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Geometric Flow Matching for Molecular Conformation Generation via Manifold Decomposition

arXiv:2605.25577v1 Announce Type: cross Abstract: The generation of accurate 3D molecular conformations is a pivotal challenge in computational chemistry and drug discovery. Recently, diffusion and flow matching models have achieved remarkable success. However, there is a critical misalignment between their mathematical formulation and the physical reality of molecules. Existing approaches predominantly treat molecules as unstructured point clouds in Cartesian space, overlooking the intrinsic hierarchical mechanics where bond lengths and bond angles are relatively stiff, whereas torsion angles constitute the dominant flexible degrees of freedom. This lack of manifold awareness forces models to relearn fundamental geometric constraints from scratch, often leading to physically implausible intermediate structures. To address this, we propose GO-Flow that aligns generative modeling with molecular geometry via manifold decomposition. Instead of forcing motion through Euclidean space, GO-Flow decomposes the generation process into three physically motivated subspaces: translation space with linear optimal transport, rotation space with geodesic flows on $SO(3)$, and conformation space with entropic optimal transport. This decomposition injects geometric inductive biases and makes the generative paths better aligned with molecular degrees of freedom. When combined with equivariant neural architectures, it encourages rotation-consistent generation and improves geometric validity. Extensive experiments on GEOM-Drugs and GEOM-QM9 demonstrate that GO-Flow achieves state-of-the-art generation quality. Notably, by learning straighter probability paths on the correct manifolds naturally, our method enables high-fidelity sampling with as few as 50 steps, effectively bridging the gap between structural precision and computational efficiency.
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MegaFake: A Theory-Driven Dataset of Fake News Generated by Large Language Models

arXiv:2408.11871v3 Announce Type: replace-cross Abstract: Fake news significantly influences decision-making processes by misleading individuals, organizations, and even governments. Large language models (LLMs), as part of generative AI, can amplify this problem by generating highly convincing fake news at scale, posing a significant threat to online information integrity. Therefore, understanding the motivations and mechanisms behind fake news generated by LLMs is crucial for effective detection and governance. In this study, we develop the LLM-Fake Theory, a theoretical framework that integrates various social psychology theories to explain machine-generated deception. Guided by this framework, we design an innovative prompt engineering pipeline that automates fake news generation using LLMs, eliminating manual annotation needs. Utilizing this pipeline, we create a theoretically informed \underline{M}achin\underline{e}-\underline{g}ener\underline{a}ted \underline{Fake} news dataset, MegaFake, derived from FakeNewsNet. Through extensive experiments with MegaFake, we advance both theoretical understanding of human-machine deception mechanisms and practical approaches to fake news detection in the LLM era.
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Reinforced Reasoning for End-to-End Retrosynthetic Planning

arXiv:2603.29723v1 Announce Type: new Abstract: Retrosynthetic planning is a fundamental task in organic chemistry, yet remains challenging due to its combinatorial complexity. To address this, conventional approaches typically rely on hybrid frameworks that combine single-step predictions with external search heuristics, inevitably fracturing the logical coherence between local molecular transformations and global planning objectives. To bridge this gap and embed sophisticated strategic foresight directly into the model's chemical reasoning, we introduce ReTriP, an end-to-end generative framework that reformulates retrosynthesis as a direct Chain-of-Thought reasoning task. We establish a path-coherent molecular representation and employ a progressive training curriculum that transitions from reasoning distillation to reinforcement learning with verifiable rewards, effectively aligning stepwise generation with practical route utility. Empirical evaluation on RetroBench demonstrates that ReTriP achieves state-of-the-art performance, exhibiting superior robustness in long-horizon planning compared to hybrid baselines.
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CUDABench: Benchmarking LLMs for Text-to-CUDA Generation

arXiv:2603.02236v1 Announce Type: cross Abstract: Recent studies have demonstrated the potential of Large Language Models (LLMs) in generating GPU Kernels. Current benchmarks focus on the translation of high-level languages into CUDA, overlooking the more general and challenging task of text-to-CUDA generation. Furthermore, given the hardware-specific and performance-critical features of GPU programming, accurately assessing the performance of LLM-generated GPU programs is nontrivial. In this work, we introduce CUDABench, a comprehensive benchmark designed to evaluate the text-to-CUDA capabilities of LLMs. First, we construct CUDABench-Set, which covers Breadth-Depth-Difficulty evaluation space in diverse application domains, including artificial intelligence, scientific computing, and data analytics, etc. Furthermore, we propose CUDABench-Score and Generative Verification Pipeline that assess (1) compilation correctness, (2) functional consistency through execution-based verification, and (3) a novel roofline-based metric, Performance-Score. Benchmarking state-of-the-art LLMs reveals insightful findings and challenges of text-to-CUDA, such as a notable mismatch between high compilation success rates and low functional correctness, a lack of domain-specific algorithmic knowledge, and suboptimal utilization of GPU hardware resources. Our benchmark is available at https://github.com/CUDA-Bench/CUDABench.
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