# Latent JEPA: Abstract Future Prediction for Latent Reasoning in Chemistry

arXiv: https://arxiv.org/abs/2610.01947 · HTML: https://mlsanity.com/paper/2610.01947/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 28 of its 37 references that are in the map.
- First posted on arXiv 1 Oct 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 28 of 28)

- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [VICReg: Variance-Invariance-Covariance Regularization for Self-Supervised Learning](https://mlsanity.com/paper/2105.04906/) (2021)
- [Self-Supervised Learning from Images with a Joint-Embedding Predictive Architecture](https://mlsanity.com/paper/2301.08243/) (2023)
- [Training Large Language Models to Reason in a Continuous Latent Space](https://mlsanity.com/paper/2412.06769/) (2024)
- [data2vec: A General Framework for Self-supervised Learning in Speech, Vision and Language](https://mlsanity.com/paper/2202.03555/) (2022)
- [Revisiting Feature Prediction for Learning Visual Representations from Video](https://mlsanity.com/paper/2404.08471/) (2024)
- [LLM2Vec: Large Language Models Are Secretly Powerful Text Encoders](https://mlsanity.com/paper/2404.05961/) (2024)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [Reasoning with Latent Thoughts: On the Power of Looped Transformers](https://mlsanity.com/paper/2502.17416/) (2025)
- [CODI: Compressing Chain-of-Thought into Continuous Space via Self-Distillation](https://mlsanity.com/paper/2502.21074/) (2025)
- [Large-Scale Chemical Language Representations Capture Molecular Structure and Properties](https://mlsanity.com/paper/2106.09553/) (2021)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [SoftCoT: Soft Chain-of-Thought for Efficient Reasoning with LLMs](https://mlsanity.com/paper/2502.12134/) (2025)
- [Intuitive physics understanding emerges from self-supervised pretraining on natural videos](https://mlsanity.com/paper/2502.11831/) (2025)
- [Paper2Poster: Towards Multimodal Poster Automation from Scientific Papers](https://mlsanity.com/paper/2505.21497/) (2025)
- [Introduction to Latent Variable Energy-Based Models: A Path Towards Autonomous Machine Intelligence](https://mlsanity.com/paper/2306.02572/) (2023)
- [Training a Scientific Reasoning Model for Chemistry](https://mlsanity.com/paper/2506.17238/) (2025)
- [Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operations](https://mlsanity.com/paper/2505.21318/) (2025)
- [LLM-JEPA: Large Language Models Meet Joint Embedding Predictive Architectures](https://mlsanity.com/paper/2509.14252/) (2025)
- [Chem-R: Learning to Reason as a Chemist](https://mlsanity.com/paper/2510.16880/) (2025)
- [Beyond Multi-Token Prediction: Pretraining LLMs with Future Summaries](https://mlsanity.com/paper/2510.14751/) (2025)
- [AOT*: Efficient Synthesis Planning via LLM-Empowered AND-OR Tree Search](https://mlsanity.com/paper/2509.20988/) (2025)
- [Semformer: Transformer Language Models with Semantic Planning](https://mlsanity.com/paper/2409.11143/) (2024)
- [LatentChem: From Textual CoT to Latent Thinking in Chemical Reasoning](https://mlsanity.com/paper/2602.07075/) (2026)
- [RetroAgent: Harnessing LLMs to Search Over Structured Memory for Agentic Retrosynthesis Planning](https://mlsanity.com/paper/2607.14512/) (2026)
- [MolEmb: Multimodal Large Language Models Can Be Strong Molecular Embedding Models](https://mlsanity.com/paper/2608.23646/) (2026)

## Abstract (arXiv)

Large language models offer a promising foundation for chemical reasoning, bringing together chemical knowledge and multistep problem solving. Chemical intuition can provide an initial sense of plausible outcomes before the details of a solution are fully worked out. Inspired by how such expectations complement explicit analysis, we study how continuous latent thoughts can be trained to anticipate informative aspects of future solutions without verbalizing every intermediate step. We introduce Latent JEPA, a framework that combines autoregressive learning with joint-embedding prediction of one or more future views. For chemical reasoning, we develop textual and molecular prediction objectives that connect latent thoughts to both subsequent reasoning and molecular outcomes. Experiments on ChemCoTBench show gains in molecular optimization and on several editing and reaction metrics. Representation analyses show that future prediction makes latent thoughts more informative about molecular outcomes and strengthens their correspondence with chemical structure. These findings support abstract future prediction as a learning principle for connecting continuous latent reasoning with scientific outcomes.