The Tokenization Bottleneck: How Vocabulary Extension Improves Chemistry Representation Learning in Pretrained Language Models

The application of large language models (LLMs) to chemistry is frequently hampered by a "tokenization bottleneck", where tokenizers tuned on general-domain text tend to fragment chemical representations such as SMILES into semantically uninformative sub-tokens. This paper introduces a principled methodology to resolve this bottleneck by unifying the representation of natural language and molecular structures within a single model. Our approach involves targeted vocabulary extension-augmenting a pretrained LLM's vocabulary with chemically salient tokens, followed by continued pretraining on chemistry-domain text to integrate this new knowledge. We provide an empirical demonstration of the effectiveness of this strategy, showing that our methodology leads to superior performance on a range of downstream chemical tasks.

Towards Transparent AI Grading: Semantic Entropy as a Signal for Human-AI Disagreement

Automated grading systems can efficiently score short-answer responses, yet they often fail to indicate when a grading decision is uncertain or potentially contentious. We introduce semantic entropy, a measure of variability across multiple GPT-4-generated explanations for the same student response, as a proxy for human grader disagreement. By clustering rationales via entailment-based similarity and computing entropy over these clusters, we quantify the diversity of justifications without relying on final output scores. We address three research questions: (1) Does semantic entropy align with human grader disagreement? (2) Does it generalize across academic subjects? (3) Is it sensitive to structural task features such as source dependency? Experiments on the ASAP-SAS dataset show that semantic entropy correlates with rater disagreement, varies meaningfully across subjects, and increases in tasks requiring interpretive reasoning. Our findings position semantic entropy as an interpretable uncertainty signal that supports more transparent and trustworthy AI-assisted grading workflows.