Tianci Liu

Tianyang Xu, Tianci Liu, Niraj Rayamajhi et al.

Gene regulatory networks (GRNs) capture transcription factor-target interactions and are central to understanding cell-state regulation and disease. Reconstructing GRNs from paired single-cell transcriptomic and chromatin accessibility data is promising but challenging: scATAC is extremely sparse, and most methods rely on fixed peak-to-gene links and weak supervision. We present EpiAwareNet, a prior-guided multi-omic Transformer framework that reconstructs GRNs from paired single-cell data using only lightweight biological priors. In Stage 1, EpiAwareNet learns joint gene-peak representations with a gene-peak cross-attention module, enabling data-driven, gene-specific aggregation of accessibility signals rather than hard-coded peak-to-gene assignments. In Stage 2, EpiAwareNet incorporates a bulk-derived GRN prior as noisy positive edges to provide weak supervision under label scarcity, refining regulatory scores while remaining robust to prior noise. In our experiments, EpiAwareNet improves GRN reconstruction over representative single- and multi-omic baselines and yields GRNs with greater biological plausibility, such as improved recovery of known regulatory interactions, suggesting that lightweight biological priors from bulk data can effectively guide single-cell GRN inference when combined with adaptive cross-modal representation learning. Code and data will be available at https://github.com/tianyang-x/EpiAwareNet_pub.

Haoxiang Jiang, Zihan Dong, Tianci Liu et al.

Pointwise reward modeling offers critical signals for LLM post-training, yet struggles with absolute scoring in subjective, non-verifiable settings. Rubric-based methods address this by decomposing evaluation into explicit criteria, but existing approaches typically depend on frontier LLMs and suffer from ties caused by hard Boolean aggregation. We present RUBRIC-ARROW, an alternating framework that jointly trains a rubric generator and a rubric-conditioned judge, with its RL stage using only pairwise preference data. Our method couples a probability-based scoring rule that reduces ties with phase-specific preference-based rewards and an alternating GRPO scheme that together train the pointwise evaluator. Extensive experiments show that RUBRIC-ARROW achieves competitive reward-modeling accuracy and yields consistent gains for downstream policy post-training.

Zeyu Zhou, Tianci Liu, Ruqi Bai et al.

In high-stake domains such as healthcare and hiring, the role of machine learning (ML) in decision-making raises significant fairness concerns. This work focuses on Counterfactual Fairness (CF), which posits that an ML model's outcome on any individual should remain unchanged if they had belonged to a different demographic group. Previous works have proposed methods that guarantee CF. Notwithstanding, their effects on the model's predictive performance remains largely unclear. To fill in this gap, we provide a theoretical study on the inherent trade-off between CF and predictive performance in a model-agnostic manner. We first propose a simple but effective method to cast an optimal but potentially unfair predictor into a fair one without losing the optimality. By analyzing its excess risk in order to achieve CF, we quantify this inherent trade-off. Further analysis on our method's performance with access to only incomplete causal knowledge is also conducted. Built upon it, we propose a performant algorithm that can be applied in such scenarios. Experiments on both synthetic and semi-synthetic datasets demonstrate the validity of our analysis and methods.

Tianci Liu, Tong Yang, Quan Zhang et al.

Incorporating a deep generative model as the prior distribution in inverse problems has established substantial success in reconstructing images from corrupted observations. Notwithstanding, the existing optimization approaches use gradient descent largely without adapting to the non-convex nature of the problem and can be sensitive to initial values, impeding further performance improvement. In this paper, we propose an efficient amortized optimization scheme for inverse problems with a deep generative prior. Specifically, the optimization task with high degrees of difficulty is decomposed into optimizing a sequence of much easier ones. We provide a theoretical guarantee of the proposed algorithm and empirically validate it on different inverse problems. As a result, our approach outperforms baseline methods qualitatively and quantitatively by a large margin.

Feijie Wu, Xingchen Wang, Yaqing Wang et al.

In federated learning (FL), accommodating clients' varied computational capacities poses a challenge, often limiting the participation of those with constrained resources in global model training. To address this issue, the concept of model heterogeneity through submodel extraction has emerged, offering a tailored solution that aligns the model's complexity with each client's computational capacity. In this work, we propose Federated Importance-Aware Submodel Extraction (FIARSE), a novel approach that dynamically adjusts submodels based on the importance of model parameters, thereby overcoming the limitations of previous static and dynamic submodel extraction methods. Compared to existing works, the proposed method offers a theoretical foundation for the submodel extraction and eliminates the need for additional information beyond the model parameters themselves to determine parameter importance, significantly reducing the overhead on clients. Extensive experiments are conducted on various datasets to showcase the superior performance of the proposed FIARSE.

Daiwei Zhang, Tianci Liu, Jian Kang

Deep neural network (DNN) models have achieved state-of-the-art predictive accuracy in a wide range of supervised learning applications. However, accurately quantifying the uncertainty in DNN predictions remains a challenging task. For continuous outcome variables, an even more difficult problem is to estimate the predictive density function, which not only provides a natural quantification of the predictive uncertainty, but also fully captures the random variation in the outcome. In this work, we propose the Bayesian Deep Noise Neural Network (B-DeepNoise), which generalizes standard Bayesian DNNs by extending the random noise variable from the output layer to all hidden layers. The latent random noise equips B-DeepNoise with the flexibility to approximate highly complex predictive distributions and accurately quantify predictive uncertainty. For posterior computation, the unique structure of B-DeepNoise leads to a closed-form Gibbs sampling algorithm that iteratively simulates from the posterior full conditional distributions of the model parameters, circumventing computationally intensive Metropolis-Hastings methods. A theoretical analysis of B-DeepNoise establishes a recursive representation of the predictive distribution and decomposes the predictive variance with respect to the latent parameters. We evaluate B-DeepNoise against existing methods on benchmark regression datasets, demonstrating its superior performance in terms of prediction accuracy, uncertainty quantification accuracy, and uncertainty quantification efficiency. To illustrate our method's usefulness in scientific studies, we apply B-DeepNoise to predict general intelligence from neuroimaging features in the Adolescent Brain Cognitive Development (ABCD) project.

Tianci Liu, Haoyu Wang, Yaqing Wang et al.

Recent years have witnessed increasing concerns towards unfair decisions made by machine learning algorithms. To improve fairness in model decisions, various fairness notions have been proposed and many fairness-aware methods are developed. However, most of existing definitions and methods focus only on single-label classification. Fairness for multi-label classification, where each instance is associated with more than one labels, is still yet to establish. To fill this gap, we study fairness-aware multi-label classification in this paper. We start by extending Demographic Parity (DP) and Equalized Opportunity (EOp), two popular fairness notions, to multi-label classification scenarios. Through a systematic study, we show that on multi-label data, because of unevenly distributed labels, EOp usually fails to construct a reliable estimate on labels with few instances. We then propose a new framework named Similarity $s$-induced Fairness ($s_γ$-SimFair). This new framework utilizes data that have similar labels when estimating fairness on a particular label group for better stability, and can unify DP and EOp. Theoretical analysis and experimental results on real-world datasets together demonstrate the advantage of over existing methods $s_γ$-SimFair on multi-label classification tasks.

Tianci Liu, Haoyu Wang, Feijie Wu et al.

Fair machine learning seeks to mitigate model prediction bias against certain demographic subgroups such as elder and female. Recently, fair representation learning (FRL) trained by deep neural networks has demonstrated superior performance, whereby representations containing no demographic information are inferred from the data and then used as the input to classification or other downstream tasks. Despite the development of FRL methods, their vulnerability under data poisoning attack, a popular protocol to benchmark model robustness under adversarial scenarios, is under-explored. Data poisoning attacks have been developed for classical fair machine learning methods which incorporate fairness constraints into shallow-model classifiers. Nonetheless, these attacks fall short in FRL due to notably different fairness goals and model architectures. This work proposes the first data poisoning framework attacking FRL. We induce the model to output unfair representations that contain as much demographic information as possible by injecting carefully crafted poisoning samples into the training data. This attack entails a prohibitive bilevel optimization, wherefore an effective approximated solution is proposed. A theoretical analysis on the needed number of poisoning samples is derived and sheds light on defending against the attack. Experiments on benchmark fairness datasets and state-of-the-art fair representation learning models demonstrate the superiority of our attack.

Ran Xu, Tianci Liu, Zihan Dong et al.

Standard reward models typically predict scalar scores that fail to capture the multifaceted nature of response quality in non-verifiable domains, such as creative writing or open-ended instruction following. To address this limitation, we propose Rubric-ARM, a framework that jointly optimizes a rubric generator and a judge using reinforcement learning from preference feedback. Unlike existing methods that rely on static rubrics or disjoint training pipelines, our approach treats rubric generation as a latent action learned to maximize judgment accuracy. We introduce an alternating optimization strategy to mitigate the non-stationarity of simultaneous updates, providing theoretical analysis that demonstrates how this schedule reduces gradient variance during training. Extensive experiments show that Rubric-ARM achieves state-of-the-art performance among baselines on multiple benchmarks and significantly improves downstream policy alignment in both offline and online reinforcement learning settings.

Sunbowen Lee, Junting Zhou, Chang Ao et al.

Model distillation is a fundamental technique in building large language models (LLMs), transferring knowledge from a teacher model to a student model. However, distillation can lead to model homogenization, reducing diversity among models and impairing their ability to robustly handle complex or novel tasks. These limitations underscore the need to systematically quantify the distillation process and its impact. In this work, we propose a framework to evaluate and quantify model distillation. Our method addresses two key aspects: (1) Identifying identity cognition contradictions to assess discrepancies in how models perceive and represent identity-related information, and (2) Analyzing multi-granularity response similarities across models to measure the extent of homogenization. Experimental results demonstrate two key insights: (1) Well-known closed-source and open-source LLMs usually exhibit high distillation degrees, except for Claude, Doubao, and Gemini. (2) Base LLMs show higher distillation degrees compared to aligned LLMs. By offering a systematic approach to improve the transparency of LLM data distillation, we call for LLMs with more independent development and more transparent technical reports to improve LLMs' robustness and safety. The code and data are available under https://github.com/Aegis1863/LLMs-Distillation-Quantification.

David Ma, Huaqing Yuan, Xingjian Wang et al.

Although long-video understanding demands that models capture hierarchical temporal information -- from clip (seconds) and shot (tens of seconds) to event (minutes) and story (hours) -- existing benchmarks either neglect this multi-scale design or scatter scale-specific questions across different videos, preventing direct comparison of model performance across timescales on the same content. To address this, we introduce ScaleLong, the first benchmark to disentangle these factors by embedding questions targeting four hierarchical timescales -- clip (seconds), shot (tens of seconds), event (minutes), and story (hours) -- all within the same video content. This within-content multi-timescale questioning design enables direct comparison of model performance across timescales on identical videos. ScaleLong features 269 long videos (avg.\ 86\,min) from 5 main categories and 36 sub-categories, with 4--8 carefully designed questions, including at least one question for each timescale. Evaluating 23 MLLMs reveals a U-shaped performance curve, with higher accuracy at the shortest and longest timescales and a dip at intermediate levels. Furthermore, ablation studies show that increased visual token capacity consistently enhances reasoning across all timescales. ScaleLong offers a fine-grained, multi-timescale benchmark for advancing MLLM capabilities in long-video understanding. The code and dataset are available https://github.com/multimodal-art-projection/ScaleLong.

Tianchun Li, Haochen Liu, Vishwa Pardeshi et al.

Small language models (SLMs) are promising for real-world deployment due to their efficiency and low operational cost. However, their limited capacity struggles with high-stakes legal reasoning tasks that require coherent statute interpretation and logically consistent deduction. Furthermore, training SLMs for such tasks demands high-quality, concise reasoning trajectories, which are prohibitively expensive to manually collect and difficult to curate via standard rejection sampling, lacking granularity beyond final verdicts. To address these challenges, we propose {LegalDrill}, a diagnosis-driven synthesis framework that extracts and iteratively refines reasoning trajectories from a capable teacher via fine-grained prompting, then a self-reflective verification is employed to adaptively select the most effective data for the SLM student. The resulting data empower SLM training through supervised fine-tuning and direct preference optimization. Extensive experiments on several legal benchmarks demonstrate that {LegalDrill} significantly bolsters the legal reasoning capabilities of representative SLMs while bypassing the need for scarce expert annotations, paving a scalable path toward practical legal reasoning systems.

Tianci Liu, Ruirui Li, Yunzhe Qi et al.

Large language models (LLMs) have achieved remarkable performance on various natural language tasks. However, they are trained on static corpora and their knowledge can become outdated quickly in the fast-changing world. This motivates the development of knowledge editing methods designed to update certain knowledge in LLMs without changing unrelated others. To make selective edits, previous efforts often sought to update a small amount of parameters in some specific layer(s) of a LLM. Nonetheless, in challenging scenarios, they still fall short in making successful edits while preserving knowledge irrelevant to the updates simultaneously, resulting in a notable editing-locality trade-off. In this work, we question if the trade-offs are caused by the fact that parameter-based updates have a global effect, i.e., edited parameters affect all inputs indiscriminately. In light of this, we explore the feasibility of representation fine-tuning, which applied some linear update to a few representations in a learned subspace, for knowledge editing. While being effective to enhance an LLM's general ability as demonstrated in the previous work, we theoretically show that this linear update imposes a tension in editing-locality trade-off. Subsequently, BaFT is proposed to break the linearity. BaFT computes a weight for each basis that spans a dimension of the subspace based on the input representation. This input-dependent weighting mechanism allows BaFT to manage different types of knowledge in an adaptive way, thereby achieving a better editing-locality trade-off. Experiments on three LLMs with five editing benchmarks in diverse scenarios show the superiority of our method.

Tianci Liu, Haoxiang Jiang, Tianze Wang et al.

Large language models (LLMs) have achieved impressive performance but face high computational costs and latency, limiting their deployment in resource-constrained settings. In contrast, small-scale LLMs (SLMs) are more efficient yet struggle to capture evolving real-world knowledge. Retrieval-augmented generation (RAG) helps by integrating external knowledge, but imperfect retrieval can introduce distracting noise that misleads SLMs. We propose RoseRAG, a robust RAG framework for SLMs via Margin-aware Preference Optimization. RoseRAG employs multi-turn prompting for detailed reasoning, rejection sampling for high-quality explanations, and contrastive preference selection to refine responses by maximizing the likelihood gap between preferred and non-preferred outputs. By integrating these components into a margin-aware optimization process, RoseRAG robustly enhances the accuracy and reliability of SLMs for RAG applications. Extensive experiments on three open-domain question answering benchmarks indicate that our innovative RoseRAG surpasses state-of-the-art baselines significantly.

Tianci Liu, Ruirui Li, Zihan Dong et al.

Large language models (LLMs) have achieved remarkable performance on various natural language tasks. However, they are trained on static corpora and their knowledge can become outdated quickly in the fast-changing world. This motivates the development of knowledge editing (KE) to update specific knowledge in LLMs without changing unrelated others or compromising their pre-trained capabilities. Previous efforts sought to update a small amount of parameters of a LLM and proved effective for making selective updates. Nonetheless, the edited LLM often exhibits degraded ability to reason about the new knowledge. In this work, we identify a key issue: heterogeneous token overfitting (HTO), where the LLM overfits different tokens in the provided knowledge at varying rates. To tackle this, we propose OVERTONE, a token-level smoothing method that mitigates HTO by adaptively refining the target distribution. Theoretically, OVERTONE offers better parameter updates with negligible computation overhead. It also induces an implicit DPO but does not require preference data pairs. Extensive experiments across four editing methods, two LLMs, and diverse scenarios demonstrate the effectiveness and versatility of our method.

Tianci Liu, Ran Xu, Tony Yu et al.

Reward modeling lies at the core of reinforcement learning from human feedback (RLHF), yet most existing reward models rely on scalar or pairwise judgments that fail to capture the multifaceted nature of human preferences. Recent studies have explored rubrics-as-rewards (RaR) that uses structured natural language criteria that capture multiple dimensions of response quality. However, producing rubrics that are both reliable and scalable remains a key challenge. In this work, we introduce OpenRubrics, a diverse, large-scale collection of (prompt, rubric) pairs for training rubric-generation and rubric-based reward models. To elicit discriminative and comprehensive evaluation signals, we introduce Contrastive Rubric Generation (CRG), which derives both hard rules (explicit constraints) and principles (implicit qualities) by contrasting preferred and rejected responses. We further improve reliability by enforcing preference-label consistency via rejection sampling to remove noisy rubrics. Across multiple reward-modeling benchmarks, our rubric-based reward model, Rubric-RM, surpasses strong size-matched baselines by 6.8%. These gains transfer to policy models on instruction-following and biomedical benchmarks. Our results show that rubrics provide scalable alignment signals that narrow the gap between costly human evaluation and automated reward modeling, enabling a new principle-driven paradigm for LLM alignment.

Tianchun Li, Tianci Liu, Xingchen Wang et al.

Large language models (LLMs) have achieved promising results in tabular data generation. However, inherent historical biases in tabular datasets often cause LLMs to exacerbate fairness issues, particularly when multiple advantaged and protected features are involved. In this work, we introduce a universal debiasing framework that minimizes group-level dependencies by simultaneously reducing the mutual information between advantaged and protected attributes. By leveraging the autoregressive structure and analytic sampling distributions of LLM-based tabular data generators, our approach efficiently computes mutual information, reducing the need for cumbersome numerical estimations. Building on this foundation, we propose two complementary methods: a direct preference optimization (DPO)-based strategy, namely UDF-DPO, that integrates seamlessly with existing models, and a targeted debiasing technique, namely UDF-MIX, that achieves debiasing without tuning the parameters of LLMs. Extensive experiments demonstrate that our framework effectively balances fairness and utility, offering a scalable and practical solution for debiasing in high-stakes applications.

Tianci Liu, Tong Yang, Quan Zhang et al.

As AI advances, copyrighted content faces growing risk of unauthorized use, whether through model training or direct misuse. Building upon invisible adversarial perturbation, recent works developed copyright protections against specific AI techniques such as unauthorized personalization through DreamBooth that are misused. However, these methods offer only short-term security, as they require retraining whenever the underlying model architectures change. To establish long-term protection aiming at better robustness, we go beyond invisible perturbation, and propose a universal approach that embeds \textit{visible} watermarks that are \textit{hard-to-remove} into images. Grounded in a new probabilistic and inverse problem-based formulation, our framework maximizes the discrepancy between the \textit{optimal} reconstruction and the original content. We develop an effective and efficient approximation algorithm to circumvent a intractable bi-level optimization. Experimental results demonstrate superiority of our approach across diverse scenarios.

Haoyu Wang, Tianci Liu, Ruirui Li et al.

Pre-trained language models, trained on large-scale corpora, demonstrate strong generalizability across various NLP tasks. Fine-tuning these models for specific tasks typically involves updating all parameters, which is resource-intensive. Parameter-efficient fine-tuning (PEFT) methods, such as the popular LoRA family, introduce low-rank matrices to learn only a few parameters efficiently. However, during inference, the product of these matrices updates all pre-trained parameters, complicating tasks like knowledge editing that require selective updates. We propose a novel PEFT method, which conducts \textbf{r}ow and c\textbf{o}lumn-wise spar\textbf{se} \textbf{lo}w-\textbf{r}ank \textbf{a}daptation (RoseLoRA), to address this challenge. RoseLoRA identifies and updates only the most important parameters for a specific task, maintaining efficiency while preserving other model knowledge. By adding a sparsity constraint on the product of low-rank matrices and converting it to row and column-wise sparsity, we ensure efficient and precise model updates. Our theoretical analysis guarantees the lower bound of the sparsity with respective to the matrix product. Extensive experiments on five benchmarks across twenty datasets demonstrate that RoseLoRA outperforms baselines in both general fine-tuning and knowledge editing tasks.

Tianci Liu, Haoyu Wang, Shiyang Wang et al.

Large language models (LLMs) have achieved impressive performance on various natural language generation tasks. Nonetheless, they suffer from generating negative and harmful contents that are biased against certain demographic groups (e.g., female), raising severe fairness concerns. As remedies, prior works intervened the generation by removing attitude or demographic information, inevitably degrading the generation quality and resulting in notable \textit{fairness-fluency} trade-offs. However, it is still under-explored to what extent the fluency \textit{has to} be affected in order to achieve a desired level of fairness. In this work, we conduct the first formal study from an information-theoretic perspective. We show that previous approaches are excessive for debiasing and propose LIDAO, a general framework to debias a (L)LM at a better fluency provably. We further robustify LIDAO in adversarial scenarios, where a carefully-crafted prompt may stimulate LLMs exhibiting instruction-following abilities to generate texts with fairness issue appears only when the prompt is also taken into account. Experiments on three LMs ranging from 0.7B to 7B parameters demonstrate the superiority of our method.

Tianci Liu, Jeffrey Regier

Generative adversarial networks (GANs) and normalizing flows are both approaches to density estimation that use deep neural networks to transform samples from an uninformative prior distribution to an approximation of the data distribution. There is great interest in both for general-purpose statistical modeling, but the two approaches have seldom been compared to each other for modeling non-image data. The difficulty of computing likelihoods with GANs, which are implicit models, makes conducting such a comparison challenging. We work around this difficulty by considering several low-dimensional synthetic datasets. An extensive grid search over GAN architectures, hyperparameters, and training procedures suggests that no GAN is capable of modeling our simple low-dimensional data well, a task we view as a prerequisite for an approach to be considered suitable for general-purpose statistical modeling. Several normalizing flows, on the other hand, excelled at these tasks, even substantially outperforming WGAN in terms of Wasserstein distance -- the metric that WGAN alone targets. Scientists and other practitioners should be wary of relying on WGAN for applications that require accurate density estimation.

Tianci Liu, Zelin Shi, Yunpeng Liu

This paper proposes a generalized framework with joint normalization which learns lower-dimensional subspaces with maximum discriminative power by making use of the Riemannian geometry. In particular, we model the similarity/dissimilarity between subspaces using various metrics defined on Grassmannian and formulate dimen-sionality reduction as a non-linear constraint optimization problem considering the orthogonalization. To obtain the linear mapping, we derive the components required to per-form Riemannian optimization (e.g., Riemannian conju-gate gradient) from the original Grassmannian through an orthonormal projection. We respect the Riemannian ge-ometry of the Grassmann manifold and search for this projection directly from one Grassmann manifold to an-other face-to-face without any additional transformations. In this natural geometry-aware way, any metric on the Grassmann manifold can be resided in our model theoreti-cally. We have combined five metrics with our model and the learning process can be treated as an unconstrained optimization problem on a Grassmann manifold. Exper-iments on several datasets demonstrate that our approach leads to a significant accuracy gain over state-of-the-art methods.