Epidemiologic and genetic studies in chronic obstructive pulmonary disease (COPD) and many complex diseases suggest subgroup disparities (e.g., by sex). We consider this problem from the standpoint of integrative analysis where we combine information from different views (e.g., genomics, proteomics, clinical data). Existing integrative analysis methods ignore the heterogeneity in subgroups, and stacking the views and accounting for subgroup heterogeneity does not model the association among the views. To address analytical challenges in the problem of our interest, we propose a statistical approach for joint association and prediction that leverages the strengths in each view to identify molecular signatures that are shared by and specific to males and females and that contribute to the variation in COPD, measured by airway wall thickness. HIP (Heterogeneity in Integration and Prediction) accounts for subgroup heterogeneity, allows for sparsity in variable selection, is applicable to multi-class and to univariate or multivariate continuous outcomes, and incorporates covariate adjustment. We develop efficient algorithms in PyTorch. Our COPD findings have identified several proteins, genes, and pathways that are common and specific to males and females, some of which have been implicated in COPD, while others could lead to new insights into sex differences in COPD mechanisms.
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Causal representation learning algorithms discover lower-dimensional representations of data that admit a decipherable interpretation of cause and effect; as achieving such interpretable representations is challenging, many causal learning algorithms utilize elements indicating prior information, such as (linear) structural causal models, interventional data, or weak supervision. Unfortunately, in exploratory causal representation learning, such elements and prior information may not be available or warranted. Alternatively, scientific datasets often have multiple modalities or physics-based constraints, and the use of such scientific, multimodal data has been shown to improve disentanglement in fully unsupervised settings. Consequently, we introduce a causal representation learning algorithm (causalPIMA) that can use multimodal data and known physics to discover important features with causal relationships. Our innovative algorithm utilizes a new differentiable parametrization to learn a directed acyclic graph (DAG) together with a latent space of a variational autoencoder in an end-to-end differentiable framework via a single, tractable evidence lower bound loss function. We place a Gaussian mixture prior on the latent space and identify each of the mixtures with an outcome of the DAG nodes; this novel identification enables feature discovery with causal relationships. Tested against a synthetic and a scientific dataset, our results demonstrate the capability of learning an interpretable causal structure while simultaneously discovering key features in a fully unsupervised setting.
FetMRQC: an open-source machine learning framework for multi-centric fetal brain MRI quality control
Fetal brain MRI is becoming an increasingly relevant complement to neurosonography for perinatal diagnosis, allowing fundamental insights into fetal brain development throughout gestation. However, uncontrolled fetal motion and heterogeneity in acquisition protocols lead to data of variable quality, potentially biasing the outcome of subsequent studies. We present FetMRQC, an open-source machine-learning framework for automated image quality assessment and quality control that is robust to domain shifts induced by the heterogeneity of clinical data. FetMRQC extracts an ensemble of quality metrics from unprocessed anatomical MRI and combines them to predict experts' ratings using random forests. We validate our framework on a pioneeringly large and diverse dataset of more than 1600 manually rated fetal brain T2-weighted images from four clinical centers and 13 different scanners. Our study shows that FetMRQC's predictions generalize well to unseen data while being interpretable. FetMRQC is a step towards more robust fetal brain neuroimaging, which has the potential to shed new insights on the developing human brain.
The accessibility of spatially distributed data, enabled by affordable sensors, field, and numerical experiments, has facilitated the development of data-driven solutions for scientific problems, including climate change, weather prediction, and urban planning. Neural Partial Differential Equations (Neural PDEs), which combine deep learning (DL) techniques with domain expertise (e.g., governing equations) for parameterization, have proven to be effective in capturing valuable correlations within spatiotemporal datasets. However, sparse and noisy measurements coupled with modeling approximation introduce aleatoric and epistemic uncertainties. Therefore, quantifying uncertainties propagated from model inputs to outputs remains a challenge and an essential goal for establishing the trustworthiness of Neural PDEs. This work evaluates various Uncertainty Quantification (UQ) approaches for both Forward and Inverse Problems in scientific applications. Specifically, we investigate the effectiveness of Bayesian methods, such as Hamiltonian Monte Carlo (HMC) and Monte-Carlo Dropout (MCD), and a more conventional approach, Deep Ensembles (DE). To illustrate their performance, we take two canonical PDEs: Burger's equation and the Navier-Stokes equation. Our results indicate that Neural PDEs can effectively reconstruct flow systems and predict the associated unknown parameters. However, it is noteworthy that the results derived from Bayesian methods, based on our observations, tend to display a higher degree of certainty in their predictions as compared to those obtained using the DE. This elevated certainty in predictions suggests that Bayesian techniques might underestimate the true underlying uncertainty, thereby appearing more confident in their predictions than the DE approach.
We consider the problem of solving a family of parametric mixed-integer linear optimization problems where some entries in the input data change. We introduce the concept of cutting-plane layer (CPL), i.e., a differentiable cutting-plane generator mapping the problem data and previous iterates to cutting planes. We propose a CPL implementation to generate split cuts, and by combining several CPLs, we devise a differentiable cutting-plane algorithm that exploits the repeated nature of parametric instances. In an offline phase, we train our algorithm by updating the internal parameters controlling the CPLs, thus altering cut generation. Once trained, our algorithm computes, with predictable execution times and a fixed number of cuts, solutions with low integrality gaps. Preliminary computational tests show that our algorithm generalizes on unseen instances and captures underlying parametric structures.
1. Automated analysis of bioacoustic recordings using machine learning (ML) methods has the potential to greatly scale biodiversity monitoring efforts. The use of ML for high-stakes applications, such as conservation research, demands a data-centric approach with a focus on utilizing carefully annotated and curated evaluation and training data that is relevant and representative. Creating annotated datasets of sound recordings presents a number of challenges, such as managing large collections of recordings with associated metadata, developing flexible annotation tools that can accommodate the diverse range of vocalization profiles of different organisms, and addressing the scarcity of expert annotators. 2. We present Whombat a user-friendly, browser-based interface for managing audio recordings and annotation projects, with several visualization, exploration, and annotation tools. It enables users to quickly annotate, review, and share annotations, as well as visualize and evaluate a set of machine learning predictions on a dataset. The tool facilitates an iterative workflow where user annotations and machine learning predictions feedback to enhance model performance and annotation quality. 3. We demonstrate the flexibility of Whombat by showcasing two distinct use cases: an project aimed at enhancing automated UK bat call identification at the Bat Conservation Trust (BCT), and a collaborative effort among the USDA Forest Service and Oregon State University researchers exploring bioacoustic applications and extending automated avian classification models in the Pacific Northwest, USA. 4. Whombat is a flexible tool that can effectively address the challenges of annotation for bioacoustic research. It can be used for individual and collaborative work, hosted on a shared server or accessed remotely, or run on a personal computer without the need for coding skills.
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous chromosomes of the human genome reveals allele-specific gene expression and allele-specific gene regulation by assessing allelic imbalance of read counts at individual sites. Here we formally describe an advanced statistical framework for detecting the allelic imbalance in allelic read counts at single-nucleotide variants detected in diverse omics studies (ChIP-Seq, ATAC-Seq, DNase-Seq, CAGE-Seq, and others). MIXALIME accounts for copy-number variants and aneuploidy, reference read mapping bias, and provides several scoring models to balance between sensitivity and specificity when scoring data with varying levels of experimental noise-caused overdispersion.
Previous studies have developed fairness methods for biased models that exhibit discriminatory behaviors towards specific subgroups. While these models have shown promise in achieving fair predictions, recent research has identified their potential vulnerability to score-based membership inference attacks (MIAs). In these attacks, adversaries can infer whether a particular data sample was used during training by analyzing the model's prediction scores. However, our investigations reveal that these score-based MIAs are ineffective when targeting fairness-enhanced models in binary classifications. The attack models trained to launch the MIAs degrade into simplistic threshold models, resulting in lower attack performance. Meanwhile, we observe that fairness methods often lead to prediction performance degradation for the majority subgroups of the training data. This raises the barrier to successful attacks and widens the prediction gaps between member and non-member data. Building upon these insights, we propose an efficient MIA method against fairness-enhanced models based on fairness discrepancy results (FD-MIA). It leverages the difference in the predictions from both the original and fairness-enhanced models and exploits the observed prediction gaps as attack clues. We also explore potential strategies for mitigating privacy leakages. Extensive experiments validate our findings and demonstrate the efficacy of the proposed method.
Human-machine interfaces (HMI) facilitate communication between humans and machines, and their importance has increased in modern technology. However, traditional HMIs are often static and do not adapt to individual user preferences or behavior. Adaptive User Interfaces (AUIs) have become increasingly important in providing personalized user experiences. Machine learning techniques have gained traction in User Experience (UX) research to provide smart adaptations that can reduce user cognitive load. This paper presents an ongoing exploration of a method for generating adaptive user interfaces by analyzing user interactions and contextual data. It also provides an illustrative example using Markov chains to predict the next step for users interacting with an app for an industrial mixing machine. Furthermore, the paper conducts an offline evaluation of the approach, focusing on the precision of the recommendations. The study emphasizes the importance of incorporating user interactions and contextual data into the design of adaptive HMIs, while acknowledging the existing challenges and potential benefits.
Accurate detection and segmentation of brain tumors is critical for medical diagnosis. However, current supervised learning methods require extensively annotated images and the state-of-the-art generative models used in unsupervised methods often have limitations in covering the whole data distribution. In this paper, we propose a novel framework Two-Stage Generative Model (TSGM) that combines Cycle Generative Adversarial Network (CycleGAN) and Variance Exploding stochastic differential equation using joint probability (VE-JP) to improve brain tumor detection and segmentation. The CycleGAN is trained on unpaired data to generate abnormal images from healthy images as data prior. Then VE-JP is implemented to reconstruct healthy images using synthetic paired abnormal images as a guide, which alters only pathological regions but not regions of healthy. Notably, our method directly learned the joint probability distribution for conditional generation. The residual between input and reconstructed images suggests the abnormalities and a thresholding method is subsequently applied to obtain segmentation results. Furthermore, the multimodal results are weighted with different weights to improve the segmentation accuracy further. We validated our method on three datasets, and compared with other unsupervised methods for anomaly detection and segmentation. The DSC score of 0.8590 in BraTs2020 dataset, 0.6226 in ITCS dataset and 0.7403 in In-house dataset show that our method achieves better segmentation performance and has better generalization.
The use of anthropomorphic robotic hands for assisting individuals in situations where human hands may be unavailable or unsuitable has gained significant importance. In this paper, we propose a novel task called human-assisting dexterous grasping that aims to train a policy for controlling a robotic hand's fingers to assist users in grasping objects. Unlike conventional dexterous grasping, this task presents a more complex challenge as the policy needs to adapt to diverse user intentions, in addition to the object's geometry. We address this challenge by proposing an approach consisting of two sub-modules: a hand-object-conditional grasping primitive called Grasping Gradient Field~(GraspGF), and a history-conditional residual policy. GraspGF learns `how' to grasp by estimating the gradient from a success grasping example set, while the residual policy determines `when' and at what speed the grasping action should be executed based on the trajectory history. Experimental results demonstrate the superiority of our proposed method compared to baselines, highlighting the user-awareness and practicality in real-world applications. The codes and demonstrations can be viewed at "//sites.google.com/view/graspgf".
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