The increased capabilities of generative AI have dramatically expanded its possible use cases in medicine. We provide a comprehensive overview of generative AI use cases for clinicians, patients, clinical trial organizers, researchers, and trainees. We then discuss the many challenges -- including maintaining privacy and security, improving transparency and interpretability, upholding equity, and rigorously evaluating models -- which must be overcome to realize this potential, and the open research directions they give rise to.

Nuclear magnetic resonance instruments are becoming available to the do-it-yourself community. The challenges encountered in the endeavor to build a magnetic resonance imaging instrument from scratch were confronted in a four-day hackathon at Singapore University of Technology and Design in spring 2024. One day was devoted to educational lectures and three days to system construction and testing. Seventy young researchers from all parts of the world formed six teams focusing on magnet, gradient coil, RF coil, console, system integration, and design, which together produced a working MRI instrument in three days. The different steps, encountered challenges, and their solutions are reported.

Cancer progression involves the sequential accumulation of genetic alterations that cumulatively shape the tumour phenotype. In prostate cancer, tumours can follow divergent evolutionary trajectories that lead to distinct subtypes, but the causes of this divergence remain unclear. While causal inference could elucidate the factors involved, conventional methods are unsuitable due to the possibility of unobserved confounders and ambiguity in the direction of causality. Here, we propose a method that circumvents these issues and apply it to genomic data from 829 prostate cancer patients. We identify several genetic alterations that drive divergence as well as others that prevent this transition, locking tumours into one trajectory. Further analysis reveals that these genetic alterations may cause each other, implying a positive-feedback loop that accelerates divergence. Our findings provide insights into how cancer subtypes emerge and offer a foundation for genomic surveillance strategies aimed at monitoring the progression of prostate cancer.

Advances in large language models (LLMs) have driven an explosion of interest about their societal impacts. Much of the discourse around how they will impact social equity has been cautionary or negative, focusing on questions like "how might LLMs be biased and how would we mitigate those biases?" This is a vital discussion: the ways in which AI generally, and LLMs specifically, can entrench biases have been well-documented. But equally vital, and much less discussed, is the more opportunity-focused counterpoint: "what promising applications do LLMs enable that could promote equity?" If LLMs are to enable a more equitable world, it is not enough just to play defense against their biases and failure modes. We must also go on offense, applying them positively to equity-enhancing use cases to increase opportunities for underserved groups and reduce societal discrimination. There are many choices which determine the impact of AI, and a fundamental choice very early in the pipeline is the problems we choose to apply it to. If we focus only later in the pipeline -- making LLMs marginally more fair as they facilitate use cases which intrinsically entrench power -- we will miss an important opportunity to guide them to equitable impacts. Here, we highlight the emerging potential of LLMs to promote equity by presenting four newly possible, promising research directions, while keeping risks and cautionary points in clear view.

Preventing Veteran suicide is a national priority. The US Department of Veterans Affairs (VA) collects, analyzes, and publishes data to inform suicide prevention strategies. Current approaches for detecting suicidal ideation mostly rely on patient self report which are inadequate and time consuming. In this research study, our goal was to automate suicidal ideation detection from acoustic and linguistic features of an individual's speech using machine learning (ML) algorithms. Using voice data collected from Veterans enrolled in a large interventional study on Gulf War Illness at the Washington DC VA Medical Center, we conducted an evaluation of the performance of different ML approaches in achieving our objective. By fitting both classical ML and deep learning models to the dataset, we identified the algorithms that were most effective for each feature set. Among classical machine learning algorithms, the Support Vector Machine (SVM) trained on acoustic features performed best in classifying suicidal Veterans. Among deep learning methods, the Convolutional Neural Network (CNN) trained on the linguistic features performed best. Our study shows that speech analysis in a machine learning pipeline is a promising approach for detecting suicidality among Veterans.

This data curation work introduces the first large-scale dataset of radial k-space and DICOM data for breast DCE-MRI acquired in diagnostic breast MRI exams. Our dataset includes case-level labels indicating patient age, menopause status, lesion status (negative, benign, and malignant), and lesion type for each case. The public availability of this dataset and accompanying reconstruction code will support research and development of fast and quantitative breast image reconstruction and machine learning methods.

Tests for racial bias commonly assess whether two people of different races are treated differently. A fundamental challenge is that, because two people may differ in many ways, factors besides race might explain differences in treatment. Here, we propose a test for bias which circumvents the difficulty of comparing two people by instead assessing whether the $\textit{same person}$ is treated differently when their race is perceived differently. We apply our method to test for bias in police traffic stops, finding that the same driver is likelier to be searched or arrested by police when they are perceived as Hispanic than when they are perceived as white. Our test is broadly applicable to other datasets where race, gender, or other identity data are perceived rather than self-reported, and the same person is observed multiple times.

Analyzing the structure of sampled features from an input data distribution is challenging when constrained by limited measurements in both the number of inputs and features. Traditional approaches often rely on the eigenvalue spectrum of the sample covariance matrix derived from finite measurement matrices; however, these spectra are sensitive to the size of the measurement matrix, leading to biased insights. In this paper, we introduce a novel algorithm that provides unbiased estimates of the spectral moments of the kernel integral operator in the limit of infinite inputs and features from finitely sampled measurement matrices. Our method, based on dynamic programming, is efficient and capable of estimating the moments of the operator spectrum. We demonstrate the accuracy of our estimator on radial basis function (RBF) kernels, highlighting its consistency with the theoretical spectra. Furthermore, we showcase the practical utility and robustness of our method in understanding the geometry of learned representations in neural networks.

Imagine an oracle that correctly predicts the outcome of every particle physics experiment, the products of every chemical reaction, or the function of every protein. Such an oracle would revolutionize science and technology as we know them. However, as scientists, we would not be satisfied with the oracle itself. We want more. We want to comprehend how the oracle conceived these predictions. This feat, denoted as scientific understanding, has frequently been recognized as the essential aim of science. Now, the ever-growing power of computers and artificial intelligence poses one ultimate question: How can advanced artificial systems contribute to scientific understanding or achieve it autonomously? We are convinced that this is not a mere technical question but lies at the core of science. Therefore, here we set out to answer where we are and where we can go from here. We first seek advice from the philosophy of science to understand scientific understanding. Then we review the current state of the art, both from literature and by collecting dozens of anecdotes from scientists about how they acquired new conceptual understanding with the help of computers. Those combined insights help us to define three dimensions of android-assisted scientific understanding: The android as a I) computational microscope, II) resource of inspiration and the ultimate, not yet existent III) agent of understanding. For each dimension, we explain new avenues to push beyond the status quo and unleash the full power of artificial intelligence's contribution to the central aim of science. We hope our perspective inspires and focuses research towards androids that get new scientific understanding and ultimately bring us closer to true artificial scientists.

In this paper, we study the efficacy and utility of recent advances in non-local, non-linear image interpolation and extrapolation algorithms, specifically, ideas based on Implicit Neural Representations (INR), as a tool for analysis of spatial transcriptomics data. We seek to utilize the microarray gene expression data sparsely sampled in the healthy human brain, and produce fully resolved spatial maps of any given gene across the whole brain at a voxel-level resolution. To do so, we first obtained the 100 top AD risk genes, whose baseline spatial transcriptional profiles were obtained from the Allen Human Brain Atlas (AHBA). We adapted Implicit Neural Representation models so that the pipeline can produce robust voxel-resolution quantitative maps of all genes. We present a variety of experiments using interpolations obtained from Abagen as a baseline/reference.

The rise of neurotechnologies, especially in combination with AI-based methods for brain data analytics, has given rise to concerns around the protection of mental privacy, mental integrity and cognitive liberty - often framed as 'neurorights' in ethical, legal and policy discussions. Several states are now looking at including 'neurorights' into their constitutional legal frameworks and international institutions and organizations, such as UNESCO and the Council of Europe, are taking an active interest in developing international policy and governance guidelines on this issue. However, in many discussions of 'neurorights' the philosophical assumptions, ethical frames of reference and legal interpretation are either not made explicit or are in conflict with each other. The aim of this multidisciplinary work here is to provide conceptual, ethical and legal foundations that allow for facilitating a common minimalist conceptual understanding of mental privacy, mental integrity and cognitive liberty to facilitate scholarly, legal and policy discussions.

The claustrum (Cl) is a thin grey matter structure located in the center of each brain hemisphere. Cl has been hypothesized as a central hub of the brain for multisensory/sensorimotor integration, consciousness, and attention. Accumulating evidence has suggested that Cl might be important in the development of severe neurological and psychiatric symptoms including epileptic seizures and psychosis. However, the specifics of the roles of Cl in human epilepsy and psychosis are largely unknown, primarily due to methodological limitations related to the thin morphology of Cl that is challenging to delineate accurately using conventional methods. The goal of this work is to develop noninvasive multimodal neuroimaging methods to delineate Cl anatomy by utilizing a large healthy adult high resolution (0.7mm3) T1-weighted MRI collected as part of the Washington University-Minnesota Consortium Human Connectome Project (WU-Minn HCP). We developed a comprehensive manual segmentation protocol to delineate Cl based on a cellular level brain atlas. The protocol involves detailed guidelines to delineate the three subregions of Cl, including the dorsal, ventral, and temporal Cl that can be parcellated based on a geometric method. As demonstrated in a representative result, Cl is large in its anterior-posterior, and the dorsal-ventral extent. Also, the volume is comparable to that of the amygdala. It is required to assess the reliability of the protocol so that it can be used for future anatomical studies of neuropsychiatric disorders, including epilepsy and schizophrenia.

Multi-task learning (MTL) refers to the paradigm of learning multiple related tasks together. In contrast, in single-task learning (STL) each individual task is learned independently. MTL often leads to better trained models because they can leverage the commonalities among related tasks. However, because MTL algorithms can ``leak" information from different models across different tasks, MTL poses a potential security risk. Specifically, an adversary may participate in the MTL process through one task and thereby acquire the model information for another task. The previously proposed privacy-preserving MTL methods protect data instances rather than models, and some of them may underperform in comparison with STL methods. In this paper, we propose a privacy-preserving MTL framework to prevent information from each model leaking to other models based on a perturbation of the covariance matrix of the model matrix. We study two popular MTL approaches for instantiation, namely, learning the low-rank and group-sparse patterns of the model matrix. Our algorithms can be guaranteed not to underperform compared with STL methods. We build our methods based upon tools for differential privacy, and privacy guarantees, utility bounds are provided, and heterogeneous privacy budgets are considered. The experiments demonstrate that our algorithms outperform the baseline methods constructed by existing privacy-preserving MTL methods on the proposed model-protection problem.

Recently, 3D medical image reconstruction (MIR) and segmentation (MIS) based on deep neural networks have been developed with promising results, and attention mechanism has been further designed to capture global contextual information for performance enhancement. However, the large size of 3D volume images poses a great computational challenge to traditional attention methods. In this paper, we propose a folded attention (FA) approach to improve the computational efficiency of traditional attention methods on 3D medical images. The main idea is that we apply tensor folding and unfolding operations with four permutations to build four small sub-affinity matrices to approximate the original affinity matrix. Through four consecutive sub-attention modules of FA, each element in the feature tensor can aggregate spatial-channel information from all other elements. Compared to traditional attention methods, with moderate improvement of accuracy, FA can substantially reduce the computational complexity and GPU memory consumption. We demonstrate the superiority of our method on two challenging tasks for 3D MIR and MIS, which are quantitative susceptibility mapping and multiple sclerosis lesion segmentation.

Resting-state functional MRI (rs-fMRI) scans hold the potential to serve as a diagnostic or prognostic tool for a wide variety of conditions, such as autism, Alzheimer's disease, and stroke. While a growing number of studies have demonstrated the promise of machine learning algorithms for rs-fMRI based clinical or behavioral prediction, most prior models have been limited in their capacity to exploit the richness of the data. For example, classification techniques applied to rs-fMRI often rely on region-based summary statistics and/or linear models. In this work, we propose a novel volumetric Convolutional Neural Network (CNN) framework that takes advantage of the full-resolution 3D spatial structure of rs-fMRI data and fits non-linear predictive models. We showcase our approach on a challenging large-scale dataset (ABIDE, with N > 2,000) and report state-of-the-art accuracy results on rs-fMRI-based discrimination of autism patients and healthy controls.

Recently, large pretrained language models have achieved compelling performance on commonsense benchmarks. Nevertheless, it is unclear what commonsense knowledge the models learn and whether they solely exploit spurious patterns. Feature attributions are popular explainability techniques that identify important input concepts for model outputs. However, commonsense knowledge tends to be implicit and rarely explicitly presented in inputs. These methods cannot infer models' implicit reasoning over mentioned concepts. We present CommonsenseVIS, a visual explanatory system that utilizes external commonsense knowledge bases to contextualize model behavior for commonsense question-answering. Specifically, we extract relevant commonsense knowledge in inputs as references to align model behavior with human knowledge. Our system features multi-level visualization and interactive model probing and editing for different concepts and their underlying relations. Through a user study, we show that CommonsenseVIS helps NLP experts conduct a systematic and scalable visual analysis of models' relational reasoning over concepts in different situations.

Estimating the prevalence of a medical condition, or the proportion of the population in which it occurs, is a fundamental problem in healthcare and public health. Accurate estimates of the relative prevalence across groups -- capturing, for example, that a condition affects women more frequently than men -- facilitate effective and equitable health policy which prioritizes groups who are disproportionately affected by a condition. However, it is difficult to estimate relative prevalence when a medical condition is underreported. In this work, we provide a method for accurately estimating the relative prevalence of underreported medical conditions, building upon the positive unlabeled learning framework. We show that under the commonly made covariate shift assumption -- i.e., that the probability of having a disease conditional on symptoms remains constant across groups -- we can recover the relative prevalence, even without restrictive assumptions commonly made in positive unlabeled learning and even if it is impossible to recover the absolute prevalence. We conduct experiments on synthetic and real health data which demonstrate our method's ability to recover the relative prevalence more accurately than do baselines, and demonstrate the method's robustness to plausible violations of the covariate shift assumption. We conclude by illustrating the applicability of our method to case studies of intimate partner violence and hate speech.