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Publications
A high-throughput phenotypic screen combined with an ultra-large-scale deep learning-based virtual screening reveals novel scaffolds of antibacterial compounds
In many data-driven applications, higher-order relationships among multiple objects are essential in capturing complex interactions. Hypergr… (see more)aphs, which generalize graphs by allowing edges to connect any number of nodes, provide a flexible and powerful framework for modeling such higher-order relationships. In this work, we introduce hypergraph diffusion wavelets and describe their favorable spectral and spatial properties. We demonstrate their utility for biomedical discovery in spatially resolved transcriptomics by applying the method to represent disease-relevant cellular niches for Alzheimer’s disease.
In many data-driven applications, higher-order relationships among multiple objects are essential in capturing complex interactions. Hypergr… (see more)aphs, which generalize graphs by allowing edges to connect any number of nodes, provide a flexible and powerful framework for modeling such higher-order relationships. In this work, we introduce hypergraph diffusion wavelets and describe their favorable spectral and spatial properties. We demonstrate their utility for biomedical discovery in spatially resolved transcriptomics by applying the method to represent disease-relevant cellular niches for Alzheimer’s disease.
Generative diffusion models, notable for their large parameter count (exceeding 100 million) and operation within high-dimensional image spa… (see more)ces, pose significant challenges for traditional uncertainty estimation methods due to computational demands. In this work, we introduce an innovative framework, Diffusion Ensembles for Capturing Uncertainty (DECU), designed for estimating epistemic uncertainty for diffusion models. The DECU framework introduces a novel method that efficiently trains ensembles of conditional diffusion models by incorporating a static set of pre-trained parameters, drastically reducing the computational burden and the number of parameters that require training. Additionally, DECU employs Pairwise-Distance Estimators (PaiDEs) to accurately measure epistemic uncertainty by evaluating the mutual information between model outputs and weights in high-dimensional spaces. The effectiveness of this framework is demonstrated through experiments on the ImageNet dataset, highlighting its capability to capture epistemic uncertainty, specifically in under-sampled image classes.
2024-09-12
Proceedings of the Fortieth Conference on Uncertainty in Artificial Intelligence (published)
Predicting molecular impact on cellular function is a core challenge in therapeutic design. Phenomic experiments, designed to capture cellul… (see more)ar morphology, utilize microscopy based techniques and demonstrate a high throughput solution for uncovering molecular impact on the cell. In this work, we learn a joint latent space between molecular structures and microscopy phenomic experiments, aligning paired samples with contrastive learning. Specifically, we study the problem ofContrastive PhenoMolecular Retrieval, which consists of zero-shot molecular structure identification conditioned on phenomic experiments. We assess challenges in multi-modal learning of phenomics and molecular modalities such as experimental batch effect, inactive molecule perturbations, and encoding perturbation concentration. We demonstrate improved multi-modal learner retrieval through (1) a uni-modal pre-trained phenomics model, (2) a novel inter sample similarity aware loss, and (3) models conditioned on a representation of molecular concentration. Following this recipe, we propose MolPhenix, a molecular phenomics model. MolPhenix leverages a pre-trained phenomics model to demonstrate significant performance gains across perturbation concentrations, molecular scaffolds, and activity thresholds. In particular, we demonstrate an 8.1x improvement in zero shot molecular retrieval of active molecules over the previous state-of-the-art, reaching 77.33% in top-1% accuracy. These results open the door for machine learning to be applied in virtual phenomics screening, which can significantly benefit drug discovery applications.
Over the past decade, Graph Neural Networks (GNNs) have achieved great success on machine learning tasks with relational data. However, rece… (see more)nt studies have found that heterophily can cause significant performance degradation of GNNs, especially on node-level tasks. Numerous heterophilic benchmark datasets have been put forward to validate the efficacy of heterophily-specific GNNs and various homophily metrics have been designed to help people recognize these malignant datasets. Nevertheless, there still exist multiple pitfalls that severely hinder the proper evaluation of new models and metrics. In this paper, we point out three most serious pitfalls: 1) a lack of hyperparameter tuning; 2) insufficient model evaluation on the real challenging heterophilic datasets; 3) missing quantitative evaluation benchmark for homophily metrics on synthetic graphs. To overcome these challenges, we first train and fine-tune baseline models on
Correction: Economic evaluation of the effect of needle and syringe programs on skin, soft tissue, and vascular infections in people who inject drugs: a microsimulation modelling approach
Deep neural networks provide Reinforcement Learning (RL) powerful function approximators to address large-scale decision-making problems. Ho… (see more)wever, these approximators introduce challenges due to the non-stationary nature of RL training. One source of the challenges in RL is that output predictions can churn, leading to uncontrolled changes after each batch update for states not included in the batch. Although such a churn phenomenon exists in each step of network training, how churn occurs and impacts RL remains under-explored. In this work, we start by characterizing churn in a view of Generalized Policy Iteration with function approximation, and we discover a chain effect of churn that leads to a cycle where the churns in value estimation and policy improvement compound and bias the learning dynamics throughout the iteration. Further, we concretize the study and focus on the learning issues caused by the chain effect in different settings, including greedy action deviation in value-based methods, trust region violation in proximal policy optimization, and dual bias of policy value in actor-critic methods. We then propose a method to reduce the chain effect across different settings, called Churn Approximated ReductIoN (CHAIN), which can be easily plugged into most existing DRL algorithms. Our experiments demonstrate the effectiveness of our method in both reducing churn and improving learning performance across online and offline, value-based and policy-based RL settings, as well as a scaling setting.
Neural network training can be accelerated when a learnable update rule is used in lieu of classic adaptive optimizers (e.g. Adam). However,… (see more) learnable update rules can be costly and unstable to train and use. Recently, Jang et al. (2023) proposed a simpler approach to accelerate training based on weight nowcaster networks (WNNs). In their approach, Adam is used for most of the optimization steps and periodically, only every few steps, a WNN nowcasts (predicts near future) parameters. We improve WNNs by proposing neuron interaction and nowcasting (NiNo) networks. In contrast to WNNs, NiNo leverages neuron connectivity and graph neural networks to more accurately nowcast parameters. We further show that in some networks, such as Transformers, modeling neuron connectivity accurately is challenging. We address this and other limitations, which allows NiNo to accelerate Adam training by up to 50% in vision and language tasks.
