Regression
Association between nutritional factors, inflammatory biomarkers and cancer types: an analysis of NHANES data using machine learning
Liu, Yuqing, Zhao, Meng, Hu, Guanlan, Zhang, Yuchen
Background. Diet and inflammation are critical factors influencing cancer risk. However, the combined impact of nutritional status and inflammatory biomarkers on cancer status and type, using machine learning (ML), remains underexplored. Objectives. This study investigates the association between nutritional factors, inflammatory biomarkers, and cancer status, and whether these relationships differ across cancer types using National Health and Nutrition Examination Survey (NHANES) data. Methods. We analyzed 24 macro- and micronutrients, C-reactive protein (CRP), and the advanced lung cancer inflammation index (ALI) in 26,409 NHANES participants (2,120 with cancer). Multivariable logistic regression assessed associations with cancer prevalence. We also examined whether these features differed across the five most common cancer types. To evaluate predictive value, we applied three ML models - Logistic Regression, Random Forest, and XGBoost - on the full feature set. Results. The cohort's mean age was 49.1 years; 34.7% were obese. Comorbidities such as anemia and liver conditions, along with nutritional factors like protein and several vitamins, were key predictors of cancer status. Among the models, Random Forest performed best, achieving an accuracy of 0.72. Conclusions. Higher-quality nutritional intake and lower levels of inflammation may offer protective effects against cancer. These findings highlight the potential of combining nutritional and inflammatory markers with ML to inform cancer prevention strategies.
Word Embedding Techniques for Classification of Star Ratings
Abdelmotaleb, Hesham, McNeile, Craig, Wojtys, Malgorzata
Telecom services are at the core of today's societies' everyday needs. The availability of numerous online forums and discussion platforms enables telecom providers to improve their services by exploring the views of their customers to learn about common issues that the customers face. Natural Language Processing (NLP) tools can be used to process the free text collected. One way of working with such data is to represent text as numerical vectors using one of many word embedding models based on neural networks. This research uses a novel dataset of telecom customers' reviews to perform an extensive study showing how different word embedding algorithms can affect the text classification process. Several state-of-the-art word embedding techniques are considered, including BERT, Word2Vec and Doc2Vec, coupled with several classification algorithms. The important issue of feature engineering and dimensionality reduction is addressed and several PCA-based approaches are explored. Moreover, the energy consumption used by the different word embeddings is investigated. The findings show that some word embedding models can lead to consistently better text classifiers in terms of precision, recall and F1-Score. In particular, for the more challenging classification tasks, BERT combined with PCA stood out with the highest performance metrics. Moreover, our proposed PCA approach of combining word vectors using the first principal component shows clear advantages in performance over the traditional approach of taking the average.
Acoustic to Articulatory Inversion of Speech; Data Driven Approaches, Challenges, Applications, and Future Scope
Pillai, Leena G, Mubarak, D. Muhammad Noorul
This review is focused on the data-driven approaches applied in different applications of Acoustic-to-Articulatory Inversion (AAI) of speech. This review paper considered the relevant works published in the last ten years (2011-2021). The selection criteria includes (a) type of AAI - Speaker Dependent and Speaker Independent AAI, (b) objectives of the work - Articulatory approximation, Articulatory Feature space selection and Automatic Speech Recognition (ASR), explore the correlation between acoustic and articulatory features, and framework for Computer-assisted language training, (c) Corpus - Simultaneously recorded speech (wav) and medical imaging models such as ElectroMagnetic Articulography (EMA), Electropalatography (EPG), Laryngography, Electroglottography (EGG), X-ray Cineradiography, Ultrasound, and real-time Magnetic Resonance Imaging (rtMRI), (d) Methods or models - recent works are considered, and therefore all the works are based on machine learning, (e) Evaluation - as AAI is a non-linear regression problem, the performance evaluation is mostly done by Correlation Coefficient (CC), Root Mean Square Error (RMSE), and also considered Mean Square Error (MSE), and Mean Format Error (MFE). The practical application of the AAI model can provide a better and user-friendly interpretable image feedback system of articulatory positions, especially tongue movement. Such trajectory feedback system can be used to provide phonetic, language, and speech therapy for pathological subjects.
On Linear Representations and Pretraining Data Frequency in Language Models
Merullo, Jack, Smith, Noah A., Wiegreffe, Sarah, Elazar, Yanai
Pretraining data has a direct impact on the behaviors and quality of language models (LMs), but we only understand the most basic principles of this relationship. While most work focuses on pretraining data's effect on downstream task behavior, we investigate its relationship to LM representations. Previous work has discovered that, in language models, some concepts are encoded `linearly' in the representations, but what factors cause these representations to form? We study the connection between pretraining data frequency and models' linear representations of factual relations. We find evidence that the formation of linear representations is strongly connected to pretraining term frequencies; specifically for subject-relation-object fact triplets, both subject-object co-occurrence frequency and in-context learning accuracy for the relation are highly correlated with linear representations. This is the case across all phases of pretraining. In OLMo-7B and GPT-J, we discover that a linear representation consistently (but not exclusively) forms when the subjects and objects within a relation co-occur at least 1k and 2k times, respectively, regardless of when these occurrences happen during pretraining. Finally, we train a regression model on measurements of linear representation quality in fully-trained LMs that can predict how often a term was seen in pretraining. Our model achieves low error even on inputs from a different model with a different pretraining dataset, providing a new method for estimating properties of the otherwise-unknown training data of closed-data models. We conclude that the strength of linear representations in LMs contains signal about the models' pretraining corpora that may provide new avenues for controlling and improving model behavior: particularly, manipulating the models' training data to meet specific frequency thresholds.
Cluster weighted models with multivariate skewed distributions for functional data
Anton, Cristina, Shreshtth, Roy Shivam Ram
Cluster weighted models with multivariate skewed distributions for functional data Cristina Anton, 1 Roy Shivam Ram Shreshtth 2 1 Department of Mathematics and Statistics, MacEwan University, 103C, 10700-104 Ave., Edmonton, AB T5J 4S2, Canada, email: popescuc@macewan.ca 2 Department of Mathematics and Statistics, Indian Institute of Technology Kanpur Abstract We propose a clustering method, funWeightClustSkew, based on mixtures of functional linear regression models and three skewed multivariate distributions: the variance-gamma distribution, the skew-t distribution, and the normal-inverse Gaussian distribution. Our approach follows the framework of the functional high dimensional data clustering (funHDDC) method, and we extend to functional data the cluster weighted models based on skewed distributions used for finite dimensional multivariate data. We consider several parsimonious models, and to estimate the parameters we construct an expectation maximization (EM) algorithm. We illustrate the performance of funWeightClustSkew for simulated data and for the Air Quality dataset. Keywords: Cluster weighted models, Functional linear regression, EM algorithm, Skewed distributions, Multivariate functional principal component analysis 1 Introduction Smart devices and other modern technologies record huge amounts of data measured continuously in time. These data are better represented as curves instead of finite-dimensional vectors, and they are analyzed using statistical methods specific to functional data (Ramsay and Silverman, 2006; Ferraty and Vieu, 2006; Horv ath and Kokoszka, 2012). Many times more than one curve is collected for one individual, e.g.
Minimax Optimal Convergence of Gradient Descent in Logistic Regression via Large and Adaptive Stepsizes
Zhang, Ruiqi, Wu, Jingfeng, Lin, Licong, Bartlett, Peter L.
We study $\textit{gradient descent}$ (GD) for logistic regression on linearly separable data with stepsizes that adapt to the current risk, scaled by a constant hyperparameter $\eta$. We show that after at most $1/\gamma^2$ burn-in steps, GD achieves a risk upper bounded by $\exp(-\Theta(\eta))$, where $\gamma$ is the margin of the dataset. As $\eta$ can be arbitrarily large, GD attains an arbitrarily small risk $\textit{immediately after the burn-in steps}$, though the risk evolution may be $\textit{non-monotonic}$. We further construct hard datasets with margin $\gamma$, where any batch (or online) first-order method requires $\Omega(1/\gamma^2)$ steps to find a linear separator. Thus, GD with large, adaptive stepsizes is $\textit{minimax optimal}$ among first-order batch methods. Notably, the classical $\textit{Perceptron}$ (Novikoff, 1962), a first-order online method, also achieves a step complexity of $1/\gamma^2$, matching GD even in constants. Finally, our GD analysis extends to a broad class of loss functions and certain two-layer networks.
Bayesian Density-Density Regression with Application to Cell-Cell Communications
Nguyen, Khai, Ni, Yang, Mueller, Peter
We introduce a scalable framework for regressing multivariate distributions onto multivariate distributions, motivated by the application of inferring cell-cell communication from population-scale single-cell data. The observed data consist of pairs of multivariate distributions for ligands from one cell type and corresponding receptors from another. For each ordered pair $e=(l,r)$ of cell types $(l \neq r)$ and each sample $i = 1, \ldots, n$, we observe a pair of distributions $(F_{ei}, G_{ei})$ of gene expressions for ligands and receptors of cell types $l$ and $r$, respectively. The aim is to set up a regression of receptor distributions $G_{ei}$ given ligand distributions $F_{ei}$. A key challenge is that these distributions reside in distinct spaces of differing dimensions. We formulate the regression of multivariate densities on multivariate densities using a generalized Bayes framework with the sliced Wasserstein distance between fitted and observed distributions. Finally, we use inference under such regressions to define a directed graph for cell-cell communications.
Differentially Private Geodesic and Linear Regression
Kulkarni, Aditya, Soto, Carlos
In statistical applications it has become increasingly common to encounter data structures that live on non-linear spaces such as manifolds. Classical linear regression, one of the most fundamental methodologies of statistical learning, captures the relationship between an independent variable and a response variable which both are assumed to live in Euclidean space. Thus, geodesic regression emerged as an extension where the response variable lives on a Riemannian manifold. The parameters of geodesic regression, as with linear regression, capture the relationship of sensitive data and hence one should consider the privacy protection practices of said parameters. We consider releasing Differentially Private (DP) parameters of geodesic regression via the K-Norm Gradient (KNG) mechanism for Riemannian manifolds. We derive theoretical bounds for the sensitivity of the parameters showing they are tied to their respective Jacobi fields and hence the curvature of the space. This corroborates recent findings of differential privacy for the Fr\'echet mean. We demonstrate the efficacy of our methodology on the sphere, $\mbS^2\subset\mbR^3$ and, since it is general to Riemannian manifolds, the manifold of Euclidean space which simplifies geodesic regression to a case of linear regression. Our methodology is general to any Riemannian manifold and thus it is suitable for data in domains such as medical imaging and computer vision.
Inferring Outcome Means of Exponential Family Distributions Estimated by Deep Neural Networks
While deep neural networks (DNNs) are widely used for prediction, inference on DNN-estimated subject-specific means for categorical or exponential family outcomes remains underexplored. We address this by proposing a DNN estimator under generalized nonparametric regression models (GNRMs) and developing a rigorous inference framework. Unlike existing approaches that assume independence between prediction errors and inputs to establish the error bound, a condition often violated in GNRMs, we allow for dependence and our theoretical analysis demonstrates the feasibility of drawing inference under GNRMs. To implement inference, we consider an Ensemble Subsampling Method (ESM) that leverages U-statistics and the Hoeffding decomposition to construct reliable confidence intervals for DNN estimates. We show that, under GNRM settings, ESM enables model-free variance estimation and accounts for heterogeneity among individuals in the population. Through simulations under nonparametric logistic, Poisson, and binomial regression models, we demonstrate the effectiveness and efficiency of our method. We further apply the method to the electronic Intensive Care Unit (eICU) dataset, a large-scale collection of anonymized health records from ICU patients, to predict ICU readmission risk and offer patient-centric insights for clinical decision-making.
Foundation models for electronic health records: representation dynamics and transferability
Burkhart, Michael C., Ramadan, Bashar, Liao, Zewei, Chhikara, Kaveri, Rojas, Juan C., Parker, William F., Beaulieu-Jones, Brett K.
Foundation models (FMs) trained on electronic health records (EHRs) have shown strong performance on a range of clinical prediction tasks. However, adapting these models to local health systems remains challenging due to limited data availability and resource constraints. In this study, we investigated what these models learn and evaluated the transferability of an FM trained on MIMIC-IV to an institutional EHR dataset at the University of Chicago Medical Center. We assessed their ability to identify outlier patients and examined representation-space patient trajectories in relation to future clinical outcomes. We also evaluated the performance of supervised fine-tuned classifiers on both source and target datasets. Our findings offer insights into the adaptability of FMs across different healthcare systems, highlight considerations for their effective implementation, and provide an empirical analysis of the underlying factors that contribute to their predictive performance.