In-Context Molecular Property Prediction with LLMs: A Blinding Study on Memorization and Knowledge Conflicts

The capabilities of large language models (LLMs) have expanded beyond natural language processing to scientific prediction tasks, including molecular property prediction. However, their effectiveness in in-context learning remains ambiguous, particularly given the potential for training data contamination in widely used benchmarks. This paper investigates whether LLMs perform genuine in-context regression on molecular properties or rely primarily on memorized values. Furthermore, we analyze the interplay between pre-trained knowledge and in-context information through a series of progressively blinded experiments. We evaluate nine LLM variants across three families (GPT-4.1, GPT-5, Gemini 2.5) on three MoleculeNet datasets (Delaney solubility, Lipophilicity, QM7 atomization energy) using a systematic blinding approach that iteratively reduces available information. Complementing this, we utilize varying in-context sample sizes (0-, 60-, and 1000-shot) as an additional control for information access. This work provides a principled framework for evaluating molecular property prediction under controlled information access, addressing concerns regarding memorization and exposing conflicts between pre-trained knowledge and in-context information.

Active partitioning: inverting the paradigm of active learning

Datasets often incorporate various functional patterns related to different aspects or regimes, which are typically not equally present throughout the dataset. We propose a novel, general-purpose partitioning algorithm that utilizes competition between models to detect and separate these functional patterns. This competition is induced by multiple models iteratively submitting their predictions for the dataset, with the best prediction for each data point being rewarded with training on that data point. This reward mechanism amplifies each model's strengths and encourages specialization in different patterns. The specializations can then be translated into a partitioning scheme. The amplification of each model's strengths inverts the active learning paradigm: while active learning typically focuses the training of models on their weaknesses to minimize the number of required training data points, our concept reinforces the strengths of each model, thus specializing them. We validate our concept -- called active partitioning -- with various datasets with clearly distinct functional patterns, such as mechanical stress and strain data in a porous structure. The active partitioning algorithm produces valuable insights into the datasets' structure, which can serve various further applications. As a demonstration of one exemplary usage, we set up modular models consisting of multiple expert models, each learning a single partition, and compare their performance on more than twenty popular regression problems with single models learning all partitions simultaneously. Our results show significant improvements, with up to 54% loss reduction, confirming our partitioning algorithm's utility.