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Send researchers to introduce proteins: LLM generalization through logic-based prototypes

Why cross-domain reasoning is important in large language models (LLMS)

The latest breakthroughs in LRMS, especially those trained using long-bed techniques, show that they can be summarized in a broad range of areas. Interestingly, models trained in tasks such as math or coding often perform well in unrelated fields such as logic puzzles or creative writing. However, making this flexibility is not entirely clear. One possible explanation is that these models learn core inference patterns, called abstract inference prototypes, which cut across domains. These shared cognitive structures allow the model to focus less on how the problem is presented and more on similar thought processes required by the solution, allowing for a wider transfer.

From COT to RL: LLM learns the transformation of reasoning

The latest advances in large language model inference have shifted from simple COT and supervised fine-tuning to RL. Models such as DeepSeek-R1 and Seed Thinking-V1.5 enhance long-term COT reasoning through mathematical problems, logical tasks, and code execution. These models utilize RL techniques guided by verifiable rewards, such as exploring complex inference paths from the accuracy in ground-based real answers. This approach enables the model to learn from errors, break down complex problems and improve solutions through iteration. Contrary to past approaches, this work introduces the concept of “reasoning prototypes” to better understand the core mindset, allowing models to span hugely different areas.

Protein Framework: Structural Reasoning with Prolog and PDDL

Researchers from Bondedance Seed and Shanghai Jiao Tong University have developed Protein News, a framework designed to enhance the reasoning of large language models by leveraging structured prototype representations such as Prolog and PDDL. The system includes an automated pipeline that translates problems into these formats, reliable verification settings using interpreters, and scalable problem synthesis without manual tagging. The models trained on these prototypes showed significant improvements in a variety of tasks, including logical reasoning (+4.7%), planning (+6.3%), general reasoning (+4.0%), and mathematics (+1.0%). Crucially, training in this structured “prototype space” leads to better generalization across similar tasks, thus supporting the idea that abstract inference patterns enhance performance across domains.

Architecture Overview: Prototype Constructors and Verification Program Systems

The protein framework improves reasoning in LLM by planning using structured prototypes, logic principles, and PDDL. It includes two core modules: a prototype constructor that transforms natural language problems into formal representations, and a verification system that checks the correctness of the solution. For Prolog, the four-step pipeline creates various logic problems and is verified using SWI-Prog. For planning, tasks like plan generation, completion, and reorder are built using PDDL and check for correctness through Val validator. The training process includes teacher model distillation for inference paths, difficulty-based sampling and filtration to ensure reliable generalization models fine-tune only high-quality data.

Evaluation shows measurable improvements in reasoning and planning

The protein framework was experimentally evaluated using a 150B parameter mixture model (15B activity) and trained in a curated set of high-quality Prolog and PDDL samples. The results show consistent improvements in logical reasoning, planning and general benchmarks, including MMLU and AIME 2024. A critical ablation study compared Prolog-based training with NL versions on matching datasets. Both formats significantly outperform the baseline, and the prologue achieves nearly equivalent performance with NL. This suggests that structured prototype training can be applied to natural language tasks. However, explicit reasoning (e.g., through thinking chains) is crucial, and low sample categories show weaker growth due to insufficient data.

Key discovery and theoretical significance of inference prototypes

In summary, protein composition is a framework based on the framework that abstract reasoning prototypes such as Prolog for Logic and PDDL are used for planning, enabling large language models to generalize across domains. Through training models of these structured representations, the study observed significant improvements in logical reasoning, planning, and general problem-solving tasks. The results support the hypothesis that shared inference patterns across domains facilitates knowledge transfer in the model. Although the empirical results are promising, the exact nature of the theoretical inference prototype has not been gradually disbanded. Future work will aim to formalize these concepts mathematically and validate discovery using open source models and datasets.


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Sana Hassan, a consulting intern at Marktechpost and a dual-degree student at IIT Madras, is passionate about applying technology and AI to address real-world challenges. He is very interested in solving practical problems, and he brings a new perspective to the intersection of AI and real-life solutions.

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