Neural additive models (NAMs) can improve the interpretability of deep neural networks by handling input features in separate additive sub-networks. However, they lack inherent mechanisms that provide calibrated uncertainties and enable selection of relevant features and interactions. Approaching NAMs from a Bayesian perspective, we enhance them in three primary ways, namely by a) providing credible intervals for the individual additive sub-networks; b) estimating the marginal likelihood to perform an implicit selection of features via an empirical Bayes procedure; and c) enabling a ranking of feature pairs as candidates for second-order interaction in fine-tuned models. In particular, we develop Laplace-approximated NAMs (LA-NAMs), which show improved empirical performance on tabular datasets and challenging real-world medical tasks.
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The field of computational pathology has witnessed remarkable progress in the development of both task-specific predictive models and task-agnostic self-supervised vision encoders. However, despite the explosive growth of generative artificial intelligence (AI), there has been limited study on building general purpose, multimodal AI assistants tailored to pathology. Here we present PathChat, a vision-language generalist AI assistant for human pathology using an in-house developed foundational vision encoder pretrained on 100 million histology images from over 100,000 patient cases and 1.18 million pathology image-caption pairs. The vision encoder is then combined with a pretrained large language model and the whole system is finetuned on over 250,000 diverse disease agnostic visual language instructions. We compare PathChat against several multimodal vision language AI assistants as well as GPT4V, which powers the commercially available multimodal general purpose AI assistant ChatGPT-4. When relevant clinical context is provided with the histology image, PathChat achieved a diagnostic accuracy of 87% on multiple-choice questions based on publicly available cases of diverse tissue origins and disease models. Additionally, using open-ended questions and human expert evaluation, we found that overall PathChat produced more accurate and pathologist-preferable responses to diverse queries related to pathology. As an interactive and general vision language AI assistant that can flexibly handle both visual and natural language inputs, PathChat can potentially find impactful applications in pathology education, research, and human-in-the-loop clinical decision making.
Bayesian optimization is a coherent, ubiquitous approach to decision-making under uncertainty, with applications including multi-arm bandits, active learning, and black-box optimization. Bayesian optimization selects decisions (i.e. objective function queries) with maximal expected utility with respect to the posterior distribution of a Bayesian model, which quantifies reducible, epistemic uncertainty about query outcomes. In practice, subjectively implausible outcomes can occur regularly for two reasons: 1) model misspecification and 2) covariate shift. Conformal prediction is an uncertainty quantification method with coverage guarantees even for misspecified models and a simple mechanism to correct for covariate shift. We propose conformal Bayesian optimization, which directs queries towards regions of search space where the model predictions have guaranteed validity, and investigate its behavior on a suite of black-box optimization tasks and tabular ranking tasks. In many cases we find that query coverage can be significantly improved without harming sample-efficiency.
Discovering causal structure from purely observational data (i.e., causal discovery), aiming to identify causal relationships among variables, is a fundamental task in machine learning. The recent invention of differentiable score-based DAG learners is a crucial enabler, which reframes the combinatorial optimization problem into a differentiable optimization with a DAG constraint over directed graph space. Despite their great success, these cutting-edge DAG learners incorporate DAG-ness independent score functions to evaluate the directed graph candidates, lacking in considering graph structure. As a result, measuring the data fitness alone regardless of DAG-ness inevitably leads to discovering suboptimal DAGs and model vulnerabilities. Towards this end, we propose a dynamic causal space for DAG structure learning, coined CASPER, that integrates the graph structure into the score function as a new measure in the causal space to faithfully reflect the causal distance between estimated and ground truth DAG. CASPER revises the learning process as well as enhances the DAG structure learning via adaptive attention to DAG-ness. Grounded by empirical visualization, CASPER, as a space, satisfies a series of desired properties, such as structure awareness and noise robustness. Extensive experiments on both synthetic and real-world datasets clearly validate the superiority of our CASPER over the state-of-the-art causal discovery methods in terms of accuracy and robustness.
Most work on the formal verification of neural networks has focused on bounding the set of outputs that correspond to a given set of inputs (for example, bounded perturbations of a nominal input). However, many use cases of neural network verification require solving the inverse problem, or over-approximating the set of inputs that lead to certain outputs. We present the INVPROP algorithm for verifying properties over the preimage of a linearly constrained output set, which can be combined with branch-and-bound to increase precision. Contrary to other approaches, our efficient algorithm is GPU-accelerated and does not require a linear programming solver. We demonstrate our algorithm for identifying safe control regions for a dynamical system via backward reachability analysis, verifying adversarial robustness, and detecting out-of-distribution inputs to a neural network. Our results show that in certain settings, we find over-approximations over 2500x tighter than prior work while being 2.5x faster. By strengthening robustness verification with output constraints, we consistently verify more properties than the previous state-of-the-art on multiple benchmarks, including a large model with 167k neurons in VNN-COMP 2023. Our algorithm has been incorporated into the $\alpha,\!\beta$-CROWN verifier, available at //abcrown.org.
The multiobjective evolutionary optimization algorithm (MOEA) is a powerful approach for tackling multiobjective optimization problems (MOPs), which can find a finite set of approximate Pareto solutions in a single run. However, under mild regularity conditions, the Pareto optimal set of a continuous MOP could be a low dimensional continuous manifold that contains infinite solutions. In addition, structure constraints on the whole optimal solution set, which characterize the patterns shared among all solutions, could be required in many real-life applications. It is very challenging for existing finite population based MOEAs to handle these structure constraints properly. In this work, we propose the first model-based algorithmic framework to learn the whole solution set with structure constraints for multiobjective optimization. In our approach, the Pareto optimality can be traded off with a preferred structure among the whole solution set, which could be crucial for many real-world problems. We also develop an efficient evolutionary learning method to train the set model with structure constraints. Experimental studies on benchmark test suites and real-world application problems demonstrate the promising performance of our proposed framework.
Graph Neural Networks (GNNs), which generalize deep neural networks to graph-structured data, have drawn considerable attention and achieved state-of-the-art performance in numerous graph related tasks. However, existing GNN models mainly focus on designing graph convolution operations. The graph pooling (or downsampling) operations, that play an important role in learning hierarchical representations, are usually overlooked. In this paper, we propose a novel graph pooling operator, called Hierarchical Graph Pooling with Structure Learning (HGP-SL), which can be integrated into various graph neural network architectures. HGP-SL incorporates graph pooling and structure learning into a unified module to generate hierarchical representations of graphs. More specifically, the graph pooling operation adaptively selects a subset of nodes to form an induced subgraph for the subsequent layers. To preserve the integrity of graph's topological information, we further introduce a structure learning mechanism to learn a refined graph structure for the pooled graph at each layer. By combining HGP-SL operator with graph neural networks, we perform graph level representation learning with focus on graph classification task. Experimental results on six widely used benchmarks demonstrate the effectiveness of our proposed model.
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
It is important to detect anomalous inputs when deploying machine learning systems. The use of larger and more complex inputs in deep learning magnifies the difficulty of distinguishing between anomalous and in-distribution examples. At the same time, diverse image and text data are available in enormous quantities. We propose leveraging these data to improve deep anomaly detection by training anomaly detectors against an auxiliary dataset of outliers, an approach we call Outlier Exposure (OE). This enables anomaly detectors to generalize and detect unseen anomalies. In extensive experiments on natural language processing and small- and large-scale vision tasks, we find that Outlier Exposure significantly improves detection performance. We also observe that cutting-edge generative models trained on CIFAR-10 may assign higher likelihoods to SVHN images than to CIFAR-10 images; we use OE to mitigate this issue. We also analyze the flexibility and robustness of Outlier Exposure, and identify characteristics of the auxiliary dataset that improve performance.
Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10% accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark data sets.
Deep neural networks (DNNs) have been found to be vulnerable to adversarial examples resulting from adding small-magnitude perturbations to inputs. Such adversarial examples can mislead DNNs to produce adversary-selected results. Different attack strategies have been proposed to generate adversarial examples, but how to produce them with high perceptual quality and more efficiently requires more research efforts. In this paper, we propose AdvGAN to generate adversarial examples with generative adversarial networks (GANs), which can learn and approximate the distribution of original instances. For AdvGAN, once the generator is trained, it can generate adversarial perturbations efficiently for any instance, so as to potentially accelerate adversarial training as defenses. We apply AdvGAN in both semi-whitebox and black-box attack settings. In semi-whitebox attacks, there is no need to access the original target model after the generator is trained, in contrast to traditional white-box attacks. In black-box attacks, we dynamically train a distilled model for the black-box model and optimize the generator accordingly. Adversarial examples generated by AdvGAN on different target models have high attack success rate under state-of-the-art defenses compared to other attacks. Our attack has placed the first with 92.76% accuracy on a public MNIST black-box attack challenge.
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