SpecMER: Fast Protein Generation with K-mer Guided Speculative Decoding
This addresses latency issues in high-throughput protein screening for researchers in computational biology, though it is incremental as it builds on existing speculative decoding methods.
The paper tackled the problem of slow autoregressive protein generation by introducing SpecMER, a framework that uses k-mer motifs to guide speculative decoding, achieving a 24-32% speedup while improving sequence plausibility and likelihoods.
Autoregressive models have transformed protein engineering by enabling the generation of novel protein sequences beyond those found in nature. However, their sequential inference introduces significant latency, limiting their utility in high-throughput protein screening. Speculative decoding accelerates generation by employing a lightweight draft model to sample tokens, which a larger target model then verifies and refines. Yet, in protein sequence generation, draft models are typically agnostic to the structural and functional constraints of the target protein, leading to biologically implausible outputs and a shift in the likelihood distribution of generated sequences. We introduce SpecMER (Speculative Decoding via k-mer Guidance), a novel framework that incorporates biological, structural, and functional priors using k-mer motifs extracted from multiple sequence alignments. By scoring candidate sequences in parallel and selecting those most consistent with known biological patterns, SpecMER significantly improves sequence plausibility while retaining the efficiency of speculative decoding. SpecMER achieves 24-32% speedup over standard autoregressive decoding, along with higher acceptance rates and improved sequence likelihoods.