Current learning machines have successfully solved hard application problems, reaching high accuracy and displaying seemingly intelligent behavior. Here we apply recent techniques for explaining ...decisions of state-of-the-art learning machines and analyze various tasks from computer vision and arcade games. This showcases a spectrum of problem-solving behaviors ranging from naive and short-sighted, to well-informed and strategic. We observe that standard performance evaluation metrics can be oblivious to distinguishing these diverse problem solving behaviors. Furthermore, we propose our semi-automated Spectral Relevance Analysis that provides a practically effective way of characterizing and validating the behavior of nonlinear learning machines. This helps to assess whether a learned model indeed delivers reliably for the problem that it was conceived for. Furthermore, our work intends to add a voice of caution to the ongoing excitement about machine intelligence and pledges to evaluate and judge some of these recent successes in a more nuanced manner.
Federated learning allows multiple parties to jointly train a deep learning model on their combined data, without any of the participants having to reveal their local data to a centralized server. ...This form of privacy-preserving collaborative learning, however, comes at the cost of a significant communication overhead during training. To address this problem, several compression methods have been proposed in the distributed training literature that can reduce the amount of required communication by up to three orders of magnitude. These existing methods, however, are only of limited utility in the federated learning setting, as they either only compress the upstream communication from the clients to the server (leaving the downstream communication uncompressed) or only perform well under idealized conditions, such as i.i.d. distribution of the client data, which typically cannot be found in federated learning. In this article, we propose sparse ternary compression (STC), a new compression framework that is specifically designed to meet the requirements of the federated learning environment. STC extends the existing compression technique of top-k gradient sparsification with a novel mechanism to enable downstream compression as well as ternarization and optimal Golomb encoding of the weight updates. Our experiments on four different learning tasks demonstrate that STC distinctively outperforms federated averaging in common federated learning scenarios. These results advocate for a paradigm shift in federated optimization toward high-frequency low-bitwidth communication, in particular in the bandwidth-constrained learning environments.
Abstract
Motivation
Inferring the properties of a protein from its amino acid sequence is one of the key problems in bioinformatics. Most state-of-the-art approaches for protein classification are ...tailored to single classification tasks and rely on handcrafted features, such as position-specific-scoring matrices from expensive database searches. We argue that this level of performance can be reached or even be surpassed by learning a task-agnostic representation once, using self-supervised language modeling, and transferring it to specific tasks by a simple fine-tuning step.
Results
We put forward a universal deep sequence model that is pre-trained on unlabeled protein sequences from Swiss-Prot and fine-tuned on protein classification tasks. We apply it to three prototypical tasks, namely enzyme class prediction, gene ontology prediction and remote homology and fold detection. The proposed method performs on par with state-of-the-art algorithms that were tailored to these specific tasks or, for two out of three tasks, even outperforms them. These results stress the possibility of inferring protein properties from the sequence alone and, on more general grounds, the prospects of modern natural language processing methods in omics. Moreover, we illustrate the prospects for explainable machine learning methods in this field by selected case studies.
Availability and implementation
Source code is available under https://github.com/nstrodt/UDSMProt.
Supplementary information
Supplementary data are available at Bioinformatics online.
With the broader and highly successful usage of machine learning (ML) in industry and the sciences, there has been a growing demand for explainable artificial intelligence (XAI). Interpretability and ...explanation methods for gaining a better understanding of the problem-solving abilities and strategies of nonlinear ML, in particular, deep neural networks, are, therefore, receiving increased attention. In this work, we aim to: 1) provide a timely overview of this active emerging field, with a focus on " post hoc " explanations, and explain its theoretical foundations; 2) put interpretability algorithms to a test both from a theory and comparative evaluation perspective using extensive simulations; 3) outline best practice aspects, i.e., how to best include interpretation methods into the standard usage of ML; and 4) demonstrate successful usage of XAI in a representative selection of application scenarios. Finally, we discuss challenges and possible future directions of this exciting foundational field of ML.
This paper provides an entry point to the problem of interpreting a deep neural network model and explaining its predictions. It is based on a tutorial given at ICASSP 2017. As a tutorial paper, the ...set of methods covered here is not exhaustive, but sufficiently representative to discuss a number of questions in interpretability, technical challenges, and possible applications. The second part of the tutorial focuses on the recently proposed layer-wise relevance propagation (LRP) technique, for which we provide theory, recommendations, and tricks, to make most efficient use of it on real data.
Deep neural networks (DNNs) have demonstrated impressive performance in complex machine learning tasks such as image classification or speech recognition. However, due to their multilayer nonlinear ...structure, they are not transparent, i.e., it is hard to grasp what makes them arrive at a particular classification or recognition decision, given a new unseen data sample. Recently, several approaches have been proposed enabling one to understand and interpret the reasoning embodied in a DNN for a single test image. These methods quantify the "importance" of individual pixels with respect to the classification decision and allow a visualization in terms of a heatmap in pixel/input space. While the usefulness of heatmaps can be judged subjectively by a human, an objective quality measure is missing. In this paper, we present a general methodology based on region perturbation for evaluating ordered collections of pixels such as heatmaps. We compare heatmaps computed by three different methods on the SUN397, ILSVRC2012, and MIT Places data sets. Our main result is that the recently proposed layer-wise relevance propagation algorithm qualitatively and quantitatively provides a better explanation of what made a DNN arrive at a particular classification decision than the sensitivity-based approach or the deconvolution method. We provide theoretical arguments to explain this result and discuss its practical implications. Finally, we investigate the use of heatmaps for unsupervised assessment of the neural network performance.
Understanding and interpreting classification decisions of automated image classification systems is of high value in many applications, as it allows to verify the reasoning of the system and ...provides additional information to the human expert. Although machine learning methods are solving very successfully a plethora of tasks, they have in most cases the disadvantage of acting as a black box, not providing any information about what made them arrive at a particular decision. This work proposes a general solution to the problem of understanding classification decisions by pixel-wise decomposition of nonlinear classifiers. We introduce a methodology that allows to visualize the contributions of single pixels to predictions for kernel-based classifiers over Bag of Words features and for multilayered neural networks. These pixel contributions can be visualized as heatmaps and are provided to a human expert who can intuitively not only verify the validity of the classification decision, but also focus further analysis on regions of potential interest. We evaluate our method for classifiers trained on PASCAL VOC 2009 images, synthetic image data containing geometric shapes, the MNIST handwritten digits data set and for the pre-trained ImageNet model available as part of the Caffe open source package.
Deep learning approaches to anomaly detection (AD) have recently improved the state of the art in detection performance on complex data sets, such as large collections of images or text. These ...results have sparked a renewed interest in the AD problem and led to the introduction of a great variety of new methods. With the emergence of numerous such methods, including approaches based on generative models, one-class classification, and reconstruction, there is a growing need to bring methods of this field into a systematic and unified perspective. In this review, we aim to identify the common underlying principles and the assumptions that are often made implicitly by various methods. In particular, we draw connections between classic "shallow" and novel deep approaches and show how this relation might cross-fertilize or extend both directions. We further provide an empirical assessment of major existing methods that are enriched by the use of recent explainability techniques and present specific worked-through examples together with practical advice. Finally, we outline critical open challenges and identify specific paths for future research in AD.
Electrocardiography (ECG) is a key non-invasive diagnostic tool for cardiovascular diseases which is increasingly supported by algorithms based on machine learning. Major obstacles for the ...development of automatic ECG interpretation algorithms are both the lack of public datasets and well-defined benchmarking procedures to allow comparison s of different algorithms. To address these issues, we put forward PTB-XL, the to-date largest freely accessible clinical 12-lead ECG-waveform dataset comprising 21837 records from 18885 patients of 10 seconds length. The ECG-waveform data was annotated by up to two cardiologists as a multi-label dataset, where diagnostic labels were further aggregated into super and subclasses. The dataset covers a broad range of diagnostic classes including, in particular, a large fraction of healthy records. The combination with additional metadata on demographics, additional diagnostic statements, diagnosis likelihoods, manually annotated signal properties as well as suggested folds for splitting training and test sets turns the dataset into a rich resource for the development and the evaluation of automatic ECG interpretation algorithms.
Text documents can be described by a number of abstract concepts such as semantic category, writing style, or sentiment. Machine learning (ML) models have been trained to automatically map documents ...to these abstract concepts, allowing to annotate very large text collections, more than could be processed by a human in a lifetime. Besides predicting the text's category very accurately, it is also highly desirable to understand how and why the categorization process takes place. In this paper, we demonstrate that such understanding can be achieved by tracing the classification decision back to individual words using layer-wise relevance propagation (LRP), a recently developed technique for explaining predictions of complex non-linear classifiers. We train two word-based ML models, a convolutional neural network (CNN) and a bag-of-words SVM classifier, on a topic categorization task and adapt the LRP method to decompose the predictions of these models onto words. Resulting scores indicate how much individual words contribute to the overall classification decision. This enables one to distill relevant information from text documents without an explicit semantic information extraction step. We further use the word-wise relevance scores for generating novel vector-based document representations which capture semantic information. Based on these document vectors, we introduce a measure of model explanatory power and show that, although the SVM and CNN models perform similarly in terms of classification accuracy, the latter exhibits a higher level of explainability which makes it more comprehensible for humans and potentially more useful for other applications.
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