arXiv subjects

Haoang Chi

Publications and source records attributed to Haoang Chi.

15 recordsLinked to original sources

arXiv2026

Gene Ontology-Guided Hierarchical Spatial Gene Expression Prediction from Histopathology Images

Predicting spatial gene expression from histopathology images enables large-scale transcriptomic profiling without the cost of direct measurement. Existing methods decode the target gene set as a flat, unstructured vector, ignoring the inter-gene dependencies arising from shared biological pathways and regulatory programs. Without explicit structural guidance, models must infer these dependencies entirely from limited paired data, constraining prediction quality. We propose MSGR (Multi-Scale Gene Refiner), which bridges this gap by incorporating the Gene Ontology (GO), a curated functional hierarchy of genes, as an explicit structural prior. MSGR organizes target genes into a four-level GO tree. Its GO-guided decoder then progressively refines predictions from coarse functional domains to fine individual genes via residual corrections under scale-weighted supervision. Operating solely on the gene side, the GO-guided decoder serves as a seamless plug-in replacement that consistently improves existing architectures without requiring any image-side modifications. Extensive experiments on nine datasets from the HEST-1k benchmark provide empirical evidence for two central claims: GO-structured decoding consistently outperforms flat decoding, even against a state-of-the-art generative baseline, and the gain is attributable to biological ontology structure rather than hierarchical decomposition per se, as confirmed by a +0.027 margin over a structurally equivalent random hierarchy.

cs.AI↗

arXiv2026

SpaCellAgent: A Self-Evolving LLM-Based Multi-Agent Framework for Trajectory Analysis

Spatial and Single-cell transcriptomics are transformative in deciphering cellular dynamics. As the fundamental paradigm for reconstructing cell developmental paths, trajectory inference (TI) is critical. However, existing methods require extensive manual intervention and proficiency in heterogeneous tools, posing a significant barrier to efficient TI analysis. To bridge this gap, we propose SpaCellAgent, an autonomous large language model (LLM) multi-agent framework that automates end-to-end spatiotemporal analysis and narrative generation. SpaCellAgent utilizes a multi-agent architecture for strategic workflow planning, a dynamic tool-orchestration engine for adaptive algorithm selection, and a self-evolution module that iteratively refines performance through feedback. We evaluate SpaCellAgent on six heterogeneous datasets encompassing complex temporal developmental trajectories, diverse sequencing platforms, and spatially-resolved tissue architectures. SpaCellAgent consistently demonstrates over 40\% improvement in analytical efficiency while maintaining expert-aligned performance. By converting natural language specifications into optimized analytical workflows and fully automating the pipeline, SpaCellAgent democratizes advanced spatiotemporal modeling and establishes a scalable, agent-driven paradigm for computational biology. The code and materials are available at https://github.com/LittleXH-shw/SpaCellAgent.

cs.AI↗

arXiv2026

Denoised Conformal Alignment for Reliable Selection of Conditional Average Treatment Effect Predictions

In selective deployment, practitioners act only on a model-chosen subset of individuals based on predicted conditional average treatment effects, but marginal conformal guarantees need not control reliability on that selected subset. We study reliable selection for black-box CATE predictors: selecting candidates whose CATE errors are below a tolerance while controlling the false discovery rate (FDR). Since CATE errors are unobservable, we construct doubly robust proxy errors from pseudo-outcomes; however, naive proxies can lose power under heteroskedasticity because variance overwhelms the reliability signal. We propose Denoised Conformal Alignment, which subtracts an estimated conditional variance component and combines conformal calibration with Benjamini--Hochberg selection. Our analysis shows that validity is governed by stability of proxy/oracle threshold labels, rather than pointwise perfection of the variance estimator. Experiments show substantially improved power while maintaining FDR control across challenging settings.

stat.ML↗

arXiv2026

MLUBench: A Benchmark for Lifelong Unlearning Evaluation in MLLMs

Multimodal large language models (MLLMs) are trained on massive multimodal data, making data unlearning increasingly important as data owners may request the removal of specific content. In practice, these requests often arrive sequentially over time, giving rise to the challenging problem of MLLM Lifelong Unlearning. However, most existing benchmarks are limited in scale and scope, failing to capture the complexities of MLLM lifelong unlearning. To fill this gap, we introduce the MLUBench, a large-scale and comprehensive benchmark featuring 127 entities across 9 classes under lifelong unlearning requests. We perform extensive experiments using MLUBench and reveal that existing unlearning methods suffer from severe, cumulative degradation. More critically, we further identify the unique challenge of this problem: unlike in unimodal models, MLLM lifelong unlearning is constrained by the need to preserve multimodal alignment. Continually unlearning from one modality could degrade the entire model. To alleviate this challenge, we propose LUMoE, an effective method. Experiments demonstrate that LUMoE significantly mitigates the degradation problem faced by baselines. The source code and the MLUBench dataset are open-sourced in https://github.com/lihe-maxsize/Lifelong_Unlearning_main.

cs.AI↗

arXiv2026

Shapley-Guided Neural Repair Approach via Derivative-Free Optimization

DNNs are susceptible to defects like backdoors, adversarial attacks, and unfairness, undermining their reliability. Existing approaches mainly involve retraining, optimization, constraint-solving, or search algorithms. However, most methods rely on gradient calculations, restricting applicability to specific activation functions (e.g., ReLU), or use search algorithms with uninterpretable localization and repair. Furthermore, they often lack generalizability across multiple properties. We propose SHARPEN, integrating interpretable fault localization with a derivative-free optimization strategy. First, SHARPEN introduces a Deep SHAP-based localization strategy quantifying each layer's and neuron's marginal contribution to erroneous outputs. Specifically, a hierarchical coarse-to-fine approach reranks layers by aggregated impact, then locates faulty neurons/filters by analyzing activation divergences between property-violating and benign states. Subsequently, SHARPEN incorporates CMA-ES to repair identified neurons. CMA-ES leverages a covariance matrix to capture variable dependencies, enabling gradient-free search and coordinated adjustments across coupled neurons. By combining interpretable localization with evolutionary optimization, SHARPEN enables derivative-free repair across architectures, being less sensitive to gradient anomalies and hyperparameters. We demonstrate SHARPEN's effectiveness on three repair tasks. Balancing property repair and accuracy preservation, it outperforms baselines in backdoor removal (+10.56%), adversarial mitigation (+5.78%), and unfairness repair (+11.82%). Notably, SHARPEN handles diverse tasks, and its modular design is plug-and-play with different derivative-free optimizers, highlighting its flexibility.

cs.SE↗

arXiv2026

Causal Representation Learning with Optimal Compression under Complex Treatments

Estimating Individual Treatment Effects (ITE) in multi-treatment scenarios faces two critical challenges: the Hyperparameter Selection Dilemma for balancing weights and the Curse of Dimensionality in computational scalability. This paper derives a novel multi-treatment generalization bound and proposes a theoretical estimator for the optimal balancing weight $\alpha$, eliminating expensive heuristic tuning. We investigate three balancing strategies: Pairwise, One-vs-All (OVA), and Treatment Aggregation. While OVA achieves superior precision in low-dimensional settings, our proposed Treatment Aggregation ensures both accuracy and O(1) scalability as the treatment space expands. Furthermore, we extend our framework to a generative architecture, Multi-Treatment CausalEGM, which preserves the Wasserstein geodesic structure of the treatment manifold. Experiments on semi-synthetic and image datasets demonstrate that our approach significantly outperforms traditional models in estimation accuracy and efficiency, particularly in large-scale intervention scenarios.

cs.LG↗

arXiv2026

Individualized Causal Effects under Network Interference with Combinatorial Treatments

Modern causal decision-making increasingly demands individualized treatment-effect estimation in networks where interventions are high-dimensional, combinatorial vectors. While network interference, effect heterogeneity, and multi-dimensional treatments have been studied separately, their intersection yields an exponentially large intervention space that makes standard identification tools and low-dimensional exposure mappings untenable. We bridge this gap with a unified framework that constructs a \emph{global potential-outcome emulator} for unit-level inference. Our method combines (1) rooted network configurations to leverage local smoothness, (2) doubly robust orthogonalization to mitigate confounding from network position and covariates, and (3) sparse spectral learning to efficiently estimate response surfaces over the $2^p$-dimensional treatment space. We also decompose networked effects into own-treatment, structural, and interaction components, and provide finite-sample error bounds and asymptotic consistency guarantees. Overall, we show that individualized causal inference remains feasible in high-dimensional networked settings without collapsing the intervention space.

stat.ME↗

arXiv2025

Breaking the Gradient Barrier: Unveiling Large Language Models for Strategic Classification

Strategic classification~(SC) explores how individuals or entities modify their features strategically to achieve favorable classification outcomes. However, existing SC methods, which are largely based on linear models or shallow neural networks, face significant limitations in terms of scalability and capacity when applied to real-world datasets with significantly increasing scale, especially in financial services and the internet sector. In this paper, we investigate how to leverage large language models to design a more scalable and efficient SC framework, especially in the case of growing individuals engaged with decision-making processes. Specifically, we introduce GLIM, a gradient-free SC method grounded in in-context learning. During the feed-forward process of self-attention, GLIM implicitly simulates the typical bi-level optimization process of SC, including both the feature manipulation and decision rule optimization. Without fine-tuning the LLMs, our proposed GLIM enjoys the advantage of cost-effective adaptation in dynamic strategic environments. Theoretically, we prove GLIM can support pre-trained LLMs to adapt to a broad range of strategic manipulations. We validate our approach through experiments with a collection of pre-trained LLMs on real-world and synthetic datasets in financial and internet domains, demonstrating that our GLIM exhibits both robustness and efficiency, and offering an effective solution for large-scale SC tasks.

cs.LG↗

arXiv2025

Transformer-Based Spatial-Temporal Counterfactual Outcomes Estimation

The real world naturally has dimensions of time and space. Therefore, estimating the counterfactual outcomes with spatial-temporal attributes is a crucial problem. However, previous methods are based on classical statistical models, which still have limitations in performance and generalization. This paper proposes a novel framework for estimating counterfactual outcomes with spatial-temporal attributes using the Transformer, exhibiting stronger estimation ability. Under mild assumptions, the proposed estimator within this framework is consistent and asymptotically normal. To validate the effectiveness of our approach, we conduct simulation experiments and real data experiments. Simulation experiments show that our estimator has a stronger estimation capability than baseline methods. Real data experiments provide a valuable conclusion to the causal effect of conflicts on forest loss in Colombia. The source code is available at https://github.com/lihe-maxsize/DeppSTCI_Release_Version-master.

stat.ME↗

arXiv2025

Unveiling Causal Reasoning in Large Language Models: Reality or Mirage?

Causal reasoning capability is critical in advancing large language models (LLMs) toward strong artificial intelligence. While versatile LLMs appear to have demonstrated capabilities in understanding contextual causality and providing responses that obey the laws of causality, it remains unclear whether they perform genuine causal reasoning akin to humans. However, current evidence indicates the contrary. Specifically, LLMs are only capable of performing shallow (level-1) causal reasoning, primarily attributed to the causal knowledge embedded in their parameters, but they lack the capacity for genuine human-like (level-2) causal reasoning. To support this hypothesis, methodologically, we delve into the autoregression mechanism of transformer-based LLMs, revealing that it is not inherently causal. Empirically, we introduce a new causal Q&A benchmark called CausalProbe-2024, whose corpora are fresh and nearly unseen for the studied LLMs. The LLMs exhibit a significant performance drop on CausalProbe-2024 compared to earlier benchmarks, indicating the fact that they primarily engage in level-1 causal reasoning. To bridge the gap towards level-2 causal reasoning, we draw inspiration from the fact that human reasoning is usually facilitated by general knowledge and intended goals. We propose G^2-Reasoner, a method that incorporates general knowledge and goal-oriented prompts into LLMs' causal reasoning processes. Experiments demonstrate that G^2-Reasoner significantly enhances LLMs' causal reasoning capability, particularly in fresh and counterfactual contexts. This work sheds light on a new path for LLMs to advance towards genuine causal reasoning, going beyond level-1 and making strides towards level-2.

cs.AI↗

arXiv2024

Look Within, Why LLMs Hallucinate: A Causal Perspective

The emergence of large language models (LLMs) is a milestone in generative artificial intelligence, achieving significant success in text comprehension and generation tasks. Despite the tremendous success of LLMs in many downstream tasks, they suffer from severe hallucination problems, posing significant challenges to the practical applications of LLMs. Most of the works about LLMs' hallucinations focus on data quality. Self-attention is a core module in transformer-based LLMs, while its potential relationship with LLMs' hallucination has been hardly investigated. To fill this gap, we study this problem from a causal perspective. We propose a method to intervene in LLMs' self-attention layers and maintain their structures and sizes intact. Specifically, we disable different self-attention layers in several popular open-source LLMs and then compare their degrees of hallucination with the original ones. We evaluate the intervened LLMs on hallucination assessment benchmarks and conclude that disabling some specific self-attention layers in the front or tail of the LLMs can alleviate hallucination issues. The study paves a new way for understanding and mitigating LLMs' hallucinations.

cs.CL↗

arXiv2024

Mixture Data for Training Cannot Ensure Out-of-distribution Generalization

Deep neural networks often face generalization problems to handle out-of-distribution (OOD) data, and there remains a notable theoretical gap between the contributing factors and their respective impacts. Literature evidence from in-distribution data has suggested that generalization error can shrink if the size of mixture data for training increases. However, when it comes to OOD samples, this conventional understanding does not hold anymore -- Increasing the size of training data does not always lead to a reduction in the test generalization error. In fact, diverse trends of the errors have been found across various shifting scenarios including those decreasing trends under a power-law pattern, initial declines followed by increases, or continuous stable patterns. Previous work has approached OOD data qualitatively, treating them merely as samples unseen during training, which are hard to explain the complicated non-monotonic trends. In this work, we quantitatively redefine OOD data as those situated outside the convex hull of mixed training data and establish novel generalization error bounds to comprehend the counterintuitive observations better. Our proof of the new risk bound agrees that the efficacy of well-trained models can be guaranteed for unseen data within the convex hull; More interestingly, but for OOD data beyond this coverage, the generalization cannot be ensured, which aligns with our observations. Furthermore, we attempted various OOD techniques to underscore that our results not only explain insightful observations in recent OOD generalization work, such as the significance of diverse data and the sensitivity to unseen shifts of existing algorithms, but it also inspires a novel and effective data selection strategy.

cs.LG↗

arXiv2023

Diversity-enhancing Generative Network for Few-shot Hypothesis Adaptation

Generating unlabeled data has been recently shown to help address the few-shot hypothesis adaptation (FHA) problem, where we aim to train a classifier for the target domain with a few labeled target-domain data and a well-trained source-domain classifier (i.e., a source hypothesis), for the additional information of the highly-compatible unlabeled data. However, the generated data of the existing methods are extremely similar or even the same. The strong dependency among the generated data will lead the learning to fail. In this paper, we propose a diversity-enhancing generative network (DEG-Net) for the FHA problem, which can generate diverse unlabeled data with the help of a kernel independence measure: the Hilbert-Schmidt independence criterion (HSIC). Specifically, DEG-Net will generate data via minimizing the HSIC value (i.e., maximizing the independence) among the semantic features of the generated data. By DEG-Net, the generated unlabeled data are more diverse and more effective for addressing the FHA problem. Experimental results show that the DEG-Net outperforms existing FHA baselines and further verifies that generating diverse data plays a vital role in addressing the FHA problem

cs.LG↗

arXiv2022

Meta Discovery: Learning to Discover Novel Classes given Very Limited Data

In novel class discovery (NCD), we are given labeled data from seen classes and unlabeled data from unseen classes, and we train clustering models for the unseen classes. However, the implicit assumptions behind NCD are still unclear. In this paper, we demystify assumptions behind NCD and find that high-level semantic features should be shared among the seen and unseen classes. Based on this finding, NCD is theoretically solvable under certain assumptions and can be naturally linked to meta-learning that has exactly the same assumption as NCD. Thus, we can empirically solve the NCD problem by meta-learning algorithms after slight modifications. This meta-learning-based methodology significantly reduces the amount of unlabeled data needed for training and makes it more practical, as demonstrated in experiments. The use of very limited data is also justified by the application scenario of NCD: since it is unnatural to label only seen-class data, NCD is sampling instead of labeling in causality. Therefore, unseen-class data should be collected on the way of collecting seen-class data, which is why they are novel and first need to be clustered.

cs.LG↗

arXiv2022

TOHAN: A One-step Approach towards Few-shot Hypothesis Adaptation

In few-shot domain adaptation (FDA), classifiers for the target domain are trained with accessible labeled data in the source domain (SD) and few labeled data in the target domain (TD). However, data usually contain private information in the current era, e.g., data distributed on personal phones. Thus, the private information will be leaked if we directly access data in SD to train a target-domain classifier (required by FDA methods). In this paper, to thoroughly prevent the privacy leakage in SD, we consider a very challenging problem setting, where the classifier for the TD has to be trained using few labeled target data and a well-trained SD classifier, named few-shot hypothesis adaptation (FHA). In FHA, we cannot access data in SD, as a result, the private information in SD will be protected well. To this end, we propose a target orientated hypothesis adaptation network (TOHAN) to solve the FHA problem, where we generate highly-compatible unlabeled data (i.e., an intermediate domain) to help train a target-domain classifier. TOHAN maintains two deep networks simultaneously, where one focuses on learning an intermediate domain and the other takes care of the intermediate-to-target distributional adaptation and the target-risk minimization. Experimental results show that TOHAN outperforms competitive baselines significantly.

cs.LG↗