Yinuo Zhang

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.

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.

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.

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.

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.

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

Simulating trajectories of multi-particle systems on complex energy landscapes is a central task in molecular dynamics (MD) and drug discovery, but remains challenging at scale due to computationally expensive and long simulations. Previous approaches leverage techniques such as flow or Schrödinger bridge matching to implicitly learn joint trajectories through data snapshots. However, many systems, including biomolecular systems and heterogeneous cell populations, undergo dynamic interactions that evolve over their trajectory and cannot be captured through static snapshots. To close this gap, we introduce Entangled Schrödinger Bridge Matching (EntangledSBM), a framework that learns the first- and second-order stochastic dynamics of interacting, multi-particle systems where the direction and magnitude of each particle's path depend dynamically on the paths of the other particles. We define the Entangled Schrödinger Bridge (EntangledSB) problem as solving a coupled system of bias forces that entangle particle velocities. We show that our framework accurately simulates heterogeneous cell populations under perturbations and rare transitions in high-dimensional biomolecular systems.

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.

Tong Chen, Yinuo Zhang, Sophia Tang et al.

Designing biological sequences that satisfy multiple, often conflicting, functional and biophysical criteria remains a central challenge in biomolecule engineering. While discrete flow matching models have recently shown promise for efficient sampling in high-dimensional sequence spaces, existing approaches address only single objectives or require continuous embeddings that can distort discrete distributions. We present Multi-Objective-Guided Discrete Flow Matching (MOG-DFM), a general framework to steer any pretrained discrete flow matching generator toward Pareto-efficient trade-offs across multiple scalar objectives. At each sampling step, MOG-DFM computes a hybrid rank-directional score for candidate transitions and applies an adaptive hypercone filter to enforce consistent multi-objective progression. We also trained two unconditional discrete flow matching models, PepDFM for diverse peptide generation and EnhancerDFM for functional enhancer DNA generation, as base generation models for MOG-DFM. We demonstrate MOG-DFM's effectiveness in generating peptide binders optimized across five properties (hemolysis, non-fouling, solubility, half-life, and binding affinity), and in designing DNA sequences with specific enhancer classes and DNA shapes. In total, MOG-DFM proves to be a powerful tool for multi-property-guided biomolecule sequence design.

Sophia Tang, Yinuo Zhang, Alexander Tong et al.

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment.

Tong Chen, Yinuo Zhang, Pranam Chatterjee

Designing sequences that satisfy multiple, often conflicting, objectives is a central challenge in therapeutic and biomolecular engineering. Existing generative frameworks largely operate in continuous spaces with single-objective guidance, while discrete approaches lack guarantees for multi-objective Pareto optimality. We introduce AReUReDi (Annealed Rectified Updates for Refining Discrete Flows), a discrete optimization algorithm with theoretical guarantees of convergence to the Pareto front. Building on Rectified Discrete Flows (ReDi), AReUReDi combines Tchebycheff scalarization, locally balanced proposals, and annealed Metropolis-Hastings updates to bias sampling toward Pareto-optimal states while preserving distributional invariance. Applied to peptide and SMILES sequence design, AReUReDi simultaneously optimizes up to five therapeutic properties (including affinity, solubility, hemolysis, half-life, and non-fouling) and outperforms both evolutionary and diffusion-based baselines. These results establish AReUReDi as a powerful, sequence-based framework for multi-property biomolecule generation.

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.