Yuchen Zhu

Chengyue Huang, Yuchen Zhu, Sichen Zhu et al.

Vision-language models (VLMs) are widely assumed to exhibit in-context learning (ICL), a property similar to that of their language-only counterparts. While recent work suggests VLMs can perform multimodal ICL (MM-ICL), studies show they often rely on shallow heuristics -- such as copying or majority voting -- rather than true task understanding. We revisit this assumption by evaluating VLMs under distribution shifts, where support examples come from a dataset different from the query. Surprisingly, performance often degrades with more demonstrations, and models tend to copy answers rather than learn from them. To investigate further, we propose a new MM-ICL with Reasoning pipeline that augments each demonstration with a generated rationale alongside the answer. We conduct extensive and comprehensive experiments on both perception- and reasoning-required datasets with open-source VLMs ranging from 3B to 72B and proprietary models such as Gemini 2.0. We conduct controlled studies varying shot count, retrieval method, rationale quality, and distribution. Our results show limited performance sensitivity across these factors, suggesting that current VLMs do not effectively utilize demonstration-level information as intended in MM-ICL.

Yuchen Zhu, Wei Guo, Jaemoo Choi et al.

Diffusion large language models (dLLMs) are promising alternatives to autoregressive large language models (AR-LLMs), as they potentially allow higher inference throughput. Reinforcement learning (RL) is a crucial component for dLLMs to achieve comparable performance with AR-LLMs on important tasks, such as reasoning. However, RL algorithms that are well-suited for dLLMs' unique characteristics have yet to be developed. This paper proposes Distribution Matching Policy Optimization (DMPO), a principled and theoretically grounded RL fine-tuning method specifically designed to enhance the reasoning capabilities of dLLMs by matching the dLLM policy distribution to the optimal, reward-tilted one through cross-entropy optimization. We identify a key challenge in the implementation with a small training batch size and propose several effective solutions through a novel weight baseline subtraction technique. DMPO exhibits superior performance on multiple reasoning benchmarks without supervised fine-tuning, with an accuracy improvement of up to $42.9\%$ over previously SOTA baselines and $55.8\%$ over the base model, underscoring the effectiveness of the distribution matching framework. Our code is available at https://github.com/yuchen-zhu-zyc/DMPO.

Sichen Zhu, Yuchen Zhu, Molei Tao et al.

Spatial Transcriptomics (ST) allows a high-resolution measurement of RNA sequence abundance by systematically connecting cell morphology depicted in Hematoxylin and Eosin (H&E) stained histology images to spatially resolved gene expressions. ST is a time-consuming, expensive yet powerful experimental technique that provides new opportunities to understand cancer mechanisms at a fine-grained molecular level, which is critical for uncovering new approaches for disease diagnosis and treatments. Here, we present $\textbf{Stem}$ ($\textbf{S}$pa$\textbf{T}$ially resolved gene $\textbf{E}$xpression inference with diffusion $\textbf{M}$odel), a novel computational tool that leverages a conditional diffusion generative model to enable in silico gene expression inference from H&E stained images. Through better capturing the inherent stochasticity and heterogeneity in ST data, $\textbf{Stem}$ achieves state-of-the-art performance on spatial gene expression prediction and generates biologically meaningful gene profiles for new H&E stained images at test time. We evaluate the proposed algorithm on datasets with various tissue sources and sequencing platforms, where it demonstrates clear improvement over existing approaches. $\textbf{Stem}$ generates high-fidelity gene expression predictions that share similar gene variation levels as ground truth data, suggesting that our method preserves the underlying biological heterogeneity. Our proposed pipeline opens up the possibility of analyzing existing, easily accessible H&E stained histology images from a genomics point of view without physically performing gene expression profiling and empowers potential biological discovery from H&E stained histology images.

Yuchen Zhu, Tianrong Chen, Evangelos A. Theodorou et al.

This article considers the generative modeling of the (mixed) states of quantum systems, and an approach based on denoising diffusion model is proposed. The key contribution is an algorithmic innovation that respects the physical nature of quantum states. More precisely, the commonly used density matrix representation of mixed-state has to be complex-valued Hermitian, positive semi-definite, and trace one. Generic diffusion models, or other generative methods, may not be able to generate data that strictly satisfy these structural constraints, even if all training data do. To develop a machine learning algorithm that has physics hard-wired in, we leverage mirror diffusion and borrow the physical notion of von Neumann entropy to design a new map, for enabling strict structure-preserving generation. Both unconditional generation and conditional generation via classifier-free guidance are experimentally demonstrated efficacious, the latter enabling the design of new quantum states when generated on unseen labels.

Kevin Rojas, Yuchen Zhu, Sichen Zhu et al.

Diffusion models have demonstrated remarkable performance in generating unimodal data across various tasks, including image, video, and text generation. On the contrary, the joint generation of multimodal data through diffusion models is still in the early stages of exploration. Existing approaches heavily rely on external preprocessing protocols, such as tokenizers and variational autoencoders, to harmonize varied data representations into a unified, unimodal format. This process heavily demands the high accuracy of encoders and decoders, which can be problematic for applications with limited data. To lift this restriction, we propose a novel framework for building multimodal diffusion models on arbitrary state spaces, enabling native generation of coupled data across different modalities. By introducing an innovative decoupled noise schedule for each modality, we enable both unconditional and modality-conditioned generation within a single model simultaneously. We empirically validate our approach for text-image generation and mixed-type tabular data synthesis, demonstrating that it achieves competitive performance.

Yuchen Zhu, Molei Tao, Yuebo Jin et al.

In quantum many-body systems, measurements can induce qualitative new features, but their simulation is hindered by the exponential complexity involved in sampling the measurement results. We propose to use machine learning to assist the simulation of measurement-induced quantum phenomena. In particular, we focus on the measurement-altered quantum criticality protocol and generate local reduced density matrices of the critical chain given random measurement results. Such generation is enabled by a physics-preserving conditional diffusion generative model, which learns an observation-indexed probability distribution of an ensemble of quantum states, and then samples from that distribution given an observation.