Zhuoyan Xu

Zhuoyan Xu, Zhenmei Shi, Yingyu Liang

Large language models (LLMs) have emerged as powerful tools for many AI problems and exhibit remarkable in-context learning (ICL) capabilities. Compositional ability, solving unseen complex tasks that combine two or more simple tasks, is an essential reasoning ability for Artificial General Intelligence. Despite the tremendous success of LLMs, how they approach composite tasks, especially those not encountered during the pretraining phase, remains an open and largely underexplored question. In this study, we delve into the ICL capabilities of LLMs on composite tasks, with only simple tasks as in-context examples. We develop a test suite of composite tasks including linguistic and logical challenges and perform empirical studies across different LLM families. We observe that models exhibit divergent behaviors: (1) For simpler composite tasks that apply distinct mapping mechanisms to different input segments, the models demonstrate decent compositional ability, while scaling up the model enhances this ability; (2) for more complex composite tasks involving reasoning multiple steps, where each step represents one task, models typically underperform, and scaling up generally provides no improvements. We offer theoretical analysis in a simplified setting, explaining that models exhibit compositional capability when the task handles different input parts separately. We believe our work sheds new light on the capabilities of LLMs in solving composite tasks regarding the nature of the tasks and model scale. Our dataset and code are available at {\url{https://github.com/OliverXUZY/LLM_Compose}}.

Zhuoyan Xu, Kris Sankaran

Spatially resolved transcriptomics (ST) measures gene expression along with the spatial coordinates of the measurements. The analysis of ST data involves significant computation complexity. In this work, we propose gene expression dimensionality reduction algorithm that retains spatial structure. We combine the wavelet transformation with matrix factorization to select spatially-varying genes. We extract a low-dimensional representation of these genes. We consider Empirical Bayes setting, imposing regularization through the prior distribution of factor genes. Additionally, We provide visualization of extracted representation genes capturing the global spatial pattern. We illustrate the performance of our methods by spatial structure recovery and gene expression reconstruction in simulation. In real data experiments, our method identifies spatial structure of gene factors and outperforms regular decomposition regarding reconstruction error. We found the connection between the fluctuation of gene patterns and wavelet technique, providing smoother visualization. We develop the package and share the workflow generating reproducible quantitative results and gene visualization. The package is available at https://github.com/OliverXUZY/waveST.

Zhuoyan Xu, Zhenmei Shi, Junyi Wei et al.

Foundation models have emerged as a powerful tool for many AI problems. Despite the tremendous success of foundation models, effective adaptation to new tasks, particularly those with limited labels, remains an open question and lacks theoretical understanding. An emerging solution with recent success in vision and NLP involves finetuning a foundation model on a selection of relevant tasks, before its adaptation to a target task with limited labeled samples. In this paper, we study the theoretical justification of this multitask finetuning approach. Our theoretical analysis reveals that with a diverse set of related tasks, this multitask finetuning leads to reduced error in the target task, in comparison to directly adapting the same pretrained model. We quantify the relationship between finetuning tasks and target tasks by diversity and consistency metrics, and further propose a practical task selection algorithm. We substantiate our theoretical claims with extensive empirical evidence. Further, we present results affirming our task selection algorithm adeptly chooses related finetuning tasks, providing advantages to the model performance on target tasks. We believe our study shed new light on the effective adaptation of foundation models to new tasks that lack abundant labels. Our code is available at https://github.com/OliverXUZY/Foudation-Model_Multitask.

Jiajun Song, Zhuoyan Xu, Yiqiao Zhong

Large language models (LLMs) such as GPT-4 sometimes appear to be creative, solving novel tasks often with a few demonstrations in the prompt. These tasks require the models to generalize on distributions different from those from training data -- which is known as out-of-distribution (OOD) generalization. Despite the tremendous success of LLMs, how they approach OOD generalization remains an open and underexplored question. We examine OOD generalization in settings where instances are generated according to hidden rules, including in-context learning with symbolic reasoning. Models are required to infer the hidden rules behind input prompts without any fine-tuning. We empirically examined the training dynamics of Transformers on a synthetic example and conducted extensive experiments on a variety of pretrained LLMs, focusing on a type of components known as induction heads. We found that OOD generalization and composition are tied together -- models can learn rules by composing two self-attention layers, thereby achieving OOD generalization. Furthermore, a shared latent subspace in the embedding (or feature) space acts as a bridge for composition by aligning early layers and later layers, which we refer to as the common bridge representation hypothesis.

Zidong Liu, Zhuoyan Xu, Zhenmei Shi et al.

Composing basic skills from simple tasks to accomplish composite tasks is crucial for modern intelligent systems. We investigate the in-context composition ability of language models to perform composite tasks that combine basic skills demonstrated in in-context examples. This is more challenging than the standard setting, where skills and their composition can be learned in training. We conduct systematic experiments on various representative open-source language models, utilizing linguistic and logical tasks designed to probe composition abilities. The results reveal that simple task examples can have a surprising negative impact on the performance, because the models generally struggle to recognize and assemble the skills correctly, even with Chain-of-Thought examples. Theoretical analysis further shows that it is crucial to align examples with the corresponding steps in the composition. This inspires a method for the probing tasks, whose improved performance provides positive support for our insights.

Yingyu Liang, Heshan Liu, Zhenmei Shi et al.

The self-attention mechanism is the key to the success of transformers in recent Large Language Models (LLMs). However, the quadratic computational cost $O(n^2)$ in the input sequence length $n$ is a notorious obstacle for further improvement and scalability in longer contexts. In this work, we leverage the convolution-like structure of attention matrices to develop an efficient approximation method for attention computation using convolution matrices. We propose a $\mathsf{conv}$ basis system, analogous to the rank basis, and show that any lower triangular matrix can always be decomposed as a sum of structured convolution matrices in this basis. We then design a fast algorithm to approximate the attention matrix via a sum of such $k$ convolution matrices. This allows us to compute the attention {\it inference} via Fast Fourier Transforms (FFT) in $O(knd \log n)$ time, where $d$ is the hidden dimension, and thus achieve almost linear time $n^{1+o(1)}$ in the practical scenario where $kd = n^{o(1)}$. Furthermore, the attention {\it training forward} and {\it backward gradient} can be computed in $n^{1+o(1)}$ as well. We provide theoretical guarantees on the run time and approximation error and conduct preliminary experiments to evaluate its effectiveness. We hope our new paradigm for accelerating attention computation in transformer models can help their application to longer contexts.

Zhuoyan Xu, Khoi Duc Nguyen, Preeti Mukherjee et al.

Multimodal Large Language Models (MLLMs) have shown impressive capabilities in visual reasoning, yet come with substantial computational cost, limiting their deployment in resource-constrained settings. Despite recent effort on improving the efficiency of MLLMs, prior solutions fall short in responding to varying runtime conditions, in particular changing resource availability (e.g., contention due to the execution of other programs on the device). To bridge this gap, we introduce AdaLLaVA, an adaptive inference framework that learns to dynamically reconfigure operations in an MLLM during inference, accounting for the input data and a latency budget. We conduct extensive experiments across benchmarks involving question-answering, reasoning, and hallucination. Our results show that AdaLLaVA effectively adheres to input latency budget, achieving varying accuracy and latency tradeoffs at runtime. Further, we demonstrate that AdaLLaVA adapts to both input latency and content, can be integrated with token selection for enhanced efficiency, and generalizes across MLLMs. Our project webpage with code release is at https://zhuoyan-xu.github.io/ada-llava/.

Sai Prasanna Teja Reddy Bogireddy, Abrar Majeedi, Viswanatha Reddy Gajjala et al.

Automated question answering (QA) over electronic health records (EHRs) can bridge critical information gaps for clinicians and patients, yet it demands both precise evidence retrieval and faithful answer generation under limited supervision. In this work, we present Neural, the runner-up in the BioNLP 2025 ArchEHR-QA shared task on evidence-grounded clinical QA. Our proposed method decouples the task into (1) sentence-level evidence identification and (2) answer synthesis with explicit citations. For each stage, we automatically explore the prompt space with DSPy's MIPROv2 optimizer, jointly tuning instructions and few-shot demonstrations on the development set. A self-consistency voting scheme further improves evidence recall without sacrificing precision. On the hidden test set, our method attains an overall score of 51.5, placing second stage while outperforming standard zero-shot and few-shot prompting by over 20 and 10 points, respectively. These results indicate that data-driven prompt optimization is a cost-effective alternative to model fine-tuning for high-stakes clinical QA, advancing the reliability of AI assistants in healthcare.