arXiv subjects

Han Liu

Publications and source records attributed to Han Liu.

At least 127 records · Page 7Linked to original sources

arXiv2025

Transformers Simulate MLE for Sequence Generation in Bayesian Networks

Transformers have achieved significant success in various fields, notably excelling in tasks involving sequential data like natural language processing. Despite these achievements, the theoretical understanding of transformers' capabilities remains limited. In this paper, we investigate the theoretical capabilities of transformers to autoregressively generate sequences in Bayesian networks based on in-context maximum likelihood estimation (MLE). Specifically, we consider a setting where a context is formed by a set of independent sequences generated according to a Bayesian network. We demonstrate that there exists a simple transformer model that can (i) estimate the conditional probabilities of the Bayesian network according to the context, and (ii) autoregressively generate a new sample according to the Bayesian network with estimated conditional probabilities. We further demonstrate in extensive experiments that such a transformer does not only exist in theory, but can also be effectively obtained through training. Our analysis highlights the potential of transformers to learn complex probabilistic models and contributes to a better understanding of large language models as a powerful class of sequence generators.

stat.ML↗

arXiv2025

EANS: Reducing Energy Consumption for UAV with an Environmental Adaptive Navigation Strategy

Unmanned Aerial Vehicles (UAVS) are limited by the onboard energy. Refinement of the navigation strategy directly affects both the flight velocity and the trajectory based on the adjustment of key parameters in the UAVS pipeline, thus reducing energy consumption. However, existing techniques tend to adopt static and conservative strategies in dynamic scenarios, leading to inefficient energy reduction. Dynamically adjusting the navigation strategy requires overcoming the challenges including the task pipeline interdependencies, the environmental-strategy correlations, and the selecting parameters. To solve the aforementioned problems, this paper proposes a method to dynamically adjust the navigation strategy of the UAVS by analyzing its dynamic characteristics and the temporal characteristics of the autonomous navigation pipeline, thereby reducing UAVS energy consumption in response to environmental changes. We compare our method with the baseline through hardware-in-the-loop (HIL) simulation and real-world experiments, showing our method 3.2X and 2.6X improvements in mission time, 2.4X and 1.6X improvements in energy, respectively.

cs.RO↗

arXiv2025

Mind the Inconspicuous: Revealing the Hidden Weakness in Aligned LLMs' Refusal Boundaries

Recent advances in Large Language Models (LLMs) have led to impressive alignment where models learn to distinguish harmful from harmless queries through supervised finetuning (SFT) and reinforcement learning from human feedback (RLHF). In this paper, we reveal a subtle yet impactful weakness in these aligned models. We find that simply appending multiple end of sequence (eos) tokens can cause a phenomenon we call context segmentation, which effectively shifts both harmful and benign inputs closer to the refusal boundary in the hidden space. Building on this observation, we propose a straightforward method to BOOST jailbreak attacks by appending eos tokens. Our systematic evaluation shows that this strategy significantly increases the attack success rate across 8 representative jailbreak techniques and 16 open-source LLMs, ranging from 2B to 72B parameters. Moreover, we develop a novel probing mechanism for commercial APIs and discover that major providers such as OpenAI, Anthropic, and Qwen do not filter eos tokens, making them similarly vulnerable. These findings highlight a hidden yet critical blind spot in existing alignment and content filtering approaches. We call for heightened attention to eos tokens' unintended influence on model behaviors, particularly in production systems. Our work not only calls for an input-filtering based defense, but also points to new defenses that make refusal boundaries more robust and generalizable, as well as fundamental alignment techniques that can defend against context segmentation attacks.

cs.AI↗

arXiv2025

VIViT: Variable-Input Vision Transformer Framework for 3D MR Image Segmentation

Self-supervised pretrain techniques have been widely used to improve the downstream tasks' performance. However, real-world magnetic resonance (MR) studies usually consist of different sets of contrasts due to different acquisition protocols, which poses challenges for the current deep learning methods on large-scale pretrain and different downstream tasks with different input requirements, since these methods typically require a fixed set of input modalities or, contrasts. To address this challenge, we propose variable-input ViT (VIViT), a transformer-based framework designed for self-supervised pretraining and segmentation finetuning for variable contrasts in each study. With this ability, our approach can maximize the data availability in pretrain, and can transfer the learned knowledge from pretrain to downstream tasks despite variations in input requirements. We validate our method on brain infarct and brain tumor segmentation, where our method outperforms current CNN and ViT-based models with a mean Dice score of 0.624 and 0.883 respectively. These results highlight the efficacy of our design for better adaptability and performance on tasks with real-world heterogeneous MR data.

eess.IV↗

arXiv2025

Cross-Domain Conditional Diffusion Models for Time Series Imputation

Cross-domain time series imputation is an underexplored data-centric research task that presents significant challenges, particularly when the target domain suffers from high missing rates and domain shifts in temporal dynamics. Existing time series imputation approaches primarily focus on the single-domain setting, which cannot effectively adapt to a new domain with domain shifts. Meanwhile, conventional domain adaptation techniques struggle with data incompleteness, as they typically assume the data from both source and target domains are fully observed to enable adaptation. For the problem of cross-domain time series imputation, missing values introduce high uncertainty that hinders distribution alignment, making existing adaptation strategies ineffective. Specifically, our proposed solution tackles this problem from three perspectives: (i) Data: We introduce a frequency-based time series interpolation strategy that integrates shared spectral components from both domains while retaining domain-specific temporal structures, constructing informative priors for imputation. (ii) Model: We design a diffusion-based imputation model that effectively learns domain-shared representations and captures domain-specific temporal dependencies with dedicated denoising networks. (iii) Algorithm: We further propose a cross-domain consistency alignment strategy that selectively regularizes output-level domain discrepancies, enabling effective knowledge transfer while preserving domain-specific characteristics. Extensive experiments on three real-world datasets demonstrate the superiority of our proposed approach. Our code implementation is available here.

cs.LG↗

arXiv2025

Nonparametric Modern Hopfield Models

We present a nonparametric interpretation for deep learning compatible modern Hopfield models and utilize this new perspective to debut efficient variants. Our key contribution stems from interpreting the memory storage and retrieval processes in modern Hopfield models as a nonparametric regression problem subject to a set of query-memory pairs. Interestingly, our framework not only recovers the known results from the original dense modern Hopfield model but also fills the void in the literature regarding efficient modern Hopfield models, by introducing \textit{sparse-structured} modern Hopfield models with sub-quadratic complexity. We establish that this sparse model inherits the appealing theoretical properties of its dense analogue -- connection with transformer attention, fixed point convergence and exponential memory capacity. Additionally, we showcase the versatility of our framework by constructing a family of modern Hopfield models as extensions, including linear, random masked, top-$K$ and positive random feature modern Hopfield models. Empirically, we validate our framework in both synthetic and realistic settings for memory retrieval and learning tasks.

stat.ML↗

arXiv2025

LLM4Vuln: A Unified Evaluation Framework for Decoupling and Enhancing LLMs' Vulnerability Reasoning

Large language models (LLMs) have demonstrated significant potential in various tasks, including those requiring human-level intelligence, such as vulnerability detection. However, recent efforts to use LLMs for vulnerability detection remain preliminary, as they lack a deep understanding of whether a subject LLM's vulnerability reasoning capability stems from the model itself or from external aids such as knowledge retrieval and tooling support. In this paper, we aim to decouple LLMs' vulnerability reasoning from other capabilities, such as vulnerability knowledge adoption, context information retrieval, and advanced prompt schemes. We introduce LLM4Vuln, a unified evaluation framework that separates and assesses LLMs' vulnerability reasoning capabilities and examines improvements when combined with other enhancements. To support this evaluation, we construct UniVul, the first benchmark that provides retrievable knowledge and context-supplementable code across three representative programming languages: Solidity, Java, and C/C++. Using LLM4Vuln and UniVul, we test six representative LLMs (GPT-4.1, Phi-3, Llama-3, o4-mini, DeepSeek-R1, and QwQ-32B) for 147 ground-truth vulnerabilities and 147 non-vulnerable cases in 3,528 controlled scenarios. Our findings reveal the varying impacts of knowledge enhancement, context supplementation, and prompt schemes. We also identify 14 zero-day vulnerabilities in four pilot bug bounty programs, resulting in $3,576 in bounties.

cs.CR↗

arXiv2025

Computational Limits of Low-Rank Adaptation (LoRA) Fine-Tuning for Transformer Models

We study the computational limits of Low-Rank Adaptation (LoRA) for finetuning transformer-based models using fine-grained complexity theory. Our key observation is that the existence of low-rank decompositions within the gradient computation of LoRA adaptation leads to possible algorithmic speedup. This allows us to (i) identify a phase transition behavior of efficiency assuming the Strong Exponential Time Hypothesis (SETH), and (ii) prove the existence of almost linear algorithms by controlling the LoRA update computation term by term. For the former, we identify a sharp transition in the efficiency of all possible rank-$r$ LoRA update algorithms for transformers, based on specific norms resulting from the multiplications of the input sequence $X$, pretrained weights ${W^\star}$, and adapter matrices $αB A/r$. Specifically, we derive a shared upper bound threshold for such norms, and show that efficient (sub-quadratic) approximation algorithms of LoRA exist only below this threshold. For the latter, we prove the existence of almost linear approximation algorithms for LoRA adaptation by utilizing the hierarchical low-rank structures of LoRA gradients and approximating the gradients with a series of chained low-rank approximations. To showcase our theory, we consider two practical scenarios: partial (e.g., only $W_V$ and $W_Q$) and full adaptations (e.g., $W_Q$, $W_V$, and $W_K$) of weights in attention heads.

cs.LG↗

arXiv2025

Fundamental Limits of Prompt Tuning Transformers: Universality, Capacity and Efficiency

We investigate the statistical and computational limits of prompt tuning for transformer-based foundation models. Our key contributions are prompt tuning on \emph{single-head} transformers with only a \emph{single} self-attention layer: (i) is universal, and (ii) supports efficient (even almost-linear time) algorithms under the Strong Exponential Time Hypothesis (SETH). Statistically, we prove that prompt tuning on such simplest possible transformers are universal approximators for sequence-to-sequence Lipschitz functions. In addition, we provide an exponential-in-$dL$ and -in-$(1/ε)$ lower bound on the required soft-prompt tokens for prompt tuning to memorize any dataset with 1-layer, 1-head transformers. Computationally, we identify a phase transition in the efficiency of prompt tuning, determined by the norm of the \emph{soft-prompt-induced} keys and queries, and provide an upper bound criterion. Beyond this criterion, no sub-quadratic (efficient) algorithm for prompt tuning exists under SETH. Within this criterion, we showcase our theory by proving the existence of almost-linear time prompt tuning inference algorithms. These fundamental limits provide important necessary conditions for designing expressive and efficient prompt tuning methods for practitioners.

cs.LG↗

arXiv2025

Minimalist Softmax Attention Provably Learns Constrained Boolean Functions

We study the computational limits of learning $k$-bit Boolean functions (specifically, $\mathrm{AND}$, $\mathrm{OR}$, and their noisy variants), using a minimalist single-head softmax-attention mechanism, where $k=Θ(d)$ relevant bits are selected from $d$ inputs. We show that these simple $\mathrm{AND}$ and $\mathrm{OR}$ functions are unsolvable with a single-head softmax-attention mechanism alone. However, with teacher forcing, the same minimalist attention is capable of solving them. These findings offer two key insights: Architecturally, solving these Boolean tasks requires only minimalist attention, without deep Transformer blocks or FFNs. Methodologically, one gradient descent update with supervision suffices and replaces the multi-step Chain-of-Thought (CoT) reasoning scheme of [Kim and Suzuki, ICLR 2025] for solving Boolean problems. Together, the bounds expose a fundamental gap between what this minimal architecture achieves under ideal supervision and what is provably impossible under standard training.

cs.LG↗

arXiv2025

A Survey of Large Language Models for Text-Guided Molecular Discovery: from Molecule Generation to Optimization

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal inputs. To advance the new field of LLM for molecular discovery, this survey provides an up-to-date and forward-looking review of the emerging use of LLMs for two central tasks: molecule generation and molecule optimization. Based on our proposed taxonomy for both problems, we analyze representative techniques in each category, highlighting how LLM capabilities are leveraged across different learning settings. In addition, we include the commonly used datasets and evaluation protocols. We conclude by discussing key challenges and future directions, positioning this survey as a resource for researchers working at the intersection of LLMs and molecular science. A continuously updated reading list is available at https://github.com/REAL-Lab-NU/Awesome-LLM-Centric-Molecular-Discovery.

cs.LG↗

arXiv2025

Statistical Guarantees for Lifelong Reinforcement Learning using PAC-Bayes Theory

Lifelong reinforcement learning (RL) has been developed as a paradigm for extending single-task RL to more realistic, dynamic settings. In lifelong RL, the "life" of an RL agent is modeled as a stream of tasks drawn from a task distribution. We propose EPIC (Empirical PAC-Bayes that Improves Continuously), a novel algorithm designed for lifelong RL using PAC-Bayes theory. EPIC learns a shared policy distribution, referred to as the world policy, which enables rapid adaptation to new tasks while retaining valuable knowledge from previous experiences. Our theoretical analysis establishes a relationship between the algorithm's generalization performance and the number of prior tasks preserved in memory. We also derive the sample complexity of EPIC in terms of RL regret. Extensive experiments on a variety of environments demonstrate that EPIC significantly outperforms existing methods in lifelong RL, offering both theoretical guarantees and practical efficacy through the use of the world policy.

cs.LG↗

arXiv2025

Let's Ask GNN: Empowering Large Language Model for Graph In-Context Learning

Textual Attributed Graphs (TAGs) are crucial for modeling complex real-world systems, yet leveraging large language models (LLMs) for TAGs presents unique challenges due to the gap between sequential text processing and graph-structured data. We introduce AskGNN, a novel approach that bridges this gap by leveraging In-Context Learning (ICL) to integrate graph data and task-specific information into LLMs. AskGNN employs a Graph Neural Network (GNN)-powered structure-enhanced retriever to select labeled nodes across graphs, incorporating complex graph structures and their supervision signals. Our learning-to-retrieve algorithm optimizes the retriever to select example nodes that maximize LLM performance on graph. Experiments across three tasks and seven LLMs demonstrate AskGNN's superior effectiveness in graph task performance, opening new avenues for applying LLMs to graph-structured data without extensive fine-tuning.

cs.LG↗

arXiv2025

Fast and Low-Cost Genomic Foundation Models via Outlier Removal

To address the challenge of scarce computational resources in genomic modeling, we introduce GERM, a genomic foundation model with strong compression performance and fast adaptability. GERM improves upon models like DNABERT-2 by eliminating outliers that hinder low-rank adaptation and post-training quantization, enhancing both efficiency and robustness. We replace the vanilla attention layer with an outlier-free mechanism inspired by associative memory models. By removing outliers during both pre-training and fine-tuning, this approach accelerates adaptation, reduces computational costs, and enhances quantization robustness within acceptable loss margins. Additionally, we propose GERM-T, a strategy that employs small-step continual learning within the outlier-free framework, leveraging original checkpoints to avoid retraining from scratch. Empirically, GERM improves fine-tuning performance by 37.98% and quantization by 64.34% over the baseline model. It also reduces average kurtosis by 92.14% and maximum infinity norm by 82.77%. Compared to leading methods, GERM consistently delivers superior performance, offering a practical solution for genomic modeling in resource-constrained settings. Code is available at https://github.com/MAGICS-LAB/GERM.

cs.LG↗

arXiv2025

SoK: Security and Privacy Risks of Healthcare AI

The integration of artificial intelligence (AI) and machine learning (ML) into healthcare systems holds great promise for enhancing patient care and care delivery efficiency; however, it also exposes sensitive data and system integrity to potential cyberattacks. Current security and privacy (S&P) research on healthcare AI is highly unbalanced in terms of healthcare deployment scenarios and threat models, and has a disconnected focus with the biomedical research community. This hinders a comprehensive understanding of the risks that healthcare AI entails. To address this gap, this paper takes a thorough examination of existing healthcare AI S&P research, providing a unified framework that allows the identification of under-explored areas. Our survey presents a systematic overview of healthcare AI attacks and defenses, and points out challenges and research opportunities for each AI-driven healthcare application domain. Through our experimental analysis of different threat models and feasibility studies on under-explored adversarial attacks, we provide compelling insights into the pressing need for cybersecurity research in the rapidly evolving field of healthcare AI.

cs.CR↗

arXiv2025

Attention Mechanism, Max-Affine Partition, and Universal Approximation

We establish the universal approximation capability of single-layer, single-head self- and cross-attention mechanisms with minimal attached structures. Our key insight is to interpret single-head attention as an input domain-partition mechanism that assigns distinct values to subregions. This allows us to engineer the attention weights such that this assignment imitates the target function. Building on this, we prove that a single self-attention layer, preceded by sum-of-linear transformations, is capable of approximating any continuous function on a compact domain under the $L_\infty$-norm. Furthermore, we extend this construction to approximate any Lebesgue integrable function under $L_p$-norm for $1\leq p <\infty$. Lastly, we also extend our techniques and show that, for the first time, single-head cross-attention achieves the same universal approximation guarantees.

cs.LG↗

arXiv2025

In-Context Deep Learning via Transformer Models

We investigate the transformer's capability to simulate the training process of deep models via in-context learning (ICL), i.e., in-context deep learning. Our key contribution is providing a positive example of using a transformer to train a deep neural network by gradient descent in an implicit fashion via ICL. Specifically, we provide an explicit construction of a $(2N+4)L$-layer transformer capable of simulating $L$ gradient descent steps of an $N$-layer ReLU network through ICL. We also give the theoretical guarantees for the approximation within any given error and the convergence of the ICL gradient descent. Additionally, we extend our analysis to the more practical setting using Softmax-based transformers. We validate our findings on synthetic datasets for 3-layer, 4-layer, and 6-layer neural networks. The results show that ICL performance matches that of direct training.

cs.LG↗

arXiv2025

AdaViT: Adaptive Vision Transformer for Flexible Pretrain and Finetune with Variable 3D Medical Image Modalities

Pretrain techniques, whether supervised or self-supervised, are widely used in deep learning to enhance model performance. In real-world clinical scenarios, different sets of magnetic resonance (MR) contrasts are often acquired for different subjects/cases, creating challenges for deep learning models assuming consistent input modalities among all the cases and between pretrain and finetune. Existing methods struggle to maintain performance when there is an input modality/contrast set mismatch with the pretrained model, often resulting in degraded accuracy. We propose an adaptive Vision Transformer (AdaViT) framework capable of handling variable set of input modalities for each case. We utilize a dynamic tokenizer to encode different input image modalities to tokens and take advantage of the characteristics of the transformer to build attention mechanism across variable length of tokens. Through extensive experiments, we demonstrate that this architecture effectively transfers supervised pretrained models to new datasets with different input modality/contrast sets, resulting in superior performance on zero-shot testing, few-shot finetuning, and backward transferring in brain infarct and brain tumor segmentation tasks. Additionally, for self-supervised pretrain, the proposed method is able to maximize the pretrain data and facilitate transferring to diverse downstream tasks with variable sets of input modalities.

eess.IV↗