Reflection Pretraining Enables Token-Level Self-Correction in Biological Sequence Models

Chain-of-Thought (CoT) prompting has significantly advanced task-solving capabilities in natural language processing with large language models. Unlike standard prompting, CoT encourages the model to generate intermediate reasoning steps, non-answer tokens, that help guide the model toward more accurate final outputs. These intermediate steps enable more complex reasoning processes such as error correction, memory management, future planning, and self-reflection. However, applying CoT to non-natural language domains, such as protein and RNA language models, is not yet possible, primarily due to the limited expressiveness of their token spaces (e.g., amino acid tokens). In this work, we propose and define the concept of language expressiveness: the ability of a given language, using its tokens and grammar, to encode information. We show that the limited expressiveness of protein language severely restricts the applicability of CoT-style reasoning. To overcome this, we introduce reflection pretraining, for the first time in a biological sequence model, which enables the model to engage in intermediate reasoning through the generation of auxiliary "thinking tokens" beyond simple answer tokens. Theoretically, we demonstrate that our augmented token set significantly enhances biological language expressiveness, thereby improving the overall reasoning capacity of the model. Experimentally, our pretraining approach teaches protein models to self-correct and leads to substantial performance gains compared to standard pretraining.

Accurate de novo sequencing of the modified proteome with OmniNovo

Post-translational modifications (PTMs) serve as a dynamic chemical language regulating protein function, yet current proteomic methods remain blind to a vast portion of the modified proteome. Standard database search algorithms suffer from a combinatorial explosion of search spaces, limiting the identification of uncharacterized or complex modifications. Here we introduce OmniNovo, a unified deep learning framework for reference-free sequencing of unmodified and modified peptides directly from tandem mass spectra. Unlike existing tools restricted to specific modification types, OmniNovo learns universal fragmentation rules to decipher diverse PTMs within a single coherent model. By integrating a mass-constrained decoding algorithm with rigorous false discovery rate estimation, OmniNovo achieves state-of-the-art accuracy, identifying 51\% more peptides than standard approaches at a 1\% false discovery rate. Crucially, the model generalizes to biological sites unseen during training, illuminating the dark matter of the proteome and enabling unbiased comprehensive analysis of cellular regulation.

CVP: Central-Peripheral Vision-Inspired Multimodal Model for Spatial Reasoning

We present a central-peripheral vision-inspired framework (CVP), a simple yet effective multimodal model for spatial reasoning that draws inspiration from the two types of human visual fields -- central vision and peripheral vision. Existing approaches primarily rely on unstructured representations, such as point clouds, voxels, or patch features, and inject scene context implicitly via coordinate embeddings. However, this often results in limited spatial reasoning capabilities due to the lack of explicit, high-level structural understanding. To address this limitation, we introduce two complementary components into a Large Multimodal Model-based architecture: target-affinity token, analogous to central vision, that guides the model's attention toward query-relevant objects; and allocentric grid, akin to peripheral vision, that captures global scene context and spatial arrangements. These components work in tandem to enable structured, context-aware understanding of complex 3D environments. Experiments show that CVP achieves state-of-the-art performance across a range of 3D scene understanding benchmarks.

MOON Embedding: Multimodal Representation Learning for E-commerce Search Advertising

We introduce MOON, our comprehensive set of sustainable iterative practices for multimodal representation learning for e-commerce applications. MOON has already been fully deployed across all stages of Taobao search advertising system, including retrieval, relevance, ranking, and so on. The performance gains are particularly significant on click-through rate (CTR) prediction task, which achieves an overall +20.00% online CTR improvement. Over the past three years, this project has delivered the largest improvement on CTR prediction task and undergone five full-scale iterations. Throughout the exploration and iteration of our MOON, we have accumulated valuable insights and practical experience that we believe will benefit the research community. MOON contains a three-stage training paradigm of "Pretraining, Post-training, and Application", allowing effective integration of multimodal representations with downstream tasks. Notably, to bridge the misalignment between the objectives of multimodal representation learning and downstream training, we define the exchange rate to quantify how effectively improvements in an intermediate metric can translate into downstream gains. Through this analysis, we identify the image-based search recall as a critical intermediate metric guiding the optimization of multimodal models. Over three years and five iterations, MOON has evolved along four critical dimensions: data processing, training strategy, model architecture, and downstream application. The lessons and insights gained through the iterative improvements will also be shared. As part of our exploration into scaling effects in the e-commerce field, we further conduct a systematic study of the scaling laws governing multimodal representation learning, examining multiple factors such as the number of training tokens, negative samples, and the length of user behavior sequences.

A Visual Perception-Based Tunable Framework and Evaluation Benchmark for H.265/HEVC ROI Encryption

ROI selective encryption, as an efficient privacy protection technique, encrypts only the key regions in the video, thereby ensuring security while minimizing the impact on coding efficiency. However, existing ROI-based video encryption methods suffer from insufficient flexibility and lack of a unified evaluation system. To address these issues, we propose a visual perception-based tunable framework and evaluation benchmark for H.265/HEVC ROI encryption. Our scheme introduces three key contributions: 1) A ROI region recognition module based on visual perception network is proposed to accurately identify the ROI region in videos. 2) A three-level tunable encryption strategy is implemented while balancing security and real-time performance. 3) A unified ROI encryption evaluation benchmark is developed to provide a standardized quantitative platform for subsequent research. This triple strategy provides new solution and significant unified performance evaluation methods for ROI selective encryption field. Experimental results indicate that the proposed benchmark can comprehensively measure the performance of the ROI selective encryption. Compared to existing ROI encryption algorithms, our proposed enhanced and advanced level encryption exhibit superior performance in multiple performance metrics. In general, the proposed framework effectively meets the privacy protection requirements in H.265/HEVC and provides a reliable solution for secure and efficient processing of sensitive video content.

PhysWorld: From Real Videos to World Models of Deformable Objects via Physics-Aware Demonstration Synthesis

Interactive world models that simulate object dynamics are crucial for robotics, VR, and AR. However, it remains a significant challenge to learn physics-consistent dynamics models from limited real-world video data, especially for deformable objects with spatially-varying physical properties. To overcome the challenge of data scarcity, we propose PhysWorld, a novel framework that utilizes a simulator to synthesize physically plausible and diverse demonstrations to learn efficient world models. Specifically, we first construct a physics-consistent digital twin within MPM simulator via constitutive model selection and global-to-local optimization of physical properties. Subsequently, we apply part-aware perturbations to the physical properties and generate various motion patterns for the digital twin, synthesizing extensive and diverse demonstrations. Finally, using these demonstrations, we train a lightweight GNN-based world model that is embedded with physical properties. The real video can be used to further refine the physical properties. PhysWorld achieves accurate and fast future predictions for various deformable objects, and also generalizes well to novel interactions. Experiments show that PhysWorld has competitive performance while enabling inference speeds 47 times faster than the recent state-of-the-art method, i.e., PhysTwin.

C3Editor: Achieving Controllable Consistency in 2D Model for 3D Editing

Existing 2D-lifting-based 3D editing methods often encounter challenges related to inconsistency, stemming from the lack of view-consistent 2D editing models and the difficulty of ensuring consistent editing across multiple views. To address these issues, we propose C3Editor, a controllable and consistent 2D-lifting-based 3D editing framework. Given an original 3D representation and a text-based editing prompt, our method selectively establishes a view-consistent 2D editing model to achieve superior 3D editing results. The process begins with the controlled selection of a ground truth (GT) view and its corresponding edited image as the optimization target, allowing for user-defined manual edits. Next, we fine-tune the 2D editing model within the GT view and across multiple views to align with the GT-edited image while ensuring multi-view consistency. To meet the distinct requirements of GT view fitting and multi-view consistency, we introduce separate LoRA modules for targeted fine-tuning. Our approach delivers more consistent and controllable 2D and 3D editing results than existing 2D-lifting-based methods, outperforming them in both qualitative and quantitative evaluations.

TimeSeriesScientist: A General-Purpose AI Agent for Time Series Analysis

Time series forecasting is central to decision-making in domains as diverse as energy, finance, climate, and public health. In practice, forecasters face thousands of short, noisy series that vary in frequency, quality, and horizon, where the dominant cost lies not in model fitting, but in the labor-intensive preprocessing, validation, and ensembling required to obtain reliable predictions. Prevailing statistical and deep learning models are tailored to specific datasets or domains and generalize poorly. A general, domain-agnostic framework that minimizes human intervention is urgently in demand. In this paper, we introduce TimeSeriesScientist (TSci), the first LLM-driven agentic framework for general time series forecasting. The framework comprises four specialized agents: Curator performs LLM-guided diagnostics augmented by external tools that reason over data statistics to choose targeted preprocessing; Planner narrows the hypothesis space of model choice by leveraging multi-modal diagnostics and self-planning over the input; Forecaster performs model fitting and validation and, based on the results, adaptively selects the best model configuration as well as ensemble strategy to make final predictions; and Reporter synthesizes the whole process into a comprehensive, transparent report. With transparent natural-language rationales and comprehensive reports, TSci transforms the forecasting workflow into a white-box system that is both interpretable and extensible across tasks. Empirical results on eight established benchmarks demonstrate that TSci consistently outperforms both statistical and LLM-based baselines, reducing forecast error by an average of 10.4% and 38.2%, respectively. Moreover, TSci produces a clear and rigorous report that makes the forecasting workflow more transparent and interpretable.

UrbanFeel: A Comprehensive Benchmark for Temporal and Perceptual Understanding of City Scenes through Human Perspective

Urban development impacts over half of the global population, making human-centered understanding of its structural and perceptual changes essential for sustainable development. While Multimodal Large Language Models (MLLMs) have shown remarkable capabilities across various domains, existing benchmarks that explore their performance in urban environments remain limited, lacking systematic exploration of temporal evolution and subjective perception of urban environment that aligns with human perception. To address these limitations, we propose UrbanFeel, a comprehensive benchmark designed to evaluate the performance of MLLMs in urban development understanding and subjective environmental perception. UrbanFeel comprises 14.3K carefully constructed visual questions spanning three cognitively progressive dimensions: Static Scene Perception, Temporal Change Understanding, and Subjective Environmental Perception. We collect multi-temporal single-view and panoramic street-view images from 11 representative cities worldwide, and generate high-quality question-answer pairs through a hybrid pipeline of spatial clustering, rule-based generation, model-assisted prompting, and manual annotation. Through extensive evaluation of 20 state-of-the-art MLLMs, we observe that Gemini-2.5 Pro achieves the best overall performance, with its accuracy approaching human expert levels and narrowing the average gap to just 1.5\%. Most models perform well on tasks grounded in scene understanding. In particular, some models even surpass human annotators in pixel-level change detection. However, performance drops notably in tasks requiring temporal reasoning over urban development. Additionally, in the subjective perception dimension, several models reach human-level or even higher consistency in evaluating dimension such as beautiful and safety.

EVDI++: Event-based Video Deblurring and Interpolation via Self-Supervised Learning

Frame-based cameras with extended exposure times often produce perceptible visual blurring and information loss between frames, significantly degrading video quality. To address this challenge, we introduce EVDI++, a unified self-supervised framework for Event-based Video Deblurring and Interpolation that leverages the high temporal resolution of event cameras to mitigate motion blur and enable intermediate frame prediction. Specifically, the Learnable Double Integral (LDI) network is designed to estimate the mapping relation between reference frames and sharp latent images. Then, we refine the coarse results and optimize overall training efficiency by introducing a learning-based division reconstruction module, enabling images to be converted with varying exposure intervals. We devise an adaptive parameter-free fusion strategy to obtain the final results, utilizing the confidence embedded in the LDI outputs of concurrent events. A self-supervised learning framework is proposed to enable network training with real-world blurry videos and events by exploring the mutual constraints among blurry frames, latent images, and event streams. We further construct a dataset with real-world blurry images and events using a DAVIS346c camera, demonstrating the generalizability of the proposed EVDI++ in real-world scenarios. Extensive experiments on both synthetic and real-world datasets show that our method achieves state-of-the-art performance in video deblurring and interpolation tasks.