Engineering topics

Bi, Jinbo

Publications and source records attributed to Bi, Jinbo.

3 records

DOE OSTI2022

A Length Adaptive Algorithm-Hardware Co-design of Transformer on FPGA Through Sparse Attention and Dynamic Pipelining

Transformers are considered one of the most important deep learning models since 2018, in part because it establishes state-of-the-art (SOTA) records and could potentially replace existing Deep Neural Networks (DNNs). Despite the remarkable triumphs, the prolonged turnaround time of Transformer models is a widely recognized roadblock. The variety of sequence lengths imposes additional computing overhead where inputs need to be zero-padded to the maximum sentence length in the batch to accommodate the parallel computing platforms. This paper targets the field-programmable gate array (FPGA) and proposes a coherent sequence length adaptive algorithm–hardware co-design for Transformer acceleration. Particularly, we develop a hardware-friendly sparse attention operator and a length-aware hardware resource scheduling algorithm. The proposed sparse attention operator brings the complexity of attention-based models down to linear complexity and alleviates the off-chip memory traffic. The proposed length-aware resource hardware scheduling algorithm dynamically allocates the hardware resources to fill up the pipeline slots and eliminates bubbles for NLP tasks. Experiments show that our design has very small accuracy loss and has 80.2 × and 2.6 × speedup compared to CPU and GPU implementation, and 4 × higher energy efficiency than state-of-the-art GPU accelerator optimized via CUBLAS GEMM.

Peng, Hongwu↗

DOE OSTI2021

Optimizing FPGA-based Accelerator Design for Large-Scale Molecular Similarity Search (Special Session Paper)

Molecular similarity search has been widely used in drug discovery to rapidly identify structurally similar compounds from large molecular databases. With the increasing size of chemical libraries, there is growing interest in the efficient ac- celeration of large-scale similarity search. Existing works mainly focus on CPU and GPU to accelerate the computation of Tatimoto coefficient in measuring the pairwise similarity between different molecular fingerprints. In this paper, we propose and optimize an FPGA-based accelerator design on exhaustive and approximate search algorithms. On exhaustive search using BitBound & fold- ing, we analyze the similarity cutoff and folding level relationship with search speedup and accuracy, and propose a scalable on- the-fly query engine on FPGAs to reduce the resource utilization and pipeline interval. We achieve a 450 million compounds-per- second processing throughput for a single query engine. On approximate search using hierarchical navigable small world (HNSW), a popular algorithm with high recall and query speed, we propose an FPGA-based graph traversal engine to utilize high throughput register array based priority queue and fine- grained distance calculation engine to increase the processing capability. Experimental results show that the proposed FPGA- based HNSW implementation achieves a 35× speedup than existing works on CPU. To the best of our knowledge, our FPGA- based implementation is the first attempt to accelerate molecular similarity search on FPGA and has the highest performance among existing approaches.

Peng, Hongwu↗

DOE OSTI2021

Discrete Graph Structure Learning for Forecasting Multiple Time Series

Time series forecasting is an extensively studied subject in statistics, economics, and computer science. Exploration of the correlation and causation among the variables in a multivariate time series shows promise in enhancing the performance of a time series model. When using deep neural networks as forecasting models, we hypothesize that exploiting the pairwise information among multiple (multivariate) time series also improves their forecast. If an explicit graph structure is known, graph neural networks (GNNs) have been demonstrated as powerful tools to exploit the structure. In this work, we propose learning the structure simultaneously with the GNN if the graph is unknown. We cast the problem as learning a probabilistic graph model through optimizing the mean performance over the graph distribution. The distribution is parameterized by a neural network so that discrete graphs can be sampled differentiably through reparameterization. Empirical evaluations show that our method is simpler, more efficient, and better performing than a recently proposed bilevel learning approach for graph structure learning, as well as a broad array of forecasting models, either deep or non-deep learning based, and graph or non-graph based.

Shang, Chao↗