Authors: Ferhat Erata, Sam Kouteili, Thanos Typaldos, Timos Antonopoulos, Robert B. Jones, Byron Cook, Ruzica Piskac
Organizations: Yale University · AWS Agentic AI
Abstract
Despite the effectiveness of Cube-and-Conquer (C&C) for solving challenging Boolean Satisfiability (SAT) problems, no prior work has shown that transformer-based models can learn effective cubing heuristics. We introduce a neuro-symbolic post-training framework for this task. We design an MCTS-based data curation pipeline that uses symbolic heuristics to explore splitting decisions over SAT competition formulas, producing preference data grounded in solver statistics and augmented with reasoning traces from a teacher model. Our two-stage post-training, supervised fine-tuning (SFT) followed by direct preference optimization (DPO), enables a 4B-parameter model to achieve a pass@5 score of 53 on 100 SAT competition benchmarks, surpassing frontier LLMs such as Claude-Sonnet-4 (50) and matching the best symbolic heuristic (53). Ablations show that SFT alone improves pass@5 from 46 to 51, with DPO adding 2 additional benchmarks; an entropy/agreement ablation on realized first-cube decisions further shows that SFT, not DPO, accounts for the root-level decision diversity that produces complementary per-run coverage over deterministic symbolic methods. This demonstrates that transformers can be trained to make effective cubing decisions in a domain traditionally dominated by symbolic methods.
Do transformers, when trained on sequential reasoning traces, build internal models of the underlying task? And if so, does the structure of those internal representations mirror the structure of the domain? We train an 8-layer transformer on Sudoku solving traces and perform a mechanistic analysis of its internal computation. We establish two results. First, the model builds a substructure world model: it does not represent the board state cell by cell, as a human analyst would expect, but organizes information around the rows, columns, and boxes that Sudoku's constraints act on. Second, we identify a naked-single circuit: a small set of dedicated neurons in the final MLP layer, each individually detecting when exactly one digit remains possible for a specific cell, and reliably promoting that digit. These findings show that the geometry of an emergent world model is shaped by the constraint algebra of the domain, not its surface presentation, and that the resulting decision circuit is sparse, monosemantic, and fully interpretable. More broadly, they demonstrate that mechanistic interpretability tools can recover an end-to-end algorithmic account of how a transformer solves a combinatorial reasoning task.
Large language models (LLMs) are increasingly used for tasks that implicitly reduce to Boolean satisfiability (SAT), yet their reasoning ability on SAT remains unclear. We present a systematic study of LLMs on 2-SAT and 3-SAT, together with two canonical reductions, Vertex Cover and discrete 3D packing, to probe representation-invariant reasoning. We first evaluate models using conventional metrics, including accuracy, precision, recall, and F1, as well as the SAT phase-transition setting. We find that these metrics can be misleading: many models obtain high scores by over-predicting satisfiable formulas, fail to reproduce the classical easy-hard-easy signature around the 3-SAT threshold, and degrade sharply as the number of variables grows. To address this problem, we introduce a paired-formula protocol based on minimally different satisfiable and unsatisfiable instances, together with Accurate Differentiation Rate (ADR), which requires both members of each pair to be classified correctly. ADR separates reasoning-oriented models from heuristic ones and correlates with witness validity. Beyond CNF, we test cross-representation consistency by converting CNF to Vertex Cover and 3-SAT to discrete 3D packing. Model decisions on CNF and on the corresponding graph or packing instances agree for most models on more than 80 percent of instances, suggesting stable decision rules across representations. Overall, our results show that SAT is a conservative probe for LLM reasoning, and that paired evaluation with ADR provides a more faithful and representation-robust assessment than conventional metrics.
Foundational optimization embeddings have recently emerged as powerful pre-trained representations for mixed-integer programming (MIP) problems. These embeddings were shown to enable cross-domain transfer and reduce reliance on solver-generated labels. In this work, we investigate whether such representations generalize beyond optimization to decision problems, focusing on Boolean satisfiability (SAT). We adapt the foundational optimization architecture to SAT by mapping CNF formulas into the same bipartite constraint-variable graph representation used for MIPs. This allows direct reuse of the pre-trained embedding model without architectural changes or supervised fine-tuning. Our results show that these embeddings capture structural regularities in SAT instances and support unsupervised tasks such as instance clustering and distribution identification. We demonstrate, for the first time, that foundational optimization embeddings can transfer to constraint satisfaction domains. Our findings is a step toward a unified representational framework for both optimization and decision problems.