DiffSpectra: Molecular Structure Elucidation from Spectra using Diffusion Models

Molecular structure elucidation from spectra is a foundational problem in chemistry, with profound implications for compound identification, synthesis, and drug development. Traditional methods rely heavily on expert interpretation and lack scalability. Pioneering machine learning methods have introduced retrieval-based strategies, but their reliance on finite libraries limits generalization to novel molecules. Generative models offer a promising alternative, yet most adopt autoregressive SMILES-based architectures that overlook 3D geometry and struggle to integrate diverse spectral modalities. In this work, we present DiffSpectra, a generative framework that directly infers both 2D and 3D molecular structures from multi-modal spectral data using diffusion models. DiffSpectra formulates structure elucidation as a conditional generation process. Its denoising network is parameterized by Diffusion Molecule Transformer, an SE(3)-equivariant architecture that integrates topological and geometric information. Conditioning is provided by SpecFormer, a transformer-based spectral encoder that captures intra- and inter-spectral dependencies from multi-modal spectra. Extensive experiments demonstrate that DiffSpectra achieves high accuracy in structure elucidation, recovering exact structures with 16.01% top-1 accuracy and 96.86% top-20 accuracy through sampling. The model benefits significantly from 3D geometric modeling, SpecFormer pre-training, and multi-modal conditioning. These results highlight the effectiveness of spectrum-conditioned diffusion modeling in addressing the challenge of molecular structure elucidation. To our knowledge, DiffSpectra is the first framework to unify multi-modal spectral reasoning and joint 2D/3D generative modeling for de novo molecular structure elucidation.

Muon Optimizes Under Spectral Norm Constraints

The pursuit of faster optimization algorithms remains an active and important research direction in deep learning. Recently, the Muon optimizer [JJB+24] has demonstrated promising empirical performance, but its theoretical foundation remains less understood. In this paper, we bridge this gap and provide a theoretical analysis of Muon by placing it within the Lion-$\mathcal{K}$ family of optimizers [CLLL24]. Specifically, we show that Muon corresponds to Lion-$\mathcal{K}$ when equipped with the nuclear norm, and we leverage the theoretical results of Lion-$\mathcal{K}$ to establish that Muon (with decoupled weight decay) implicitly solves an optimization problem that enforces a constraint on the spectral norm of weight matrices. This perspective not only demystifies the implicit regularization effects of Muon but also leads to natural generalizations through varying the choice of convex map $\mathcal{K}$, allowing for the exploration of a broader class of implicitly regularized and constrained optimization algorithms.

Reinforcing Spatial Reasoning in Vision-Language Models with Interwoven Thinking and Visual Drawing

As textual reasoning with large language models (LLMs) has advanced significantly, there has been growing interest in enhancing the multimodal reasoning capabilities of large vision-language models (LVLMs). However, existing methods primarily approach multimodal reasoning in a straightforward, text-centric manner, where both reasoning and answer derivation are conducted purely through text, with the only difference being the presence of multimodal input. As a result, these methods often encounter fundamental limitations in spatial reasoning tasks that demand precise geometric understanding and continuous spatial tracking-capabilities that humans achieve through mental visualization and manipulation. To address the limitations, we propose drawing to reason in space, a novel paradigm that enables LVLMs to reason through elementary drawing operations in the visual space. By equipping models with basic drawing operations, including annotating bounding boxes and drawing auxiliary lines, we empower them to express and analyze spatial relationships through direct visual manipulation, meanwhile avoiding the performance ceiling imposed by specialized perception tools in previous tool-integrated reasoning approaches. To cultivate this capability, we develop a three-stage training framework: cold-start training with synthetic data to establish basic drawing abilities, reflective rejection sampling to enhance self-reflection behaviors, and reinforcement learning to directly optimize for target rewards. Extensive experiments demonstrate that our model, named VILASR, consistently outperforms existing methods across diverse spatial reasoning benchmarks, involving maze navigation, static spatial reasoning, video-based reasoning, and multi-view-based reasoning tasks, with an average improvement of 18.4%.

Flow Matching Meets PDEs: A Unified Framework for Physics-Constrained Generation

Generative machine learning methods, such as diffusion models and flow matching, have shown great potential in modeling complex system behaviors and building efficient surrogate models. However, these methods typically learn the underlying physics implicitly from data. We propose Physics-Based Flow Matching (PBFM), a novel generative framework that explicitly embeds physical constraints, both PDE residuals and algebraic relations, into the flow matching objective. We also introduce temporal unrolling at training time that improves the accuracy of the final, noise-free sample prediction. Our method jointly minimizes the flow matching loss and the physics-based residual loss without requiring hyperparameter tuning of their relative weights. Additionally, we analyze the role of the minimum noise level, $\sigma_{\min}$, in the context of physical constraints and evaluate a stochastic sampling strategy that helps to reduce physical residuals. Through extensive benchmarks on three representative PDE problems, we show that our approach yields up to an $8\times$ more accurate physical residuals compared to FM, while clearly outperforming existing algorithms in terms of distributional accuracy. PBFM thus provides a principled and efficient framework for surrogate modeling, uncertainty quantification, and accelerated simulation in physics and engineering applications.

VersaVid-R1: A Versatile Video Understanding and Reasoning Model from Question Answering to Captioning Tasks

Recent advancements in multimodal large language models have successfully extended the Reason-Then-Respond paradigm to image-based reasoning, yet video-based reasoning remains an underdeveloped frontier, primarily due to the scarcity of high-quality reasoning-oriented data and effective training methodologies. To bridge this gap, we introduce DarkEventInfer and MixVidQA, two novel datasets specifically designed to stimulate the model's advanced video understanding and reasoning abilities. DarkEventinfer presents videos with masked event segments, requiring models to infer the obscured content based on contextual video cues. MixVidQA, on the other hand, presents interleaved video sequences composed of two distinct clips, challenging models to isolate and reason about one while disregarding the other. Leveraging these carefully curated training samples together with reinforcement learning guided by diverse reward functions, we develop VersaVid-R1, the first versatile video understanding and reasoning model under the Reason-Then-Respond paradigm capable of handling multiple-choice and open-ended question answering, as well as video captioning tasks. Extensive experiments demonstrate that VersaVid-R1 significantly outperforms existing models across a broad spectrum of benchmarks, covering video general understanding, cognitive reasoning, and captioning tasks.

MonkeyOCR: Document Parsing with a Structure-Recognition-Relation Triplet Paradigm

We introduce MonkeyOCR, a vision-language model for document parsing that advances the state of the art by leveraging a Structure-Recognition-Relation (SRR) triplet paradigm. This design simplifies what would otherwise be a complex multi-tool pipeline (as in MinerU's modular approach) and avoids the inefficiencies of processing full pages with giant end-to-end models (e.g., large multimodal LLMs like Qwen-VL). In SRR, document parsing is abstracted into three fundamental questions - "Where is it?" (structure), "What is it?" (recognition), and "How is it organized?" (relation) - corresponding to layout analysis, content identification, and logical ordering. This focused decomposition balances accuracy and speed: it enables efficient, scalable processing without sacrificing precision. To train and evaluate this approach, we introduce the MonkeyDoc (the most comprehensive document parsing dataset to date), with 3.9 million instances spanning over ten document types in both Chinese and English. Experiments show that MonkeyOCR outperforms MinerU by an average of 5.1%, with particularly notable improvements on challenging content such as formulas (+15.0%) and tables (+8.6%). Remarkably, our 3B-parameter model surpasses much larger and top-performing models, including Qwen2.5-VL (72B) and Gemini 2.5 Pro, achieving state-of-the-art average performance on English document parsing tasks. In addition, MonkeyOCR processes multi-page documents significantly faster (0.84 pages per second compared to 0.65 for MinerU and 0.12 for Qwen2.5-VL-7B). The 3B model can be efficiently deployed for inference on a single NVIDIA 3090 GPU. Code and models will be released at https://github.com/Yuliang-Liu/MonkeyOCR.

Using In-Context Learning for Automatic Defect Labelling of Display Manufacturing Data

This paper presents an AI-assisted auto-labeling system for display panel defect detection that leverages in-context learning capabilities. We adopt and enhance the SegGPT architecture with several domain-specific training techniques and introduce a scribble-based annotation mechanism to streamline the labeling process. Our two-stage training approach, validated on industrial display panel datasets, demonstrates significant improvements over the baseline model, achieving an average IoU increase of 0.22 and a 14% improvement in recall across multiple product types, while maintaining approximately 60% auto-labeling coverage. Experimental results show that models trained on our auto-labeled data match the performance of those trained on human-labeled data, offering a practical solution for reducing manual annotation efforts in industrial inspection systems.

PDE-Transformer: Efficient and Versatile Transformers for Physics Simulations

We introduce PDE-Transformer, an improved transformer-based architecture for surrogate modeling of physics simulations on regular grids. We combine recent architectural improvements of diffusion transformers with adjustments specific for large-scale simulations to yield a more scalable and versatile general-purpose transformer architecture, which can be used as the backbone for building large-scale foundation models in physical sciences. We demonstrate that our proposed architecture outperforms state-of-the-art transformer architectures for computer vision on a large dataset of 16 different types of PDEs. We propose to embed different physical channels individually as spatio-temporal tokens, which interact via channel-wise self-attention. This helps to maintain a consistent information density of tokens when learning multiple types of PDEs simultaneously. We demonstrate that our pre-trained models achieve improved performance on several challenging downstream tasks compared to training from scratch and also beat other foundation model architectures for physics simulations.

Divide-Then-Align: Honest Alignment based on the Knowledge Boundary of RAG

Large language models (LLMs) augmented with retrieval systems have significantly advanced natural language processing tasks by integrating external knowledge sources, enabling more accurate and contextually rich responses. To improve the robustness of such systems against noisy retrievals, Retrieval-Augmented Fine-Tuning (RAFT) has emerged as a widely adopted method. However, RAFT conditions models to generate answers even in the absence of reliable knowledge. This behavior undermines their reliability in high-stakes domains, where acknowledging uncertainty is critical. To address this issue, we propose Divide-Then-Align (DTA), a post-training approach designed to endow RAG systems with the ability to respond with "I don't know" when the query is out of the knowledge boundary of both the retrieved passages and the model's internal knowledge. DTA divides data samples into four knowledge quadrants and constructs tailored preference data for each quadrant, resulting in a curated dataset for Direct Preference Optimization (DPO). Experimental results on three benchmark datasets demonstrate that DTA effectively balances accuracy with appropriate abstention, enhancing the reliability and trustworthiness of retrieval-augmented systems.

REACT: Representation Extraction And Controllable Tuning to Overcome Overfitting in LLM Knowledge Editing

Large language model editing methods frequently suffer from overfitting, wherein factual updates can propagate beyond their intended scope, overemphasizing the edited target even when it's contextually inappropriate. To address this challenge, we introduce REACT (Representation Extraction And Controllable Tuning), a unified two-phase framework designed for precise and controllable knowledge editing. In the initial phase, we utilize tailored stimuli to extract latent factual representations and apply Principal Component Analysis with a simple learnbale linear transformation to compute a directional "belief shift" vector for each instance. In the second phase, we apply controllable perturbations to hidden states using the obtained vector with a magnitude scalar, gated by a pre-trained classifier that permits edits only when contextually necessary. Relevant experiments on EVOKE benchmarks demonstrate that REACT significantly reduces overfitting across nearly all evaluation metrics, and experiments on COUNTERFACT and MQuAKE shows that our method preserves balanced basic editing performance (reliability, locality, and generality) under diverse editing scenarios.