Yinuo Zhang

Hanqun Cao, Aastha Pal, Sophia Tang et al.

Protein function is often controlled by ligands that bias the direction of state transitions, such as agonists and antagonists, rather than stabilizing a single conformation. This is especially important for clinically relevant G protein-coupled receptors (GPCRs), where therapeutic efficacy depends on functional directionality. Structure-based design methods optimize binding to static conformations and cannot represent non-reversible, directional effects or systematically distinguish agonist from antagonist behavior. To address this gap, we introduce Transition-Directed Discrete Diffusion for Allosteric Binder Design (TD3B), a sequence-based generative framework that designs binders with specified agonist or antagonist behavior via a directional transition control objective. TD3B combines a target-aware Direction Oracle, a soft binding-affinity gate, and amortized fine-tuning of a pre-trained discrete diffusion model, enabling targeted agonist and antagonist generation decoupled from binding affinity and unattainable by equilibrium-based or inference-only guidance baselines. The code and checkpoints are available at https://huggingface.co/ChatterjeeLab/TD3B.

Yuhua Jiang, Yijun Guo, Hongbing Yang et al.

World action models (WAMs) provide a powerful generative framework for embodied control, yet transferring knowledge across heterogeneous WAMs remains challenging due to mismatched latent interfaces, high adaptation cost, and the rigidity of conventional distillation objectives. We propose \textbf{CKT-WAM}, a parameter-efficient \textbf{C}ontext \textbf{K}nowledge \textbf{T}ransfer framework that transfers teacher WAM's knowledge into a student WAM through a compact context in the text embedding space, rather than output imitation or dense hidden-state matching. Specifically, CKT-WAM extracts intermediate teacher hidden states, reduces the number of tokens via compressors' learnable-query cross attention (LQCA), and transforms them through an always-on generalized adapter, a lightweight router, and sparsely activated specialized adapters. The resulting context is then appended to the student's conditioning textual embeddings, thereby injecting the transferred knowledge into the student with minimal architectural modification. Experiments show that CKT-WAM consistently improves zero-shot generalization and achieves the best overall performance on LIBERO-Plus, reaching 86.1\% total success rate with only 1.17\% trainable parameters, while approaching full fine-tuning performance. Beyond simulation, CKT-WAM also demonstrates strong real-world long-horizon manipulation ability, achieving the best average success rate of 83.3\% across four multi-step and long-horizon tasks. Code is available at https://github.com/YuhuaJiang2002/CKT-WAM.

Qi Mao, Tinghan Yang, Yinuo Zhang et al.

Recent advances in generative compression methods have demonstrated remarkable progress in enhancing the perceptual quality of compressed data, especially in scenarios with low bitrates. However, their efficacy and applicability to achieve extreme compression ratios ($<0.05$ bpp) remain constrained. In this work, we propose a simple yet effective coding framework by introducing vector quantization (VQ)--based generative models into the image compression domain. The main insight is that the codebook learned by the VQGAN model yields a strong expressive capacity, facilitating efficient compression of continuous information in the latent space while maintaining reconstruction quality. Specifically, an image can be represented as VQ-indices by finding the nearest codeword, which can be encoded using lossless compression methods into bitstreams. We propose clustering a pre-trained large-scale codebook into smaller codebooks through the K-means algorithm, yielding variable bitrates and different levels of reconstruction quality within the coding framework. Furthermore, we introduce a transformer to predict lost indices and restore images in unstable environments. Extensive qualitative and quantitative experiments on various benchmark datasets demonstrate that the proposed framework outperforms state-of-the-art codecs in terms of perceptual quality-oriented metrics and human perception at extremely low bitrates ($\le 0.04$ bpp). Remarkably, even with the loss of up to $20\%$ of indices, the images can be effectively restored with minimal perceptual loss.

Sawan Patel, Sophia Tang, Yesol Kim et al.

Therapeutic mRNA design requires coordinating multiple interacting sequence features across the full transcript, where codon usage, untranslated regions (UTRs), and their coupling jointly determine stability, translation efficiency, and protein expression. Here, we present mRNA generation via unrolled trajectories and informed latent updates (mRNAutilus), a framework for simultaneous codon optimization and de novo UTR design directly from sequence. mRNAutilus combines a masked discrete diffusion model trained on millions of full-length mRNAs with Monte Carlo Tree Guidance to generate Pareto-efficient sequences under multiple functional objectives, using lightweight regressors over model embeddings to predict half-life, translation efficiency, and protein abundance. Unlike recent methods that design coding sequences and UTRs separately or rely on post hoc assembly and screening, mRNAutilus generates complete transcripts in a single process optimized across properties. Across diverse targets, zero-shot mRNAs encoding P. pyralis luciferase achieve over 400-fold higher expression than wild-type and outperform commercial and machine learning-designed baselines, including zero-shot generative approaches. Zero-shot SARS-CoV-2 Spike mRNAs exceed clinically used and commercial constructs and match or surpass lab-optimized designs with improved durability. We further demonstrate generality in therapeutic settings, including prime editing (PEMax) and programmable proteome modulation, where mRNAutilus-designed constructs enhance expression of peptide-guided E3 ligases (uAbs) for beta-catenin degradation. These results establish a sequence-based, multi-objective framework for generating functional mRNAs tailored to diverse biological applications.

Xinrui Zhan, Xuyang Chang, Daoyu Li et al.

Image sensing often relies on a high-quality machine vision system with a large field of view and high resolution. It requires fine imaging optics, has high computational costs, and requires a large communication bandwidth between image sensors and computing units. In this paper, we propose a novel image-free sensing framework for resource-efficient image classification, where the required number of measurements can be reduced by up to two orders of magnitude. In the proposed framework for single-pixel detection, the optical field for a target is first scattered by an optical diffuser and then two-dimensionally modulated by a spatial light modulator. The optical diffuser simultaneously serves as a compressor and an encryptor for the target information, effectively narrowing the field of view and improving the system's security. The one-dimensional sequence of intensity values, which is measured with time-varying patterns on the spatial light modulator, is then used to extract semantic information based on end-to-end deep learning. The proposed sensing framework is shown to obtain over a 95\% accuracy at sampling rates of 1% and 5% for classification on the MNIST dataset and the recognition of Chinese license plates, respectively, and the framework is up to 24% more efficient than the approach without an optical diffuser. The proposed framework represents a significant breakthrough in high-throughput machine intelligence for scene analysis with low bandwidth, low costs, and strong encryption.

Yinuo Zhang, Zhulin Tao, Xi Wang et al.

This paper describes our approach to the multi-modal fact verification (FACTIFY) challenge at AAAI2023. In recent years, with the widespread use of social media, fake news can spread rapidly and negatively impact social security. Automatic claim verification becomes more and more crucial to combat fake news. In fact verification involving multiple modal data, there should be a structural coherence between claim and document. Therefore, we proposed a structure coherence-based multi-modal fact verification scheme to classify fake news. Our structure coherence includes the following four aspects: sentence length, vocabulary similarity, semantic similarity, and image similarity. Specifically, CLIP and Sentence BERT are combined to extract text features, and ResNet50 is used to extract image features. In addition, we also extract the length of the text as well as the lexical similarity. Then the features were concatenated and passed through the random forest classifier. Finally, our weighted average F1 score has reached 0.8079, achieving 2nd place in FACTIFY2.

Sophia Tang, Yinuo Zhang, Pranam Chatterjee

We present PepTune, a multi-objective discrete diffusion model for simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with a novel bond-dependent masking schedule and invalid loss function. To guide the diffusion process, we introduce Monte Carlo Tree Guidance (MCTG), an inference-time multi-objective guidance algorithm that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTG integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity. Using PepTune, we generate diverse, chemically-modified peptides simultaneously optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling for various disease-relevant targets. In total, our results demonstrate that MCTG for masked discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces.

Yinuo Zhang, Guangshun Wei, Yuanfeng Zhou et al.

High frame-rate RGB-D videos are crucial for a variety of downstream tasks, including motion analysis, dynamic scene understanding, and 3D reconstruction. However, due to hardware and sensing constraints, practical RGB-D cameras are typically limited to low frame rates, making it difficult to capture rapid scene dynamics. Existing video interpolation methods have achieved strong performance on RGB data, but they are not readily applicable to RGB-D scenarios, where they often yield blurry boundaries, visible artifacts, and degraded geometric consistency. Furthermore, motion estimation from only two boundary frames is inherently under-constrained in complex dynamic scenes. Event cameras, by contrast, provide asynchronous measurements with ultra-high temporal resolution, offering dense motion cues. In this paper, we propose a unified multimodal framework for RGB-D video interpolation that jointly exploits RGB appearance, depth geometry, and event-based temporal cues. Specifically, it first extracts and fuses RGB, depth and event cues, then estimates bidirectional flow with motion basis refinement for RGB and Z-axial refinement for depth, and finally synthesizes the target RGB-D frame via bidirectional warping and soft blending. In addition, we construct a new RGB-D-Event dataset to alleviate the scarcity of tri-modal training data. Extensive experiments on a public benchmark and the proposed dataset demonstrate that our method achieves superior photometric fidelity for RGB interpolation and stronger geometric accuracy for depth interpolation than existing approaches.

Sophia Tang, Yinuo Zhang, Alexander Tong et al.

Predicting the intermediate trajectories between an initial and target distribution is a central problem in generative modeling. Existing approaches, such as flow matching and Schrödinger Bridge Matching, effectively learn mappings between two distributions by modeling a single stochastic path. However, these methods are inherently limited to unimodal transitions and cannot capture branched or divergent evolution from a common origin to multiple distinct outcomes. To address this, we introduce Branched Schrödinger Bridge Matching (BranchSBM), a novel framework that learns branched Schrödinger bridges. BranchSBM parameterizes multiple time-dependent velocity fields and growth processes, enabling the representation of population-level divergence into multiple terminal distributions. We show that BranchSBM is not only more expressive but also essential for tasks involving multi-path surface navigation, modeling cell fate bifurcations from homogeneous progenitor states, and simulating diverging cellular responses to perturbations.