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Chen Wei

Publications and source records attributed to Chen Wei.

At least 37 records · Page 2Linked to original sources
arXiv2026

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design

Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit ligand constraints. Although continuous diffusion and flow-based models support ligand-aware design in coordinate or latent spaces, existing discrete diffusion protein language models mainly operate over sequence or structure tokens without direct small-molecule conditioning. We introduce \textbf{ProtLiD$^2$}, a \textbf{Prot}ein \textbf{L}igand-conditioned \textbf{D}iscrete \textbf{D}iffusion model for protein sequence-structure co-design. ProtLiD$^2$ jointly generates amino-acid sequence and discrete structure tokens while incorporating ligand chemical and geometric information through geometry-aware cross-attention. Trained on over one million ligand-protein complexes, ProtLiD$^2$ extends masked discrete diffusion to ligand-aware functional protein design. We further propose maximum confidence-margin guided ReMask decoding, an inference-time self-correction strategy that retains confident predictions and remasks uncertain tokens. ProtLiD$^2$ improves global fold confidence over Complexa in whole-protein design, increasing TM-score from 0.672 to 0.802 and pLDDT from 64.55 to 73.00. In pocket co-design, ProtLiD$^2$ reduces active-site BB-RMSD from 3.46/3.40Å for FAIR/PocketGen to 1.97Å, and improves ligand-aware pass rates over PocketGen from 14.86% to 59.73% and from 6.08% to 23.49% under stricter docking thresholds. These results support ligand-conditioned discrete diffusion as an effective token-space framework for functional protein co-design. Code will be available at https://github.com/auroua/ProtLiD.

q-bio.BM↗
arXiv2026

Higher order Magnus expansions for driven two-level quantum dynamics

We investigate the Magnus expansion for a generic time-dependent two-level system under single-axis driving.By virtue of the su(2) Lie algebra, the expansion is decomposed into a commutator-free form. To illustrate the usefulness of the gained expression, we then revisit the Landau-Zener-Stückelberg-Majorana model, with a focus on non-adiabatic transitions as well as the Stokes phase. In addition, the semiclassical Rabi model is systematically treated by determining the Floquet quasienergy up to different orders. We demonstrate how to employ suitable picture transformations as well as on how to enforce the symmetry of the underlying model in order to guarantee convergence of the expansion as well as to achieve satisfactory agreement with the exact results. For both models that we studied it turns out that a third order approximation yields results that are in next to perfect agreement with exact analytical ones. Surprisingly, in the case of the semiclassical Rabi model, even the second order Magnus approximation in the adiabatic picture produces almost exact results for a large parameter range.

quant-ph↗
arXiv2026

The Perceptual Bandwidth Bottleneck in Vision-Language Models: Active Visual Reasoning via Sequential Experimental Design

Visual perception in modern Vision-Language Models (VLMs) is constrained by a perceptual bandwidth bottleneck: a broad field of view preserves global context but sacrifices the fine-grained details required for complex reasoning. We argue that high-resolution visual reasoning is therefore not only semantic reasoning but also task-relevant evidence acquisition under limited perceptual bandwidth. Inspired by active vision and information foraging, we formalise this process as sequential Bayesian optimal experimental design (S-BOED), where an agent decides which visual evidence to acquire before answering. Since exact Bayesian inference is intractable in continuous gigapixel spaces, we derive a tractable coverage--resolution objective as a proxy for task-relevant information gain. We instantiate this framework with FOVEA, a training-free procedure that refines VLM crop proposals through evidence-oriented probing. Experiments on high-resolution benchmarks show consistent gains over direct and ReAct-style baselines, with particularly strong improvements in search-dominated remote-sensing settings.

cs.CV↗
arXiv2026

Taming Outlier Tokens in Diffusion Transformers

We study outlier tokens in Diffusion Transformers (DiTs) for image generation. Prior work has shown that Vision Transformers (ViTs) can produce a small number of high-norm tokens that attract disproportionate attention while carrying limited local information, but their role in generative models remains underexplored. We show that this phenomenon appears in both the encoder and denoiser of modern Representation Autoencoder (RAE)-DiT pipelines: pretrained ViT encoders can produce outlier representations, and DiTs themselves can develop internal outlier tokens, especially in intermediate layers. Moreover, simply masking high-norm tokens does not improve performance, indicating that the problem is not only caused by a few extreme values, but is more closely related to corrupted local patch semantics. To address this issue, we introduce Dual-Stage Registers (DSR), a register-based intervention for both components: trained registers when available, recursive test-time registers otherwise, and diffusion registers for the denoiser. Across ImageNet and large-scale text-to-image generation, these interventions consistently reduce outlier artifacts and improve generation quality. Our results highlight outlier-token control as an important ingredient in building stronger DiTs.

cs.CV↗
arXiv2026

Learning Rate Engineering: From Coarse Single Parameter to Layered Evolution

Learning rate scheduling has evolved from the single global fixed rate of early SGD to sophisticated layer-wise adaptive strategies. We systematize this evolution into five generations: (Gen1) global fixed learning rates, (Gen2) global scheduling, (Gen3) parameter-level adaptation, (Gen4) layer-level differentiation, and (Gen5) joint layer-time scheduling. We trace the fundamental motivation behind each transition, showing how the shift from one-size-fits-all to tailoring by layer and time addresses the impossible trinity of transfer learning: lower layers require small updates to preserve general knowledge while higher layers need large updates to adapt to new tasks. Building on this taxonomy, we propose Discriminative Adaptive Layer Scaling (DALS), a unified framework that integrates phase-adaptive cosine scheduling, depth-aware Grokfast gradient filtering, and LARS-style trust ratios into a single coherent optimizer. We benchmark 18 strategies including three DALS variants across all five generations on five datasets: synthetic, CIFAR-10 (from scratch), RTE, TREC-6, and IMDb (fine-tuning). On synthetic, DALS achieves the best accuracy at 98.0%, while DALS-Fast reaches 90% in just 3 epochs. The cross-dataset analysis reveals striking regime-dependent patterns -- no single strategy wins across all regimes. Critically, STLR+Discriminative, the ULMFiT champion, catastrophically fails on from-scratch tasks (43.6% on TREC-6 from scratch vs. 96.8% with RAdam), confirming that directional decay biases are harmful without pretrained features. DALS avoids either extreme, achieving the best synthetic result while maintaining competitive fine-tuning performance.

cs.AI↗
arXiv2026

A geometry aware framework enhances noninvasive mapping of whole human brain dynamics

Non-invasive electrophysiology lacks methods that accurately reconstruct whole-brain spatiotemporal dynamics while incorporating individual cortical geometry, leaving current electroencephalography and magnetoencephalography source imaging limited by simplistic or biologically implausible priors. Here, we show that embedding participant-specific Geometric Basis Functions (GBFs), eigenmodes derived from each individual's cortical surface, provides a powerful anatomic constraint that resolves the inverse problem and improves reconstruction fidelity. The method reconstructs neural sources as linear combinations of geometric basis functions, thereby aligning source estimates with the geometric organization of neural dynamics. We validate GBF across the Meta-Source Benchmark, task-evoked data, resting-state networks, intracranial stimulation, and epilepsy data. The results demonstrate that GBF yields high localization accuracy and captures fast spatiotemporal dynamics consistent with anatomical pathways. These findings suggest that both spontaneous and evoked whole-brain activity can be described by hundreds of geometric modes, providing a compact yet accurate representation of neural sources. By linking cortical geometry to electrophysiological dynamics, GBF offers a versatile source imaging tool for both scientific and clinical applications.

q-bio.NC↗
arXiv2026

A novel LSTM music generator based on the fractional time-frequency feature extraction

In this paper, we propose a novel approach for generating music based on an artificial intelligence (AI) system. We analyze the features of music and use them to fit and predict the music. The fractional Fourier transform (FrFT) and the long short-term memory (LSTM) network are the foundations of our method. The FrFT method is used to extract the spectral features of a music piece, where the music signal is expressed on the time and frequency domains. The LSTM network is used to generate new music based on the extracted features, where we predict the music according to the hidden layer features and real-time inputs using GiantMIDI-Piano dataset. The results of our experiments show that our proposed system is capable of generating high-quality music that is comparable to human-generated music.

cs.SD↗
arXiv2026

Agentic Discovery with Active Hypothesis Exploration for Visual Recognition

We introduce HypoExplore, an agentic framework that formulates neural architecture discovery for visual recognition as a hypothesis-driven scientific inquiry. Given a human-specified high-level research direction, HypoExplore ideates, implements, evaluates, and improves neural architectures through evolutionary branching. New hypotheses are created using a large language model by selecting a parent hypothesis to build upon, guided by a dual strategy that balances exploiting validated principles with resolving uncertain ones. Our proposed framework maintains a Trajectory Tree that records the lineage of all proposed architectures, and a Hypothesis Memory Bank that actively tracks confidence scores acquired through experimental evidence. After each experiment, multiple feedback agents analyze the results from different perspectives and consolidate their findings into hypothesis confidence updates. Our framework is tested on discovering lightweight vision architectures on CIFAR-10, with the best achieving 94.11% accuracy evolved from a root node baseline that starts at 18.91%, and generalizes to CIFAR-100 and Tiny-ImageNet. We further demonstrate applicability to a specialized domain by conducting independent architecture discovery runs on MedMNIST, which yield a state-of-the-art performance. We show that hypothesis confidence scores grow increasingly predictive as evidence accumulates, and that the learned principles transfer across independent evolutionary lineages, suggesting that HypoExplore not only discovers stronger architectures, but can help build a genuine understanding of the design space.

cs.CV↗
arXiv2026

MiroEval: Benchmarking Multimodal Deep Research Agents in Process and Outcome

Recent progress in deep research systems has been impressive, but evaluation still lags behind real user needs. Existing benchmarks predominantly assess final reports using fixed rubrics, failing to evaluate the underlying research process. Most also offer limited multimodal coverage, rely on synthetic tasks that do not reflect real-world query complexity, and cannot be refreshed as knowledge evolves. To address these gaps, we introduce MiroEval, a benchmark and evaluation framework for deep research systems. The benchmark comprises 100 tasks (70 text-only, 30 multimodal), all grounded in real user needs and constructed via a dual-path pipeline that supports periodic updates, enabling a live and evolving setting. The proposed evaluation suite assesses deep research systems along three complementary dimensions: adaptive synthesis quality evaluation with task-specific rubrics, agentic factuality verification via active retrieval and reasoning over both web sources and multimodal attachments, and process-centric evaluation audits how the system searches, reasons, and refines throughout its investigation. Evaluation across 13 systems yields three principal findings: the three evaluation dimensions capture complementary aspects of system capability, with each revealing distinct strengths and weaknesses across systems; process quality serves as a reliable predictor of overall outcome while revealing weaknesses invisible to output-level metrics; and multimodal tasks pose substantially greater challenges, with most systems declining by 3 to 10 points. The MiroThinker series achieves the most balanced performance, with MiroThinker-H1 ranking the highest overall in both settings. Human verification and robustness results confirm the reliability of the benchmark and evaluation framework. MiroEval provides a holistic diagnostic tool for the next generation of deep research agents.

cs.AI↗
arXiv2026

The Quest for Generalizable Motion Generation: Data, Model, and Evaluation

Despite recent advances in 3D human motion generation (MoGen) on standard benchmarks, existing text-to-motion models still face a fundamental bottleneck in their generalization capability. In contrast, adjacent generative fields, most notably video generation (ViGen), have demonstrated remarkable generalization in modeling human behaviors, highlighting transferable insights that MoGen can leverage. Motivated by this observation, we present a comprehensive framework that systematically transfers knowledge from ViGen to MoGen across three key pillars: data, modeling, and evaluation. First, we introduce ViMoGen-228K, a large-scale dataset comprising 228,000 high-quality motion samples that integrates high-fidelity optical MoCap data with semantically annotated motions from web videos and synthesized samples generated by state-of-the-art ViGen models. The dataset includes both text-motion pairs and text-video-motion triplets, substantially expanding semantic diversity. Second, we propose ViMoGen, a flow-matching-based diffusion transformer that unifies priors from MoCap data and ViGen models through gated multimodal conditioning. To enhance efficiency, we further develop ViMoGen-light, a distilled variant that eliminates video generation dependencies while preserving strong generalization. Finally, we present MBench, a hierarchical benchmark designed for fine-grained evaluation across motion quality, prompt fidelity, and generalization ability. Extensive experiments show that our framework significantly outperforms existing approaches in both automatic and human evaluations. The code, data, and benchmark will be made publicly available. Homepage: https://motrixlab.github.io/2026_iclr_vimogen.

cs.CV↗
arXiv2026

Scaling Spatial Intelligence with Multimodal Foundation Models

Despite remarkable progress, multimodal foundation models still exhibit surprising deficiencies in spatial intelligence. In this work, we explore scaling up multimodal foundation models to cultivate spatial intelligence within the SenseNova-SI family, built upon established multimodal foundations including visual understanding models (i.e., Qwen3-VL and InternVL3) and unified understanding and generation models (i.e., Bagel). We take a principled approach to constructing high-performing and robust spatial intelligence by systematically curating SenseNova-SI-8M: eight million diverse data samples under a rigorous taxonomy of spatial capabilities. SenseNova-SI demonstrates unprecedented performance across a broad range of spatial intelligence benchmarks: 68.8% on VSI-Bench, 43.3% on MMSI, 85.7% on MindCube, 54.7% on ViewSpatial, 47.7% on SITE, 63.9% on BLINK, 55.5% on 3DSR, and 72.0% on EmbSpatial, while maintaining strong general multimodal understanding (e.g., 84.9% on MMBench-En). More importantly, we analyze the impact of data scaling, discuss early signs of emergent generalization capabilities enabled by diverse data training, analyze the risk of overfitting and language shortcuts, present a preliminary study on spatial chain-of-thought reasoning, and validate the potential downstream application. All newly trained multimodal foundation models are publicly released.

cs.CV↗
arXiv2026

Chiral Epitaxy: Enantioselective Growth of Chiral Nanowires on Low-Symmetry Two-Dimensional Materials

Chiral crystals exhibit useful handedness-dependent properties, including spin selectivity and circularly polarized light sensitivity, yet controlling which enantiomer forms during synthesis remains a central challenge. Existing approaches utilize molecules in solution to template crystal growth, which restricts processing conditions and introduces organic contaminants incompatible with device fabrication. Enantioselective growth of a chiral crystal on a chiral surface via vapor-phase synthesis (chiral epitaxy) has not yet been demonstrated. Here, we show chiral epitaxy of aligned tellurium nanowires on a low-symmetry two-dimensional material, ReSe2. In situ electron microscopies suggest a mechanism where handedness is determined at nucleation by the interface energy difference between Te enantiomers and the chiral substrate surface. Chiral epitaxy provides a solvent-free, vapor-solid route to homochiral crystals compatible with semiconductor and quantum manufacturing processes.

cond-mat.mtrl-sci↗
arXiv2026

LexInstructEval: Lexical Instruction Following Evaluation for Large Language Models

The ability of Large Language Models (LLMs) to precisely follow complex and fine-grained lexical instructions is a cornerstone of their utility and controllability. However, evaluating this capability remains a significant challenge. Current methods either rely on subjective and costly human evaluation or on automated LLM-as-a-judge systems, which suffer from inherent biases and unreliability. Existing programmatic benchmarks, while objective, often lack the expressiveness to test intricate, compositional constraints at a granular level. To address these limitations, we introduce LexInstructEval, a new benchmark and evaluation framework for fine-grained lexical instruction following. Our framework is built upon a formal, rule-based grammar that deconstructs complex instructions into a canonical triplet. This grammar enables the systematic generation of a diverse dataset through a multi-stage, human-in-the-loop pipeline and facilitates objective verification via a transparent, programmatic engine. We release our dataset and open-source evaluation tools to facilitate further research into the controllability and reliability of LLMs.

cs.CL↗
arXiv2026

MEMO: Memory-Augmented Model Context Optimization for Robust Multi-Turn Multi-Agent LLM Games

Multi-turn, multi-agent LLM game evaluations often exhibit substantial run-to-run variance. In long-horizon interactions, small early deviations compound across turns and are amplified by multi-agent coupling. This biases win rate estimates and makes rankings unreliable across repeated tournaments. Prompt choice worsens this further by producing different effective policies. We address both instability and underperformance with MEMO (Memory-augmented MOdel context optimization), a self-play framework that optimizes inference-time context by coupling retention and exploration. Retention maintains a persistent memory bank that stores structured insights from self-play trajectories and injects them as priors during later play. Exploration runs tournament-style prompt evolution with uncertainty-aware selection via TrueSkill, and uses prioritized replay to revisit rare and decisive states. Across five text-based games, MEMO raises mean win rate from 25.1% to 49.5% for GPT-4o-mini and from 20.9% to 44.3% for Qwen-2.5-7B-Instruct, using $2,000$ self-play games per task. Run-to-run variance also drops, giving more stable rankings across prompt variations. These results suggest that multi-agent LLM game performance and robustness have substantial room for improvement through context optimization. MEMO achieves the largest gains in negotiation and imperfect-information games, while RL remains more effective in perfect-information settings. All code is open-source and available here: https://github.com/openverse-ai/MEMO

cs.AI↗
arXiv2026

Chain of World: World Model Thinking in Latent Motion

Vision-Language-Action (VLA) models are a promising path toward embodied intelligence, yet they often overlook the predictive and temporal-causal structure underlying visual dynamics. World-model VLAs address this by predicting future frames, but waste capacity reconstructing redundant backgrounds. Latent-action VLAs encode frame-to-frame transitions compactly, but lack temporally continuous dynamic modeling and world knowledge. To overcome these limitations, we introduce CoWVLA (Chain-of-World VLA), a new "Chain of World" paradigm that unifies world-model temporal reasoning with a disentangled latent motion representation. First, a pretrained video VAE serves as a latent motion extractor, explicitly factorizing video segments into structure and motion latents. Then, during pre-training, the VLA learns from an instruction and an initial frame to infer a continuous latent motion chain and predict the segment's terminal frame. Finally, during co-fine-tuning, this latent dynamic is aligned with discrete action prediction by jointly modeling sparse keyframes and action sequences in a unified autoregressive decoder. This design preserves the world-model benefits of temporal reasoning and world knowledge while retaining the compactness and interpretability of latent actions, enabling efficient visuomotor learning. Extensive experiments on robotic simulation benchmarks show that CoWVLA outperforms existing world-model and latent-action approaches and achieves moderate computational efficiency, highlighting its potential as a more effective VLA pretraining paradigm. The project website can be found at https://fx-hit.github.io/cowvla-io.

cs.CV↗
arXiv2026

PyVision-RL: Forging Open Agentic Vision Models via RL

Reinforcement learning for agentic multimodal models often suffers from interaction collapse, where models learn to reduce tool usage and multi-turn reasoning, limiting the benefits of agentic behavior. We introduce PyVision-RL, a reinforcement learning framework for open-weight multimodal models that stabilizes training and sustains interaction. Our approach combines an oversampling-filtering-ranking rollout strategy with an accumulative tool reward to prevent collapse and encourage multi-turn tool use. Using a unified training pipeline, we develop PyVision-Image and PyVision-Video for image and video understanding. For video reasoning, PyVision-Video employs on-demand context construction, selectively sampling task-relevant frames during reasoning to significantly reduce visual token usage. Experiments show strong performance and improved efficiency, demonstrating that sustained interaction and on-demand visual processing are critical for scalable multimodal agents.

cs.AI↗
arXiv2026

Local Intrinsic Dimension of Representations Predicts Alignment and Generalization in AI Models and Human Brain

Recent work has found that neural networks with stronger generalization tend to exhibit higher representational alignment with one another across architectures and training paradigms. In this work, we show that models with stronger generalization also align more strongly with human neural activity. Moreover, generalization performance, model--model alignment, and model--brain alignment are all significantly correlated with each other. We further show that these relationships can be explained by a single geometric property of learned representations: the local intrinsic dimension of embeddings. Lower local dimension is consistently associated with stronger model--model alignment, stronger model--brain alignment, and better generalization, whereas global dimension measures fail to capture these effects. Finally, we find that increasing model capacity and training data scale systematically reduces local intrinsic dimension, providing a geometric account of the benefits of scaling. Together, our results identify local intrinsic dimension as a unifying descriptor of representational convergence in artificial and biological systems.

cs.LG↗
arXiv2026

Understanding Generalization from Embedding Dimension and Distributional Convergence

Deep neural networks often generalize well despite heavy over-parameterization, challenging classical parameter-based analyses. We study generalization from a representation-centric perspective and analyze how the geometry of learned embeddings controls predictive performance for a fixed trained model. We show that population risk can be bounded by two factors: (i) the intrinsic dimension of the embedding distribution, which determines the convergence rate of empirical embedding distribution to the population distribution in Wasserstein distance, and (ii) the sensitivity of the downstream mapping from embeddings to predictions, characterized by Lipschitz constants. Together, these yield an embedding-dependent error bound that does not rely on parameter counts or hypothesis class complexity. At the final embedding layer, architectural sensitivity vanishes and the bound is dominated by embedding dimension, explaining its strong empirical correlation with generalization performance. Experiments across architectures and datasets validate the theory and demonstrate the utility of embedding-based diagnostics.

cs.LG↗