We propose a novel class of language models, Latent Thought Models (LTMs), which incorporate explicit latent thought vectors that follow an explicit prior model in latent space. These latent thought vectors guide the autoregressive generation of ground tokens through a Transformer decoder. Training employs a dual-rate optimization process within the classical variational Bayes framework: fast learning of local variational parameters for the posterior distribution of latent vectors (inference-time computation), and slow learning of global decoder parameters. Empirical studies reveal that LTMs possess additional scaling dimensions beyond traditional Large Language Models (LLMs), such as the number of iterations in inference-time computation and number of latent thought vectors. Higher sample efficiency can be achieved by increasing training compute per token, with further gains possible by trading model size for more inference steps. Designed based on these scaling properties, LTMs demonstrate superior sample and parameter efficiency compared to autoregressive models and discrete diffusion models. They significantly outperform these counterparts in validation perplexity and zero-shot language modeling tasks. Additionally, LTMs exhibit emergent few-shot in-context reasoning capabilities that scale with model size, and achieve competitive performance in conditional and unconditional text generation. The project page is available at https://deqiankong.github.io/blogs/ltm.

This work explores the challenging problem of molecule design by framing it as a conditional generative modeling task, where target biological properties or desired chemical constraints serve as conditioning variables. We propose the Latent Prompt Transformer (LPT), a novel generative model comprising three components: (1) a latent vector with a learnable prior distribution modeled by a neural transformation of Gaussian white noise; (2) a molecule generation model based on a causal Transformer, which uses the latent vector as a prompt; and (3) a property prediction model that predicts a molecule's target properties and/or constraint values using the latent prompt. LPT can be learned by maximum likelihood estimation on molecule-property pairs. During property optimization, the latent prompt is inferred from target properties and constraints through posterior sampling and then used to guide the autoregressive molecule generation. After initial training on existing molecules and their properties, we adopt an online learning algorithm to progressively shift the model distribution towards regions that support desired target properties. Experiments demonstrate that LPT not only effectively discovers useful molecules across single-objective, multi-objective, and structure-constrained optimization tasks, but also exhibits strong sample efficiency.