Brian Caffo

Eric W. Bridgeford, Jaewon Chung, Brian Gilbert et al.

Causal inference studies whether the presence of a variable influences an observed outcome. As measured by quantities such as the "average treatment effect," this paradigm is employed across numerous biological fields, from vaccine and drug development to policy interventions. Unfortunately, the majority of these methods are often limited to univariate outcomes. Our work generalizes causal estimands to outcomes with any number of dimensions or any measurable space, and formulates traditional causal estimands for nominal variables as causal discrepancy tests. We propose a simple technique for adjusting universally consistent conditional independence tests and prove that these tests are universally consistent causal discrepancy tests. Numerical experiments illustrate that our method, Causal CDcorr, leads to improvements in both finite sample validity and power when compared to existing strategies. Our methods are all open source and available at github.com/ebridge2/cdcorr.

Ruxiao Duan, Brian Caffo, Harrison X. Bai et al.

Uncertainty quantification of deep neural networks has become an active field of research and plays a crucial role in various downstream tasks such as active learning. Recent advances in evidential deep learning shed light on the direct quantification of aleatoric and epistemic uncertainties with a single forward pass of the model. Most traditional approaches adopt an entropy-based method to derive evidential uncertainty in classification, quantifying uncertainty at the sample level. However, the variance-based method that has been widely applied in regression problems is seldom used in the classification setting. In this work, we adapt the variance-based approach from regression to classification, quantifying classification uncertainty at the class level. The variance decomposition technique in regression is extended to class covariance decomposition in classification based on the law of total covariance, and the class correlation is also derived from the covariance. Experiments on cross-domain datasets are conducted to illustrate that the variance-based approach not only results in similar accuracy as the entropy-based one in active domain adaptation but also brings information about class-wise uncertainties as well as between-class correlations. The code is available at https://github.com/KerryDRX/EvidentialADA. This alternative means of evidential uncertainty quantification will give researchers more options when class uncertainties and correlations are important in their applications.

Noam H. Rotenberg, Andreia V. Faria, Brian Caffo

Ordinal data is widely prevalent in clinical and other domains, yet there is a lack of both modern, machine-learning based methods and publicly available software to address it. In this paper, we present a model-agnostic method of ordinal classification, which can apply any non-ordinal classification method in an ordinal fashion. We also provide an open-source implementation of these algorithms, in the form of a Python package. We apply these models on multiple real-world datasets to show their performance across domains. We show that they often outperform non-ordinal classification methods, especially when the number of datapoints is relatively small or when there are many classes of outcomes. This work, including the developed software, facilitates the use of modern, more powerful machine learning algorithms to handle ordinal data.

Zan Chaudhry, Noam H. Rotenberg, Brian Caffo et al.

Machine learning classification systems are susceptible to poor performance when trained with incorrect ground truth labels, even when data is well-curated by expert annotators. As machine learning becomes more widespread, it is increasingly imperative to identify and correct mislabeling to develop more powerful models. In this work, we motivate and describe Adaptive Label Error Detection (ALED), a novel method of detecting mislabeling. ALED extracts an intermediate feature space from a deep convolutional neural network, denoises the features, models the reduced manifold of each class with a multidimensional Gaussian distribution, and performs a simple likelihood ratio test to identify mislabeled samples. We show that ALED has markedly increased sensitivity, without compromising precision, compared to established label error detection methods, on multiple medical imaging datasets. We demonstrate an example where fine-tuning a neural network on corrected data results in a 33.8% decrease in test set errors, providing strong benefits to end users. The ALED detector is deployed in the Python package statlab.

Sohaib Naim, Brian Caffo, Haris I Sair et al.

Purpose: The aim of this work is to develop a neural network training framework for continual training of small amounts of medical imaging data and create heuristics to assess training in the absence of a hold-out validation or test set. Materials and Methods: We formulated a retrospective sequential learning approach that would train and consistently update a model on mini-batches of medical images over time. We address problems that impede sequential learning such as overfitting, catastrophic forgetting, and concept drift through PyTorch convolutional neural networks (CNN) and publicly available Medical MNIST and NIH Chest X-Ray imaging datasets. We begin by comparing two methods for a sequentially trained CNN with and without base pre-training. We then transition to two methods of unique training and validation data recruitment to estimate full information extraction without overfitting. Lastly, we consider an example of real-life data that shows how our approach would see mainstream research implementation. Results: For the first experiment, both approaches successfully reach a ~95% accuracy threshold, although the short pre-training step enables sequential accuracy to plateau in fewer steps. The second experiment comparing two methods showed better performance with the second method which crosses the ~90% accuracy threshold much sooner. The final experiment showed a slight advantage with a pre-training step that allows the CNN to cross ~60% threshold much sooner than without pre-training. Conclusion: We have displayed sequential learning as a serviceable multi-classification technique statistically comparable to traditional CNNs that can acquire data in small increments feasible for clinically realistic scenarios.

Jacob Renn, Ian Sotnek, Benjamin Harvey et al.

Neural networks have seen an explosion of usage and research in the past decade, particularly within the domains of computer vision and natural language processing. However, only recently have advancements in neural networks yielded performance improvements beyond narrow applications and translated to expanded multitask models capable of generalizing across multiple data types and modalities. Simultaneously, it has been shown that neural networks are overparameterized to a high degree, and pruning techniques have proved capable of significantly reducing the number of active weights within the network while largely preserving performance. In this work, we identify a methodology and network representational structure which allows a pruned network to employ previously unused weights to learn subsequent tasks. We employ these methodologies on well-known benchmarking datasets for testing purposes and show that networks trained using our approaches are able to learn multiple tasks, which may be related or unrelated, in parallel or in sequence without sacrificing performance on any task or exhibiting catastrophic forgetting.

Arunkumar Kannan, Martin A. Lindquist, Brian Caffo

Recent advances in deep learning have made it possible to predict phenotypic measures directly from functional magnetic resonance imaging (fMRI) brain volumes, sparking significant interest in the neuroimaging community. However, existing approaches, primarily based on convolutional neural networks or transformer architectures, often struggle to model the complex relationships inherent in fMRI data, limited by their inability to capture long-range spatial and temporal dependencies. To overcome these shortcomings, we introduce BrainMT, a novel hybrid framework designed to efficiently learn and integrate long-range spatiotemporal attributes in fMRI data. Our framework operates in two stages: (1) a bidirectional Mamba block with a temporal-first scanning mechanism to capture global temporal interactions in a computationally efficient manner; and (2) a transformer block leveraging self-attention to model global spatial relationships across the deep features processed by the Mamba block. Extensive experiments on two large-scale public datasets, UKBioBank and the Human Connectome Project, demonstrate that BrainMT achieves state-of-the-art performance on both classification (sex prediction) and regression (cognitive intelligence prediction) tasks, outperforming existing methods by a significant margin. Our code and implementation details will be made publicly available at this https://github.com/arunkumar-kannan/BrainMT-fMRI

Shijia Zhang, Xiyu Ding, Brian Caffo et al.

Early diagnosis of Alzheimer's disease (AD) is critical for intervention before irreversible neurodegeneration occurs. Structural MRI (sMRI) is widely used for AD diagnosis, but conventional deep learning approaches primarily rely on intensity-based features, which require large datasets to capture subtle structural changes. Jacobian determinant maps (JSM) provide complementary information by encoding localized brain deformations, yet existing multimodal fusion strategies fail to fully integrate these features with sMRI. We propose a cross-attention fusion framework to model the intrinsic relationship between sMRI intensity and JSM-derived deformations for AD classification. Using the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset, we compare cross-attention, pairwise self-attention, and bottleneck attention with four pre-trained 3D image encoders. Cross-attention fusion achieves superior performance, with mean ROC-AUC scores of 0.903 (+/-0.033) for AD vs. cognitively normal (CN) and 0.692 (+/-0.061) for mild cognitive impairment (MCI) vs. CN. Despite its strong performance, our model remains highly efficient, with only 1.56 million parameters--over 40 times fewer than ResNet-34 (63M) and Swin UNETR (61.98M). These findings demonstrate the potential of cross-attention fusion for improving AD diagnosis while maintaining computational efficiency.

Ashwin De Silva, Rahul Ramesh, Lyle Ungar et al.

Learning is a process which can update decision rules, based on past experience, such that future performance improves. Traditionally, machine learning is often evaluated under the assumption that the future will be identical to the past in distribution or change adversarially. But these assumptions can be either too optimistic or pessimistic for many problems in the real world. Real world scenarios evolve over multiple spatiotemporal scales with partially predictable dynamics. Here we reformulate the learning problem to one that centers around this idea of dynamic futures that are partially learnable. We conjecture that certain sequences of tasks are not retrospectively learnable (in which the data distribution is fixed), but are prospectively learnable (in which distributions may be dynamic), suggesting that prospective learning is more difficult in kind than retrospective learning. We argue that prospective learning more accurately characterizes many real world problems that (1) currently stymie existing artificial intelligence solutions and/or (2) lack adequate explanations for how natural intelligences solve them. Thus, studying prospective learning will lead to deeper insights and solutions to currently vexing challenges in both natural and artificial intelligences.

Gagan Sidhu, Brian Caffo

This manuscript uses machine learning techniques to exploit baseball pitchers' decision making, so-called "Baseball IQ," by modeling the at-bat information, pitch selection and counts, as a Markov Decision Process (MDP). Each state of the MDP models the pitcher's current pitch selection in a Markovian fashion, conditional on the information immediately prior to making the current pitch. This includes the count prior to the previous pitch, his ensuing pitch selection, the batter's ensuing action and the result of the pitch.

Huitong Qiu, Fang Han, Han Liu et al.

In this manuscript we consider the problem of jointly estimating multiple graphical models in high dimensions. We assume that the data are collected from n subjects, each of which consists of T possibly dependent observations. The graphical models of subjects vary, but are assumed to change smoothly corresponding to a measure of closeness between subjects. We propose a kernel based method for jointly estimating all graphical models. Theoretically, under a double asymptotic framework, where both (T,n) and the dimension d can increase, we provide the explicit rate of convergence in parameter estimation. It characterizes the strength one can borrow across different individuals and impact of data dependence on parameter estimation. Empirically, experiments on both synthetic and real resting state functional magnetic resonance imaging (rs-fMRI) data illustrate the effectiveness of the proposed method.