the design is migrated to different FPGAs. We demonstrate that correct parameter sizing, based on the application, can reduce latency by 20% on average. Further, we show that in an application with tightly coupled data-path and latency constraints, having a large amount of computing resources can actually reduce performance. Moreover, since the FPGA does not require batch processing of inputs, it can operate with ultra-low latency in order to meet real-time constraints. Using mass-spectrometry benchmarks, our proposed FPGA design outperforms both CPU and GPU implementations with average speedups of 144x and 21x,respectively.
This work is supported in part by the National Science Foundation through Awards CNS-1405695 and CCF-1618303/7960; by a grant from Red Hat; by Altera through donated FPGAs, tools, and IP; and by Gidel through discounted FPGA boards and daughter cards. This research used the resources of the Argonne Leadership Computing Facility, which is a U.S. Department of Energy (DoE) Office of Science User Facility supported under Contract DE-AC02-06CH11357. We gratefully acknowledge the computing resources provided and operated by the Joint Laboratory for System Evaluation (JLSE) at Argonne National Laboratory. The authors would also like to thank Hafsah Shahzad for valuable comments and suggestions to improve the quality of this paper.
Publication costs were funded by a grant from Microsoft.
Availability of data and materials
The datasets generated and/or analyzed during the current study are available in the FDA-NCI Clinical Proteomics Program Databank.
About this supplement
This article has been published as part of BMC Bioinformatics Volume 19 Supplement 18, 2018: Selected Articles from the Computational Approaches for Cancer at SC17 workshop. The full contents of the supplement are available online at https://bmcbioinformatics.biomedcentral.com/articles/supplements/volume-19-supplement-18.;
AS and CY developed the proposed architecture. YA and KZ provided the work on MLP applications and datasets. MH contributed to all aspects of the work including background, architecture design and benchmarking. All authors have read and approved of the final manuscript.
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