Thomas Walton

Thomas Walton, Ayan Goel, Amirali Aghazadeh

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.

Anastasia Zhukova, Thomas Walton, Christian E. Matt et al.

Knowledge management (KM) is vital in the process industry for optimizing operations, ensuring safety, and enabling continuous improvement through effective use of operational data and past insights. A key challenge in this domain is the fragmented nature of event logs in shift books, where related records, e.g., entries documenting issues related to equipment or processes and the corresponding solutions, may remain disconnected. This fragmentation hinders the recommendation of previous solutions to the users. To address this problem, we investigate record linking (RL) as link prediction, commonly studied in graph-based machine learning, by framing it as a cross-document coreference resolution (CDCR) task enhanced with natural language inference (NLI) and semantic text similarity (STS) by shifting it into the causal inference (CI). We adapt CDCR, traditionally applied in the news domain, into an RL model to operate at the passage level, similar to NLI and STS, while accommodating the process industry's specific text formats, which contain unstructured text and structured record attributes. Our RL model outperformed the best versions of NLI- and STS-driven baselines by 28% (11.43 points) and 27% (11.21 points), respectively. Our work demonstrates how domain adaptation of the state-of-the-art CDCR models, enhanced with reasoning capabilities, can be effectively tailored to the process industry, improving data quality and connectivity in shift logs.

Thomas Walton, Darin Tsui, Aryan Musharaf et al.

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.