Pengfei Yu

Andrea Yaoyun Cui, Pengfei Yu

Language models are essentially probability distributions over token sequences. Auto-regressive models generate sentences by iteratively computing and sampling from the distribution of the next token. This iterative sampling introduces stochasticity, leading to the assumption that language models make probabilistic decisions, similar to sampling from unknown distributions. Building on this assumption, prior research has used simulated Gibbs sampling, inspired by experiments designed to elicit human priors, to infer the priors of language models. In this paper, we revisit a critical question: Do language models possess Bayesian brains? Our findings show that under certain conditions, language models can exhibit near-deterministic decision-making, such as producing maximum likelihood estimations, even with a non-zero sampling temperature. This challenges the sampling assumption and undermines previous methods for eliciting human-like priors. Furthermore, we demonstrate that without proper scrutiny, a system with deterministic behavior undergoing simulated Gibbs sampling can converge to a "false prior." To address this, we propose a straightforward approach to distinguish between stochastic and deterministic decision patterns in Gibbs sampling, helping to prevent the inference of misleading language model priors. We experiment on a variety of large language models to identify their decision patterns under various circumstances. Our results provide key insights in understanding decision making of large language models.

Kexuan Xin, Qingyun Wang, Junyu Chen et al.

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.