Motivation: We explored how explainable AI (XAI) can help to shed light into the inner workings of neural networks for protein function prediction, by extending the widely used XAI method of integrated gradients such that latent representations inside of transformer models, which were finetuned to Gene Ontology term and Enzyme Commission number prediction, can be inspected too. Results: The approach enabled us to identify amino acids in the sequences that the transformers pay particular attention to, and to show that these relevant sequence parts reflect expectations from biology and chemistry, both in the embedding layer and inside of the model, where we identified transformer heads with a statistically significant correspondence of attribution maps with ground truth sequence annotations (e.g., transmembrane regions, active sites) across many proteins. Availability and Implementation: Source code can be accessed at //github.com/markuswenzel/xai-proteins .
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Deep neural networks (DNNs) often accept high-dimensional media data (e.g., photos, text, and audio) and understand their perceptual content (e.g., a cat). To test DNNs, diverse inputs are needed to trigger mis-predictions. Some preliminary works use byte-level mutations or domain-specific filters (e.g., foggy), whose enabled mutations may be limited and likely error-prone. SOTA works employ deep generative models to generate (infinite) inputs. Also, to keep the mutated inputs perceptually valid (e.g., a cat remains a "cat" after mutation), existing efforts rely on imprecise and less generalizable heuristics. This study revisits two key objectives in media input mutation - perception diversity (DIV) and validity (VAL) - in a rigorous manner based on manifold, a well-developed theory capturing perceptions of high-dimensional media data in a low-dimensional space. We show important results that DIV and VAL inextricably bound each other, and prove that SOTA generative model-based methods fundamentally fail to mutate real-world media data (either sacrificing DIV or VAL). In contrast, we discuss the feasibility of mutating real-world media data with provably high DIV and VAL based on manifold. We concretize the technical solution of mutating media data of various formats (images, audios, text) via a unified manner based on manifold. Specifically, when media data are projected into a low-dimensional manifold, the data can be mutated by walking on the manifold with certain directions and step sizes. When contrasted with the input data, the mutated data exhibit encouraging DIV in the perceptual traits (e.g., lying vs. standing dog) while retaining reasonably high VAL (i.e., a dog remains a dog). We implement our techniques in DEEPWALK for testing DNNs. DEEPWALK outperforms prior methods in testing comprehensiveness and can find more error-triggering inputs with higher quality.
Backpropagation within neural networks leverages a fundamental element of automatic differentiation, which is referred to as the reverse mode differentiation, or vector Jacobian Product (VJP) or, in the context of differential geometry, known as the pull-back process. The computation of gradient is important as update of neural network parameters is performed using gradient descent method. In this study, we present a genric randomized method, which updates the parameters of neural networks by using directional derivatives of loss functions computed efficiently by using forward mode AD or Jacobian vector Product (JVP). These JVP are computed along the random directions sampled from different probability distributions e.g., Bernoulli, Normal, Wigner, Laplace and Uniform distributions. The computation of gradient is performed during the forward pass of the neural network. We also present a rigorous analysis of the presented methods providing the rate of convergence along with the computational experiments deployed in scientific Machine learning in particular physics-informed neural networks and Deep Operator Networks.
Graph neural networks (GNNs) are widely used for modeling complex interactions between entities represented as vertices of a graph. Despite recent efforts to theoretically analyze the expressive power of GNNs, a formal characterization of their ability to model interactions is lacking. The current paper aims to address this gap. Formalizing strength of interactions through an established measure known as separation rank, we quantify the ability of certain GNNs to model interaction between a given subset of vertices and its complement, i.e. between the sides of a given partition of input vertices. Our results reveal that the ability to model interaction is primarily determined by the partition's walk index -- a graph-theoretical characteristic defined by the number of walks originating from the boundary of the partition. Experiments with common GNN architectures corroborate this finding. As a practical application of our theory, we design an edge sparsification algorithm named Walk Index Sparsification (WIS), which preserves the ability of a GNN to model interactions when input edges are removed. WIS is simple, computationally efficient, and in our experiments has markedly outperformed alternative methods in terms of induced prediction accuracy. More broadly, it showcases the potential of improving GNNs by theoretically analyzing the interactions they can model.
Structural entropy is a metric that measures the amount of information embedded in graph structure data under a strategy of hierarchical abstracting. To measure the structural entropy of a dynamic graph, we need to decode the optimal encoding tree corresponding to the optimal hierarchical community partitioning of the graph. However, the current structural entropy methods do not support efficient incremental updating of encoding trees. To address this issue, we propose Incre-2dSE, a novel incremental measurement framework that dynamically adjusts the community partitioning and efficiently computes the updated structural entropy for each snapshot of dynamic graphs. Incre-2dSE consists of an online module and an offline module. The online module includes dynamic measurement algorithms based on two dynamic adjustment strategies for two-dimensional encoding trees, i.e., the naive adjustment strategy and the node-shifting adjustment strategy, which supports theoretical analysis of the updated structural entropy and incrementally adjusts the community partitioning towards a lower structural entropy. In contrast, the offline module globally constructs the encoding tree for the updated graph using static community detection methods and calculates the structural entropy by definition. We conduct experiments on an artificial dynamic graph dataset generated by Hawkes Process and 3 real-world datasets. Experimental results confirm that our dynamic measurement algorithms effectively capture the dynamic evolution of the communities, reduce time consumption, and provide great interpretability.
Accurate uncertainty quantification in graph neural networks (GNNs) is essential, especially in high-stakes domains where GNNs are frequently employed. Conformal prediction (CP) offers a promising framework for quantifying uncertainty by providing $\textit{valid}$ prediction sets for any black-box model. CP ensures formal probabilistic guarantees that a prediction set contains a true label with a desired probability. However, the size of prediction sets, known as $\textit{inefficiency}$, is influenced by the underlying model and data generating process. On the other hand, Bayesian learning also provides a credible region based on the estimated posterior distribution, but this region is $\textit{well-calibrated}$ only when the model is correctly specified. Building on a recent work that introduced a scaling parameter for constructing valid credible regions from posterior estimate, our study explores the advantages of incorporating a temperature parameter into Bayesian GNNs within CP framework. We empirically demonstrate the existence of temperatures that result in more efficient prediction sets. Furthermore, we conduct an analysis to identify the factors contributing to inefficiency and offer valuable insights into the relationship between CP performance and model calibration.
Graph neural networks (GNNs) have been demonstrated to be a powerful algorithmic model in broad application fields for their effectiveness in learning over graphs. To scale GNN training up for large-scale and ever-growing graphs, the most promising solution is distributed training which distributes the workload of training across multiple computing nodes. However, the workflows, computational patterns, communication patterns, and optimization techniques of distributed GNN training remain preliminarily understood. In this paper, we provide a comprehensive survey of distributed GNN training by investigating various optimization techniques used in distributed GNN training. First, distributed GNN training is classified into several categories according to their workflows. In addition, their computational patterns and communication patterns, as well as the optimization techniques proposed by recent work are introduced. Second, the software frameworks and hardware platforms of distributed GNN training are also introduced for a deeper understanding. Third, distributed GNN training is compared with distributed training of deep neural networks, emphasizing the uniqueness of distributed GNN training. Finally, interesting issues and opportunities in this field are discussed.
The generalization mystery in deep learning is the following: Why do over-parameterized neural networks trained with gradient descent (GD) generalize well on real datasets even though they are capable of fitting random datasets of comparable size? Furthermore, from among all solutions that fit the training data, how does GD find one that generalizes well (when such a well-generalizing solution exists)? We argue that the answer to both questions lies in the interaction of the gradients of different examples during training. Intuitively, if the per-example gradients are well-aligned, that is, if they are coherent, then one may expect GD to be (algorithmically) stable, and hence generalize well. We formalize this argument with an easy to compute and interpretable metric for coherence, and show that the metric takes on very different values on real and random datasets for several common vision networks. The theory also explains a number of other phenomena in deep learning, such as why some examples are reliably learned earlier than others, why early stopping works, and why it is possible to learn from noisy labels. Moreover, since the theory provides a causal explanation of how GD finds a well-generalizing solution when one exists, it motivates a class of simple modifications to GD that attenuate memorization and improve generalization. Generalization in deep learning is an extremely broad phenomenon, and therefore, it requires an equally general explanation. We conclude with a survey of alternative lines of attack on this problem, and argue that the proposed approach is the most viable one on this basis.
The dominating NLP paradigm of training a strong neural predictor to perform one task on a specific dataset has led to state-of-the-art performance in a variety of applications (eg. sentiment classification, span-prediction based question answering or machine translation). However, it builds upon the assumption that the data distribution is stationary, ie. that the data is sampled from a fixed distribution both at training and test time. This way of training is inconsistent with how we as humans are able to learn from and operate within a constantly changing stream of information. Moreover, it is ill-adapted to real-world use cases where the data distribution is expected to shift over the course of a model's lifetime. The first goal of this thesis is to characterize the different forms this shift can take in the context of natural language processing, and propose benchmarks and evaluation metrics to measure its effect on current deep learning architectures. We then proceed to take steps to mitigate the effect of distributional shift on NLP models. To this end, we develop methods based on parametric reformulations of the distributionally robust optimization framework. Empirically, we demonstrate that these approaches yield more robust models as demonstrated on a selection of realistic problems. In the third and final part of this thesis, we explore ways of efficiently adapting existing models to new domains or tasks. Our contribution to this topic takes inspiration from information geometry to derive a new gradient update rule which alleviate catastrophic forgetting issues during adaptation.
Deep neural networks (DNNs) are successful in many computer vision tasks. However, the most accurate DNNs require millions of parameters and operations, making them energy, computation and memory intensive. This impedes the deployment of large DNNs in low-power devices with limited compute resources. Recent research improves DNN models by reducing the memory requirement, energy consumption, and number of operations without significantly decreasing the accuracy. This paper surveys the progress of low-power deep learning and computer vision, specifically in regards to inference, and discusses the methods for compacting and accelerating DNN models. The techniques can be divided into four major categories: (1) parameter quantization and pruning, (2) compressed convolutional filters and matrix factorization, (3) network architecture search, and (4) knowledge distillation. We analyze the accuracy, advantages, disadvantages, and potential solutions to the problems with the techniques in each category. We also discuss new evaluation metrics as a guideline for future research.
Deep convolutional neural networks (CNNs) have recently achieved great success in many visual recognition tasks. However, existing deep neural network models are computationally expensive and memory intensive, hindering their deployment in devices with low memory resources or in applications with strict latency requirements. Therefore, a natural thought is to perform model compression and acceleration in deep networks without significantly decreasing the model performance. During the past few years, tremendous progress has been made in this area. In this paper, we survey the recent advanced techniques for compacting and accelerating CNNs model developed. These techniques are roughly categorized into four schemes: parameter pruning and sharing, low-rank factorization, transferred/compact convolutional filters, and knowledge distillation. Methods of parameter pruning and sharing will be described at the beginning, after that the other techniques will be introduced. For each scheme, we provide insightful analysis regarding the performance, related applications, advantages, and drawbacks etc. Then we will go through a few very recent additional successful methods, for example, dynamic capacity networks and stochastic depths networks. After that, we survey the evaluation matrix, the main datasets used for evaluating the model performance and recent benchmarking efforts. Finally, we conclude this paper, discuss remaining challenges and possible directions on this topic.
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