Traditional instrumental variable (IV) estimators face a fundamental constraint: they can only accommodate as many endogenous treatment variables as available instruments. This limitation becomes particularly challenging in settings where the treatment is presented in a high-dimensional and unstructured manner (e.g. descriptions of patient treatment pathways in a hospital). In such settings, researchers typically resort to applying unsupervised dimension reduction techniques to learn a low-dimensional treatment representation prior to implementing IV regression analysis. We show that such methods can suffer from substantial omitted variable bias due to implicit regularization in the representation learning step. We propose a novel approach to construct treatment representations by explicitly incorporating instrumental variables during the representation learning process. Our approach provides a framework for handling high-dimensional endogenous variables with limited instruments. We demonstrate both theoretically and empirically that fitting IV models on these instrument-informed representations ensures identification of directions that optimize outcome prediction. Our experiments show that our proposed methodology improves upon the conventional two-stage approaches that perform dimension reduction without incorporating instrument information.
Varying coefficient models are popular for estimating nonlinear regression functions in functional data models. Their Bayesian variants have received limited attention in large data applications, primarily due to prohibitively slow posterior computations using Markov chain Monte Carlo (MCMC) algorithms. We introduce Bayesian data sketching for varying coefficient models to obviate computational challenges presented by large sample sizes. To address the challenges of analyzing large data, we compress the functional response vector and predictor matrix by a random linear transformation to achieve dimension reduction and conduct inference on the compressed data. Our approach distinguishes itself from several existing methods for analyzing large functional data in that it requires neither the development of new models or algorithms, nor any specialized computational hardware while delivering fully model-based Bayesian inference. Well-established methods and algorithms for varying coefficient regression models can be applied to the compressed data.
This paper proposes an innovative extension of Principal Component Analysis (PCA) that transcends the traditional assumption of data lying in Euclidean space, enabling its application to data on Riemannian manifolds. The primary challenge addressed is the lack of vector space operations on such manifolds. Fletcher et al., in their work {\em Principal Geodesic Analysis for the Study of Nonlinear Statistics of Shape}, proposed Principal Geodesic Analysis (PGA) as a geometric approach to analyze data on Riemannian manifolds, particularly effective for structured datasets like medical images, where the manifold's intrinsic structure is apparent. However, PGA's applicability is limited when dealing with general datasets that lack an implicit local distance notion. In this work, we introduce a generalized framework, termed {\em Riemannian Principal Component Analysis (R-PCA)}, to extend PGA for any data endowed with a local distance structure. Specifically, we adapt the PCA methodology to Riemannian manifolds by equipping data tables with local metrics, enabling the incorporation of manifold geometry. This framework provides a unified approach for dimensionality reduction and statistical analysis directly on manifolds, opening new possibilities for datasets with region-specific or part-specific distance notions, ensuring respect for their intrinsic geometric properties.
Cell-free DNA (cfDNA) analysis is a powerful, minimally invasive tool for monitoring disease progression, treatment response, and early detection. A major challenge, however, is accurately determining the tissue of origin, especially in complex or heterogeneous disease contexts. To address this, we developed a machine learning framework that leverages tissue-specific DNA methylation signatures to classify both tissue and disease origin from cfDNA data. Our model integrates methylation datasets across diverse epigenomic platforms, including Whole Genome Bisulfite Sequencing (WGBS), Illumina Infinium Bead Arrays, and Enzymatic Methyl-seq (EM-seq). To account for platform variability and data sparsity, we applied imputation strategies and harmonized CpG features to enable cross-platform learning. Dimensionality reduction revealed clear tissue-specific clustering of methylation profiles. A random forest classifier trained on these features achieved consistent classification performance (accuracy 0.75-0.8 across test sets and platforms). Notably, our model distinguished clinically relevant tissues such as inflamed synovium and peripheral blood mononuclear cells (PBMCs) in arthritis patients and deconvoluted synthetic cfDNA mixtures mimicking real-world liquid biopsy samples. The predicted tissue proportions closely matched the true values, demonstrating the model's potential for both classification and quantitative inference. These results support the feasibility of using cross-platform methylation data and machine learning for scalable, generalizable cfDNA diagnostics and lay the groundwork for future integration of disease-specific epigenetic features to guide clinical decision-making in precision medicine.
A recent breakthrough in biologically-plausible normative frameworks for dimensionality reduction is based upon the similarity matching cost function and the low-rank matrix approximation problem. Despite clear biological interpretation, successful application in several domains, and experimental validation, a formal complete convergence analysis remains elusive. Building on this framework, we consider and analyze a continuous-time neural network, the \emph{similarity matching network}, for principal subspace projection. Derived from a min-max-min objective, this biologically-plausible network consists of three coupled dynamics evolving at different time scales: neural dynamics, lateral synaptic dynamics, and feedforward synaptic dynamics at the fast, intermediate, and slow time scales, respectively. The feedforward and lateral synaptic dynamics consist of Hebbian and anti-Hebbian learning rules, respectively. By leveraging a multilevel optimization framework, we prove convergence of the dynamics in the offline setting. Specifically, at the first level (fast time scale), we show strong convexity of the cost function and global exponential convergence of the corresponding gradient-flow dynamics. At the second level (intermediate time scale), we prove strong concavity of the cost function and exponential convergence of the corresponding gradient-flow dynamics within the space of positive definite matrices. At the third and final level (slow time scale), we study a non-convex and non-smooth cost function, provide explicit expressions for its global minima, and prove almost sure convergence of the corresponding gradient-flow dynamics to the global minima. These results rely on two empirically motivated conjectures that are supported by thorough numerical experiments. Finally, we validate the effectiveness of our approach via a numerical example.
An alternative data-driven modeling approach has been proposed and employed to gain fundamental insights into robot motion interaction with granular terrain at certain length scales. The approach is based on an integration of dimension reduction (Sequentially Truncated Higher-Order Singular Value Decomposition), surrogate modeling (Gaussian Process), and data assimilation techniques (Reduced Order Particle Filter). This approach can be used online and is based on offline data, obtained from the offline collection of high-fidelity simulation data and a set of sparse experimental data. The results have shown that orders of magnitude reduction in computational time can be obtained from the proposed data-driven modeling approach compared with physics-based high-fidelity simulations. With only simulation data as input, the data-driven prediction technique can generate predictions that have comparable accuracy as simulations. With both simulation data and sparse physical experimental measurement as input, the data-driven approach with its embedded data assimilation techniques has the potential in outperforming only high-fidelity simulations for the long-horizon predictions. In addition, it is demonstrated that the data-driven modeling approach can also reproduce the scaling relationship recovered by physics-based simulations for maximum resistive forces, which may indicate its general predictability beyond a case-by-case basis. The results are expected to help robot navigation and exploration in unknown and complex terrains during both online and offline phases.
Oral cancer presents a formidable challenge in oncology, necessitating early diagnosis and accurate prognosis to enhance patient survival rates. Recent advancements in machine learning and data mining have revolutionized traditional diagnostic methodologies, providing sophisticated and automated tools for differentiating between benign and malignant oral lesions. This study presents a comprehensive review of cutting-edge data mining methodologies, including Neural Networks, K-Nearest Neighbors (KNN), Support Vector Machines (SVM), and ensemble learning techniques, specifically applied to the diagnosis and prognosis of oral cancer. Through a rigorous comparative analysis, our findings reveal that Neural Networks surpass other models, achieving an impressive classification accuracy of 93,6 % in predicting oral cancer. Furthermore, we underscore the potential benefits of integrating feature selection and dimensionality reduction techniques to enhance model performance. These insights underscore the significant promise of advanced data mining techniques in bolstering early detection, optimizing treatment strategies, and ultimately improving patient outcomes in the realm of oral oncology.
This study conducts an empirical examination of MLP networks investigated through a rigorous methodical experimentation process involving three diverse datasets: TinyFace, Heart Disease, and Iris. Study Overview: The study includes three key methods: a) a baseline training using the default settings for the Multi-Layer Perceptron (MLP), b) feature selection using Genetic Algorithm (GA) based refinement c) Principal Component Analysis (PCA) based dimension reduction. The results show important information on how such techniques affect performance. While PCA had showed benefits in low-dimensional and noise-free datasets GA consistently increased accuracy in complex datasets by accurately identifying critical features. Comparison reveals that feature selection and dimensionality reduction play interdependent roles in enhancing MLP performance. The study contributes to the literature on feature engineering and neural network parameter optimization, offering practical guidelines for a wide range of machine learning tasks
We consider the problem of propagating the uncertainty from a possibly large number of random inputs through a computationally expensive model. Stratified sampling is a well-known variance reduction strategy, but its application, thus far, has focused on models with a limited number of inputs due to the challenges of creating uniform partitions in high dimensions. To overcome these challenges, we perform stratification with respect to the uniform distribution defined over the unit interval, and then derive the corresponding strata in the original space using nonlinear dimensionality reduction. We show that our approach is effective in high dimensions and can be used to further reduce the variance of multifidelity Monte Carlo estimators.
We propose an efficient thermodynamics-informed latent space dynamics identification (tLaSDI) framework for the reduced-order modeling of parametric nonlinear dynamical systems. This framework integrates autoencoders for dimensionality reduction with newly developed parametric GENERIC formalism-informed neural networks (pGFINNs), which enable efficient learning of parametric latent dynamics while preserving key thermodynamic principles such as free energy conservation and entropy generation across the parameter space. To further enhance model performance, a physics-informed active learning strategy is incorporated, leveraging a greedy, residual-based error indicator to adaptively sample informative training data, outperforming uniform sampling at equivalent computational cost. Numerical experiments on the Burgers' equation and the 1D/1V Vlasov-Poisson equation demonstrate that the proposed method achieves up to 3,528x speed-up with 1-3% relative errors, and significant reduction in training (50-90%) and inference (57-61%) cost. Moreover, the learned latent space dynamics reveal the underlying thermodynamic behavior of the system, offering valuable insights into the physical-space dynamics.
This study proposes a universal flow field prediction framework based on knowledge transfer from large language model (LLM), addressing the high computational costs of traditional computational fluid dynamics (CFD) methods and the limited cross-condition transfer capability of existing deep learning models. The framework innovatively integrates Proper Orthogonal Decomposition (POD) dimensionality reduction with fine-tuning strategies for pretrained LLM, where POD facilitates compressed representation of flow field features while the fine-tuned model learns to encode system dynamics in state space. To enhance the model's adaptability to flow field data, we specifically designed fluid dynamics-oriented text templates that improve predictive performance through enriched contextual semantic information. Experimental results demonstrate that our framework outperforms conventional Transformer models in few-shot learning scenarios while exhibiting exceptional generalization across various inflow conditions and airfoil geometries. Ablation studies reveal the contributions of key components in the FlowBERT architecture. Compared to traditional Navier-Stokes equation solvers requiring hours of computation, our approach reduces prediction time to seconds while maintaining over 90% accuracy. The developed knowledge transfer paradigm establishes a new direction for rapid fluid dynamics prediction, with potential applications extending to aerodynamic optimization, flow control, and other engineering domains.
Natural disasters have caused significant losses to human society, and the timely and efficient acquisition of post-disaster environmental information is crucial for the effective implementation of rescue operations. Due to the complexity of post-disaster environments, existing sensing technologies face challenges such as weak environmental adaptability, insufficient specialized sensing capabilities, and limited practicality of sensing solutions. This paper explores the heterogeneous multi-agent online autonomous collaborative scheduling algorithm HoAs-PALN, aimed at achieving efficient collection of post-disaster environmental information. HoAs-PALN is realized through adaptive dimensionality reduction in the matching process and local Nash equilibrium game, facilitating autonomous collaboration among time-dependent UAVs, workers and vehicles to enhance sensing scheduling. (1) In terms of adaptive dimensionality reduction during the matching process, HoAs-PALN significantly reduces scheduling decision time by transforming a five-dimensional matching process into two categories of three-dimensional matching processes; (2) Regarding the local Nash equilibrium game, HoAs-PALN combines the softmax function to optimize behavior selection probabilities and introduces a local Nash equilibrium determination mechanism to ensure scheduling decision performance. Finally, we conducted detailed experiments based on extensive real-world and simulated data. Compared with the baselines (GREEDY, K-WTA, MADL and MARL), HoAs-PALN improves task completion rates by 64.12%, 46.48%, 16.55%, and 14.03% on average, respectively, while each online scheduling decision takes less than 10 seconds, demonstrating its effectiveness in dynamic post-disaster environments.
Randomized dimensionality reduction is a widely-used algorithmic technique for speeding up large-scale Euclidean optimization problems. In this paper, we study dimension reduction for a variety of maximization problems, including max-matching, max-spanning tree, max TSP, as well as various measures for dataset diversity. For these problems, we show that the effect of dimension reduction is intimately tied to the \emph{doubling dimension} $\lambda_X$ of the underlying dataset $X$ -- a quantity measuring intrinsic dimensionality of point sets. Specifically, we prove that a target dimension of $O(\lambda_X)$ suffices to approximately preserve the value of any near-optimal solution,which we also show is necessary for some of these problems. This is in contrast to classical dimension reduction results, whose dependence increases with the dataset size $|X|$. We also provide empirical results validating the quality of solutions found in the projected space, as well as speedups due to dimensionality reduction.
Gene selection in high-dimensional genomic data is essential for understanding disease mechanisms and improving therapeutic outcomes. Traditional feature selection methods effectively identify predictive genes but often ignore complex biological pathways and regulatory networks, leading to unstable and biologically irrelevant signatures. Prior approaches, such as Lasso-based methods and statistical filtering, either focus solely on individual gene-outcome associations or fail to capture pathway-level interactions, presenting a key challenge: how to integrate biological pathway knowledge while maintaining statistical rigor in gene selection? To address this gap, we propose a novel two-stage framework that integrates statistical selection with biological pathway knowledge using multi-agent reinforcement learning (MARL). First, we introduce a pathway-guided pre-filtering strategy that leverages multiple statistical methods alongside KEGG pathway information for initial dimensionality reduction. Next, for refined selection, we model genes as collaborative agents in a MARL framework, where each agent optimizes both predictive power and biological relevance. Our framework incorporates pathway knowledge through Graph Neural Network-based state representations, a reward mechanism combining prediction performance with gene centrality and pathway coverage, and collaborative learning strategies using shared memory and a centralized critic component. Extensive experiments on multiple gene expression datasets demonstrate that our approach significantly improves both prediction accuracy and biological interpretability compared to traditional methods.
We present a study on how and where personas -- defined by distinct sets of human characteristics, values, and beliefs -- are encoded in the representation space of large language models (LLMs). Using a range of dimension reduction and pattern recognition methods, we first identify the model layers that show the greatest divergence in encoding these representations. We then analyze the activations within a selected layer to examine how specific personas are encoded relative to others, including their shared and distinct embedding spaces. We find that, across multiple pre-trained decoder-only LLMs, the analyzed personas show large differences in representation space only within the final third of the decoder layers. We observe overlapping activations for specific ethical perspectives -- such as moral nihilism and utilitarianism -- suggesting a degree of polysemy. In contrast, political ideologies like conservatism and liberalism appear to be represented in more distinct regions. These findings help to improve our understanding of how LLMs internally represent information and can inform future efforts in refining the modulation of specific human traits in LLM outputs. Warning: This paper includes potentially offensive sample statements.
Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) systems are increasingly deployed in industry applications, yet their reliability remains hampered by challenges in detecting hallucinations. While supervised state-of-the-art (SOTA) methods that leverage LLM hidden states -- such as activation tracing and representation analysis -- show promise, their dependence on extensively annotated datasets limits scalability in real-world applications. This paper addresses the critical bottleneck of data annotation by investigating the feasibility of reducing training data requirements for two SOTA hallucination detection frameworks: Lookback Lens, which analyzes attention head dynamics, and probing-based approaches, which decode internal model representations. We propose a methodology combining efficient classification algorithms with dimensionality reduction techniques to minimize sample size demands while maintaining competitive performance. Evaluations on standardized question-answering RAG benchmarks show that our approach achieves performance comparable to strong proprietary LLM-based baselines with only 250 training samples. These results highlight the potential of lightweight, data-efficient paradigms for industrial deployment, particularly in annotation-constrained scenarios.
Video generative models can be regarded as world simulators due to their ability to capture dynamic, continuous changes inherent in real-world environments. These models integrate high-dimensional information across visual, temporal, spatial, and causal dimensions, enabling predictions of subjects in various status. A natural and valuable research direction is to explore whether a fully trained video generative model in high-dimensional space can effectively support lower-dimensional tasks such as controllable image generation. In this work, we propose a paradigm for video-to-image knowledge compression and task adaptation, termed \textit{Dimension-Reduction Attack} (\texttt{DRA-Ctrl}), which utilizes the strengths of video models, including long-range context modeling and flatten full-attention, to perform various generation tasks. Specially, to address the challenging gap between continuous video frames and discrete image generation, we introduce a mixup-based transition strategy that ensures smooth adaptation. Moreover, we redesign the attention structure with a tailored masking mechanism to better align text prompts with image-level control. Experiments across diverse image generation tasks, such as subject-driven and spatially conditioned generation, show that repurposed video models outperform those trained directly on images. These results highlight the untapped potential of large-scale video generators for broader visual applications. \texttt{DRA-Ctrl} provides new insights into reusing resource-intensive video models and lays foundation for future unified generative models across visual modalities. The project page is https://dra-ctrl-2025.github.io/DRA-Ctrl/.
Principal component analysis (PCA) is a key tool in the field of data dimensionality reduction. Various methods have been proposed to extend PCA to the union of subspace (UoS) setting for clustering data that come from multiple subspaces like K-Subspaces (KSS). However, some applications involve heterogeneous data that vary in quality due to noise characteristics associated with each data sample. Heteroscedastic methods aim to deal with such mixed data quality. This paper develops a heteroscedastic-focused subspace clustering method, named ALPCAHUS, that can estimate the sample-wise noise variances and use this information to improve the estimate of the subspace bases associated with the low-rank structure of the data. This clustering algorithm builds on K-Subspaces (KSS) principles by extending the recently proposed heteroscedastic PCA method, named LR-ALPCAH, for clusters with heteroscedastic noise in the UoS setting. Simulations and real-data experiments show the effectiveness of accounting for data heteroscedasticity compared to existing clustering algorithms. Code available at https://github.com/javiersc1/ALPCAHUS.
Enterprise search systems often struggle to retrieve accurate, domain-specific information due to semantic mismatches and overlapping terminologies. These issues can degrade the performance of downstream applications such as knowledge management, customer support, and retrieval-augmented generation agents. To address this challenge, we propose a scalable hard-negative mining framework tailored specifically for domain-specific enterprise data. Our approach dynamically selects semantically challenging but contextually irrelevant documents to enhance deployed re-ranking models. Our method integrates diverse embedding models, performs dimensionality reduction, and uniquely selects hard negatives, ensuring computational efficiency and semantic precision. Evaluation on our proprietary enterprise corpus (cloud services domain) demonstrates substantial improvements of 15\% in MRR@3 and 19\% in MRR@10 compared to state-of-the-art baselines and other negative sampling techniques. Further validation on public domain-specific datasets (FiQA, Climate Fever, TechQA) confirms our method's generalizability and readiness for real-world applications.
Probabilistic principal component analysis (PCA) and its Bayesian variant (BPCA) are widely used for dimension reduction in machine learning and statistics. The main advantage of probabilistic PCA over the traditional formulation is allowing uncertainty quantification. The parameters of BPCA are typically learned using mean-field variational inference, and in particular, the coordinate ascent variational inference (CAVI) algorithm. So far, the convergence speed of CAVI for BPCA has not been characterized. In our paper, we fill this gap in the literature. Firstly, we prove a precise exponential convergence result in the case where the model uses a single principal component (PC). Interestingly, this result is established through a connection with the classical $\textit{power iteration algorithm}$ and it indicates that traditional PCA is retrieved as points estimates of the BPCA parameters. Secondly, we leverage recent tools to prove exponential convergence of CAVI for the model with any number of PCs, thus leading to a more general result, but one that is of a slightly different flavor. To prove the latter result, we additionally needed to introduce a novel lower bound for the symmetric Kullback--Leibler divergence between two multivariate normal distributions, which, we believe, is of independent interest in information theory.