arXiv subjects

Thomas Walton

Publications and source records attributed to Thomas Walton.

3 recordsLinked to original sources

arXiv2026

Structure-Aware Masking for Protein Representation Learning

Masked language modeling (MLM) is the standard objective for training protein language models, typically implemented by randomly masking individual residues at a fixed rate (e.g., 15%). This practice implicitly assumes that all sequence positions contribute equally to representation learning. In downstream fitness prediction tasks, however, protein sequences are governed by three-dimensional structural dependencies and long-range residue contacts that induce strong nonlocal couplings between residues. We introduce Bucket Masking, a structure-aware masking strategy that selects groups of residues based on their proximity in three-dimensional space, preferentially masking structurally coupled regions during training. By conditioning the masking distribution on residue contacts, Bucket Masking shifts the learning objective toward modeling long-range interactions that are critical for protein function. Across four downstream protein fitness prediction tasks, Bucket Masking enables up to a 14% improvement over standard random masking, excelling at predicting higher-order mutational interactions. Through controlled ablations, we show that these improvements arise from mask placement rather than span size, establishing masking as a positional inductive bias.

cs.LG↗

arXiv2025

SpecMER: Fast Protein Generation with K-mer Guided Speculative Decoding

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.

cs.LG↗

arXiv2025

Link Prediction for Event Logs in the Process Industry

In the era of graph-based retrieval-augmented generation (RAG), link prediction is a significant preprocessing step for improving the quality of fragmented or incomplete domain-specific data for the graph retrieval. Knowledge management in the process industry uses RAG-based applications to optimize operations, ensure safety, and facilitate continuous improvement by effectively leveraging operational data and past insights. A key challenge in this domain is the fragmented nature of event logs in shift books, where related records are often kept separate, even though they belong to a single event or process. This fragmentation hinders the recommendation of previously implemented solutions to users, which is crucial in the timely problem-solving at live production sites. To address this problem, we develop a record linking model, which we define as a cross-document coreference resolution (CDCR) task. Record linking adapts the task definition of CDCR and combines two state-of-the-art CDCR models with the principles of natural language inference (NLI) and semantic text similarity (STS) to perform link prediction. The evaluation shows that our record linking model outperformed the best versions of our baselines, i.e., NLP and STS, by 28% (11.43 p) and 27.4% (11.21 p), respectively. Our work demonstrates that common NLP tasks can be combined and adapted to a domain-specific setting of the German process industry, improving data quality and connectivity in shift logs.

cs.CL↗