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Denoising diffusion probabilistic models (DDPMs) have recently taken the field of generative modeling by storm, pioneering new state-of-the-art results in disciplines such as computer vision and computational biology for diverse tasks ranging from text-guided image generation to structure-guided protein design. Along this latter line of research, methods have recently been proposed for generating 3D molecules using equivariant graph neural networks (GNNs) within a DDPM framework. However, such methods are unable to learn important geometric and physical properties of 3D molecules during molecular graph generation, as they adopt molecule-agnostic and non-geometric GNNs as their 3D graph denoising networks, which negatively impacts their ability to effectively scale to datasets of large 3D molecules. In this work, we address these gaps by introducing the Geometry-Complete Diffusion Model (GCDM) for 3D molecule generation, which outperforms existing 3D molecular diffusion models by significant margins across conditional and unconditional settings for the QM9 dataset as well as for the larger GEOM-Drugs dataset. Importantly, we demonstrate that the geometry-complete denoising process GCDM learns for 3D molecule generation allows the model to generate realistic and stable large molecules at the scale of GEOM-Drugs, whereas previous methods fail to do so with the features they learn. Additionally, we show that extensions of GCDM can not only effectively design 3D molecules for specific protein pockets but also that GCDM's geometric features can effectively be repurposed to directly optimize the geometry and chemical composition of existing 3D molecules for specific molecular properties, demonstrating new, real-world versatility of molecular diffusion models. Our source code and data are freely available at //github.com/BioinfoMachineLearning/Bio-Diffusion.

Ordinary differential equation (ODE) is an important tool to study the dynamics of a system of biological and physical processes. A central question in ODE modeling is to infer the significance of individual regulatory effect of one signal variable on another. However, building confidence band for ODE with unknown regulatory relations is challenging, and it remains largely an open question. In this article, we construct post-regularization confidence band for individual regulatory function in ODE with unknown functionals and noisy data observations. Our proposal is the first of its kind, and is built on two novel ingredients. The first is a new localized kernel learning approach that combines reproducing kernel learning with local Taylor approximation, and the second is a new de-biasing method that tackles infinite-dimensional functionals and additional measurement errors. We show that the constructed confidence band has the desired asymptotic coverage probability, and the recovered regulatory network approaches the truth with probability tending to one. We establish the theoretical properties when the number of variables in the system can be either smaller or larger than the number of sampling time points, and we study the regime-switching phenomenon. We demonstrate the efficacy of the proposed method through both simulations and illustrations with two data applications.

Document-level translation models are usually evaluated using general metrics such as BLEU, which are not informative about the benefits of context. Current work on context-aware evaluation, such as contrastive methods, only measure translation accuracy on words that need context for disambiguation. Such measures cannot reveal whether the translation model uses the correct supporting context. We propose to complement accuracy-based evaluation with measures of context utilization. We find that perturbation-based analysis (comparing models' performance when provided with correct versus random context) is an effective measure of overall context utilization. For a finer-grained phenomenon-specific evaluation, we propose to measure how much the supporting context contributes to handling context-dependent discourse phenomena. We show that automatically-annotated supporting context gives similar conclusions to human-annotated context and can be used as alternative for cases where human annotations are not available. Finally, we highlight the importance of using discourse-rich datasets when assessing context utilization.

Deep neural networks have exhibited remarkable performance in a variety of computer vision fields, especially in semantic segmentation tasks. Their success is often attributed to multi-level feature fusion, which enables them to understand both global and local information from an image. However, we found that multi-level features from parallel branches are on different scales. The scale disequilibrium is a universal and unwanted flaw that leads to detrimental gradient descent, thereby degrading performance in semantic segmentation. We discover that scale disequilibrium is caused by bilinear upsampling, which is supported by both theoretical and empirical evidence. Based on this observation, we propose injecting scale equalizers to achieve scale equilibrium across multi-level features after bilinear upsampling. Our proposed scale equalizers are easy to implement, applicable to any architecture, hyperparameter-free, implementable without requiring extra computational cost, and guarantee scale equilibrium for any dataset. Experiments showed that adopting scale equalizers consistently improved the mIoU index across various target datasets, including ADE20K, PASCAL VOC 2012, and Cityscapes, as well as various decoder choices, including UPerHead, PSPHead, ASPPHead, SepASPPHead, and FCNHead.

The advent of foundation models has revolutionized the fields of natural language processing and computer vision, paving the way for their application in autonomous driving (AD). This survey presents a comprehensive review of more than 40 research papers, demonstrating the role of foundation models in enhancing AD. Large language models contribute to planning and simulation in AD, particularly through their proficiency in reasoning, code generation and translation. In parallel, vision foundation models are increasingly adapted for critical tasks such as 3D object detection and tracking, as well as creating realistic driving scenarios for simulation and testing. Multi-modal foundation models, integrating diverse inputs, exhibit exceptional visual understanding and spatial reasoning, crucial for end-to-end AD. This survey not only provides a structured taxonomy, categorizing foundation models based on their modalities and functionalities within the AD domain but also delves into the methods employed in current research. It identifies the gaps between existing foundation models and cutting-edge AD approaches, thereby charting future research directions and proposing a roadmap for bridging these gaps.

Predictive multiplicity refers to the phenomenon in which classification tasks may admit multiple competing models that achieve almost-equally-optimal performance, yet generate conflicting outputs for individual samples. This presents significant concerns, as it can potentially result in systemic exclusion, inexplicable discrimination, and unfairness in practical applications. Measuring and mitigating predictive multiplicity, however, is computationally challenging due to the need to explore all such almost-equally-optimal models, known as the Rashomon set, in potentially huge hypothesis spaces. To address this challenge, we propose a novel framework that utilizes dropout techniques for exploring models in the Rashomon set. We provide rigorous theoretical derivations to connect the dropout parameters to properties of the Rashomon set, and empirically evaluate our framework through extensive experimentation. Numerical results show that our technique consistently outperforms baselines in terms of the effectiveness of predictive multiplicity metric estimation, with runtime speedup up to $20\times \sim 5000\times$. With efficient Rashomon set exploration and metric estimation, mitigation of predictive multiplicity is then achieved through dropout ensemble and model selection.

The digitization of healthcare data coupled with advances in computational capabilities has propelled the adoption of machine learning (ML) in healthcare. However, these methods can perpetuate or even exacerbate existing disparities, leading to fairness concerns such as the unequal distribution of resources and diagnostic inaccuracies among different demographic groups. Addressing these fairness problem is paramount to prevent further entrenchment of social injustices. In this survey, we analyze the intersection of fairness in machine learning and healthcare disparities. We adopt a framework based on the principles of distributive justice to categorize fairness concerns into two distinct classes: equal allocation and equal performance. We provide a critical review of the associated fairness metrics from a machine learning standpoint and examine biases and mitigation strategies across the stages of the ML lifecycle, discussing the relationship between biases and their countermeasures. The paper concludes with a discussion on the pressing challenges that remain unaddressed in ensuring fairness in healthcare ML, and proposes several new research directions that hold promise for developing ethical and equitable ML applications in healthcare.

Submodular functions, as well as the sub-class of decomposable submodular functions, and their optimization appear in a wide range of applications in machine learning, recommendation systems, and welfare maximization. However, optimization of decomposable submodular functions with millions of component functions is computationally prohibitive. Furthermore, the component functions may be private (they might represent user preference function, for example) and cannot be widely shared. To address these issues, we propose a {\em federated optimization} setting for decomposable submodular optimization. In this setting, clients have their own preference functions, and a weighted sum of these preferences needs to be maximized. We implement the popular {\em continuous greedy} algorithm in this setting where clients take parallel small local steps towards the local solution and then the local changes are aggregated at a central server. To address the large number of clients, the aggregation is performed only on a subsampled set. Further, the aggregation is performed only intermittently between stretches of parallel local steps, which reduces communication cost significantly. We show that our federated algorithm is guaranteed to provide a good approximate solution, even in the presence of above cost-cutting measures. Finally, we show how the federated setting can be incorporated in solving fundamental discrete submodular optimization problems such as Maximum Coverage and Facility Location.

The inductive biases of graph representation learning algorithms are often encoded in the background geometry of their embedding space. In this paper, we show that general directed graphs can be effectively represented by an embedding model that combines three components: a pseudo-Riemannian metric structure, a non-trivial global topology, and a unique likelihood function that explicitly incorporates a preferred direction in embedding space. We demonstrate the representational capabilities of this method by applying it to the task of link prediction on a series of synthetic and real directed graphs from natural language applications and biology. In particular, we show that low-dimensional cylindrical Minkowski and anti-de Sitter spacetimes can produce equal or better graph representations than curved Riemannian manifolds of higher dimensions.

Approaches based on deep neural networks have achieved striking performance when testing data and training data share similar distribution, but can significantly fail otherwise. Therefore, eliminating the impact of distribution shifts between training and testing data is crucial for building performance-promising deep models. Conventional methods assume either the known heterogeneity of training data (e.g. domain labels) or the approximately equal capacities of different domains. In this paper, we consider a more challenging case where neither of the above assumptions holds. We propose to address this problem by removing the dependencies between features via learning weights for training samples, which helps deep models get rid of spurious correlations and, in turn, concentrate more on the true connection between discriminative features and labels. Extensive experiments clearly demonstrate the effectiveness of our method on multiple distribution generalization benchmarks compared with state-of-the-art counterparts. Through extensive experiments on distribution generalization benchmarks including PACS, VLCS, MNIST-M, and NICO, we show the effectiveness of our method compared with state-of-the-art counterparts.