Aqueous solubility is a valuable yet challenging property to predict. Computing solubility using first-principles methods requires accounting for the competing effects of entropy and enthalpy, resulting in long computations for relatively poor accuracy. Data-driven approaches, such as deep learning, offer improved accuracy and computational efficiency but typically lack uncertainty quantification. Additionally, ease of use remains a concern for any computational technique, resulting in the sustained popularity of group-based contribution methods. In this work, we addressed these problems with a deep learning model with predictive uncertainty that runs on a static website (without a server). This approach moves computing needs onto the website visitor without requiring installation, removing the need to pay for and maintain servers. Our model achieves satisfactory results in solubility prediction. Furthermore, we demonstrate how to create molecular property prediction models that balance uncertainty and ease of use. The code is available at //github.com/ur-whitelab/mol.dev, and the model is usable at //mol.dev.
相關內容
Bayesian inference for complex models with an intractable likelihood can be tackled using algorithms performing many calls to computer simulators. These approaches are collectively known as "simulation-based inference" (SBI). Recent SBI methods have made use of neural networks (NN) to provide approximate, yet expressive constructs for the unavailable likelihood function and the posterior distribution. However, they do not generally achieve an optimal trade-off between accuracy and computational demand. In this work, we propose an alternative that provides both approximations to the likelihood and the posterior distribution, using structured mixtures of probability distributions. Our approach produces accurate posterior inference when compared to state-of-the-art NN-based SBI methods, while exhibiting a much smaller computational footprint. We illustrate our results on several benchmark models from the SBI literature.
High-performing out-of-distribution (OOD) detection, both anomaly and novel class, is an important prerequisite for the practical use of classification models. In this paper, we focus on the species recognition task in images concerned with large databases, a large number of fine-grained hierarchical classes, severe class imbalance, and varying image quality. We propose a framework for combining individual OOD measures into one combined OOD (COOD) measure using a supervised model. The individual measures are several existing state-of-the-art measures and several novel OOD measures developed with novel class detection and hierarchical class structure in mind. COOD was extensively evaluated on three large-scale (500k+ images) biodiversity datasets in the context of anomaly and novel class detection. We show that COOD outperforms individual, including state-of-the-art, OOD measures by a large margin in terms of TPR@1% FPR in the majority of experiments, e.g., improving detecting ImageNet images (OOD) from 54.3% to 85.4% for the iNaturalist 2018 dataset. SHAP (feature contribution) analysis shows that different individual OOD measures are essential for various tasks, indicating that multiple OOD measures and combinations are needed to generalize. Additionally, we show that explicitly considering ID images that are incorrectly classified for the original (species) recognition task is important for constructing high-performing OOD detection methods and for practical applicability. The framework can easily be extended or adapted to other tasks and media modalities.
Active learning can improve the efficiency of training prediction models by identifying the most informative new labels to acquire. However, non-response to label requests can impact active learning's effectiveness in real-world contexts. We conceptualise this degradation by considering the type of non-response present in the data, demonstrating that biased non-response is particularly detrimental to model performance. We argue that biased non-response is likely in contexts where the labelling process, by nature, relies on user interactions. To mitigate the impact of biased non-response, we propose a cost-based correction to the sampling strategy--the Upper Confidence Bound of the Expected Utility (UCB-EU)--that can, plausibly, be applied to any active learning algorithm. Through experiments, we demonstrate that our method successfully reduces the harm from labelling non-response in many settings. However, we also characterise settings where the non-response bias in the annotations remains detrimental under UCB-EU for specific sampling methods and data generating processes. Finally, we evaluate our method on a real-world dataset from an e-commerce platform. We show that UCB-EU yields substantial performance improvements to conversion models that are trained on clicked impressions. Most generally, this research serves to both better conceptualise the interplay between types of non-response and model improvements via active learning, and to provide a practical, easy-to-implement correction that mitigates model degradation.
Change-point detection, detecting an abrupt change in the data distribution from sequential data, is a fundamental problem in statistics and machine learning. CUSUM is a popular statistical method for online change-point detection due to its efficiency from recursive computation and constant memory requirement, and it enjoys statistical optimality. CUSUM requires knowing the precise pre- and post-change distribution. However, post-change distribution is usually unknown a priori since it represents anomaly and novelty. Classic CUSUM can perform poorly when there is a model mismatch with actual data. While likelihood ratio-based methods encounter challenges facing high dimensional data, neural networks have become an emerging tool for change-point detection with computational efficiency and scalability. In this paper, we introduce a neural network CUSUM (NN-CUSUM) for online change-point detection. We also present a general theoretical condition when the trained neural networks can perform change-point detection and what losses can achieve our goal. We further extend our analysis by combining it with the Neural Tangent Kernel theory to establish learning guarantees for the standard performance metrics, including the average run length (ARL) and expected detection delay (EDD). The strong performance of NN-CUSUM is demonstrated in detecting change-point in high-dimensional data using both synthetic and real-world data.
Efficient and accurate algorithms are necessary to reconstruct particles in the highly granular detectors anticipated at the High-Luminosity Large Hadron Collider and the Future Circular Collider. We study scalable machine learning models for event reconstruction in electron-positron collisions based on a full detector simulation. Particle-flow reconstruction can be formulated as a supervised learning task using tracks and calorimeter clusters. We compare a graph neural network and kernel-based transformer and demonstrate that we can avoid quadratic operations while achieving realistic reconstruction. We show that hyperparameter tuning significantly improves the performance of the models. The best graph neural network model shows improvement in the jet transverse momentum resolution by up to 50% compared to the rule-based algorithm. The resulting model is portable across Nvidia, AMD and Habana hardware. Accurate and fast machine-learning based reconstruction can significantly improve future measurements at colliders.
Distributed control increases system scalability, flexibility, and redundancy. Foundational to such decentralisation is consensus formation, by which decision-making and coordination are achieved. However, decentralised multi-agent systems are inherently vulnerable to disruption. To develop a resilient consensus approach, inspiration is taken from the study of social systems and their dynamics; specifically, the Deffuant Model. A dynamic algorithm is presented enabling efficient consensus to be reached with an unknown number of disruptors present within a multi-agent system. By inverting typical social tolerance, agents filter out extremist non-standard opinions that would drive them away from consensus. This approach allows distributed systems to deal with unknown disruptions, without knowledge of the network topology or the numbers and behaviours of the disruptors. A disruptor-agnostic algorithm is particularly suitable to real-world applications where this information is typically unknown. Faster and tighter convergence can be achieved across a range of scenarios with the social dynamics inspired algorithm, compared with standard Mean-Subsequence-Reduced-type methods.
In large-scale systems there are fundamental challenges when centralised techniques are used for task allocation. The number of interactions is limited by resource constraints such as on computation, storage, and network communication. We can increase scalability by implementing the system as a distributed task-allocation system, sharing tasks across many agents. However, this also increases the resource cost of communications and synchronisation, and is difficult to scale. In this paper we present four algorithms to solve these problems. The combination of these algorithms enable each agent to improve their task allocation strategy through reinforcement learning, while changing how much they explore the system in response to how optimal they believe their current strategy is, given their past experience. We focus on distributed agent systems where the agents' behaviours are constrained by resource usage limits, limiting agents to local rather than system-wide knowledge. We evaluate these algorithms in a simulated environment where agents are given a task composed of multiple subtasks that must be allocated to other agents with differing capabilities, to then carry out those tasks. We also simulate real-life system effects such as networking instability. Our solution is shown to solve the task allocation problem to 6.7% of the theoretical optimal within the system configurations considered. It provides 5x better performance recovery over no-knowledge retention approaches when system connectivity is impacted, and is tested against systems up to 100 agents with less than a 9% impact on the algorithms' performance.
We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
小貼士
登錄享
相關主題
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191