LightNobel: Improving Sequence Length Limitation in Protein Structure Prediction Model via Adaptive Activation Quantization

Recent advances in Protein Structure Prediction Models (PPMs), such as AlphaFold2 and ESMFold, have revolutionized computational biology by achieving unprecedented accuracy in predicting three-dimensional protein folding structures. However, these models face significant scalability challenges, particularly when processing proteins with long amino acid sequences (e.g., sequence length > 1,000). The primary bottleneck that arises from the exponential growth in activation sizes is driven by the unique data structure in PPM, which introduces an additional dimension that leads to substantial memory and computational demands. These limitations have hindered the effective scaling of PPM for real-world applications, such as analyzing large proteins or complex multimers with critical biological and pharmaceutical relevance. In this paper, we present LightNobel, the first hardware-software co-designed accelerator developed to overcome scalability limitations on the sequence length in PPM. At the software level, we propose Token-wise Adaptive Activation Quantization (AAQ), which leverages unique token-wise characteristics, such as distogram patterns in PPM activations, to enable fine-grained quantization techniques without compromising accuracy. At the hardware level, LightNobel integrates the multi-precision reconfigurable matrix processing unit (RMPU) and versatile vector processing unit (VVPU) to enable the efficient execution of AAQ. Through these innovations, LightNobel achieves up to 8.44x, 8.41x speedup and 37.29x, 43.35x higher power efficiency over the latest NVIDIA A100 and H100 GPUs, respectively, while maintaining negligible accuracy loss. It also reduces the peak memory requirement up to 120.05x in PPM, enabling scalable processing for proteins with long sequences.

Oaken: Fast and Efficient LLM Serving with Online-Offline Hybrid KV Cache Quantization

Modern Large Language Model serving system batches multiple requests to achieve high throughput, while batching attention operations is challenging, rendering memory bandwidth a critical bottleneck. The community relies on high-end GPUs with multiple high-bandwidth memory channels. Unfortunately, HBM's high bandwidth often comes at the expense of limited memory capacity, which reduces core utilization and increases costs. Recent advancements enabling longer contexts for LLMs have substantially increased the key-value cache size, further intensifying the pressures on memory capacity. The literature has explored KV cache quantization techniques, which commonly use low bitwidth for most values, selectively using higher bitwidth for outlier values. While this approach helps achieve high accuracy and low bitwidth simultaneously, it comes with the limitation that cost for online outlier detection is excessively high, negating the advantages. We propose Oaken, an acceleration solution that achieves high accuracy and high performance simultaneously through co-designing algorithm and hardware. To effectively find a sweet spot in the accuracy-performance trade-off space of KV cache quantization, Oaken employs an online-offline hybrid approach, setting outlier thresholds offline, which are then used to determine the quantization scale online. To translate the proposed algorithmic technique into tangible performance gains, Oaken also comes with custom quantization engines and memory management units that can be integrated with any LLM accelerators. We built an Oaken accelerator on top of an LLM accelerator, LPU, and conducted a comprehensive evaluation. Our experiments show that for a batch size of 256, Oaken achieves up to 1.58x throughput improvement over NVIDIA A100 GPU, incurring a minimal accuracy loss of only 0.54\% on average, compared to state-of-the-art KV cache quantization techniques.