Cancer remains one of the most challenging diseases to treat in the medical field. Machine learning has enabled in-depth analysis of rich multi-omics profiles and medical imaging for cancer diagnosis and prognosis. Despite these advancements, machine learning models face challenges stemming from limited labeled sample sizes, the intricate interplay of high-dimensionality data types, the inherent heterogeneity observed among patients and within tumors, and concerns about interpretability and consistency with existing biomedical knowledge. One approach to surmount these challenges is to integrate biomedical knowledge into data-driven models, which has proven potential to improve the accuracy, robustness, and interpretability of model results. Here, we review the state-of-the-art machine learning studies that adopted the fusion of biomedical knowledge and data, termed knowledge-informed machine learning, for cancer diagnosis and prognosis. Emphasizing the properties inherent in four primary data types including clinical, imaging, molecular, and treatment data, we highlight modeling considerations relevant to these contexts. We provide an overview of diverse forms of knowledge representation and current strategies of knowledge integration into machine learning pipelines with concrete examples. We conclude the review article by discussing future directions to advance cancer research through knowledge-informed machine learning.

Local explanation methods highlight the input tokens that have a considerable impact on the outcome of classifying the document at hand. For example, the Anchor algorithm applies a statistical analysis of the sensitivity of the classifier to changes in the token. Aggregating local explanations over a dataset provides a global explanation of the model. Such aggregation aims to detect words with the most impact, giving valuable insights about the model, like what it has learned in training and which adversarial examples expose its weaknesses. However, standard aggregation methods bear a high computational cost: a na\"ive implementation applies a costly algorithm to each token of each document, and hence, it is infeasible for a simple user running in the scope of a short analysis session. % We devise techniques for accelerating the global aggregation of the Anchor algorithm. Specifically, our goal is to compute a set of top-$k$ words with the highest global impact according to different aggregation functions. Some of our techniques are lossless and some are lossy. We show that for a very mild loss of quality, we are able to accelerate the computation by up to 30$\times$, reducing the computation from hours to minutes. We also devise and study a probabilistic model that accounts for noise in the Anchor algorithm and diminishes the bias toward words that are frequent yet low in impact.

Partial differential equations are often used in the spatial-temporal modeling of complex dynamical systems in many engineering applications. In this work, we build on the recent progress of operator learning and present a data-driven modeling framework that is continuous in both space and time. A key feature of the proposed model is the resolution-invariance with respect to both spatial and temporal discretizations, without demanding abundant training data in different temporal resolutions. To improve the long-term performance of the calibrated model, we further propose a hybrid optimization scheme that leverages both gradient-based and derivative-free optimization methods and efficiently trains on both short-term time series and long-term statistics. We investigate the performance of the spatial-temporal continuous learning framework with three numerical examples, including the viscous Burgers' equation, the Navier-Stokes equations, and the Kuramoto-Sivashinsky equation. The results confirm the resolution-invariance of the proposed modeling framework and also demonstrate stable long-term simulations with only short-term time series data. In addition, we show that the proposed model can better predict long-term statistics via the hybrid optimization scheme with a combined use of short-term and long-term data.

This paper presents a theoretical analysis of linear interpolation as a principled method for stabilizing (large-scale) neural network training. We argue that instabilities in the optimization process are often caused by the nonmonotonicity of the loss landscape and show how linear interpolation can help by leveraging the theory of nonexpansive operators. We construct a new optimization scheme called relaxed approximate proximal point (RAPP), which is the first 1-SCLI method to achieve last iterate convergence rates for $\rho$-comonotone problems while only requiring $\rho > -\tfrac{1}{2L}$. The construction extends to constrained and regularized settings. By replacing the inner optimizer in RAPP we rediscover the family of Lookahead algorithms for which we establish convergence in cohypomonotone problems even when the base optimizer is taken to be gradient descent ascent. The range of cohypomonotone problems in which Lookahead converges is further expanded by exploiting that Lookahead inherits the properties of the base optimizer. We corroborate the results with experiments on generative adversarial networks which demonstrates the benefits of the linear interpolation present in both RAPP and Lookahead.

Recent research works have proposed machine learning models for classifying IoT devices connected to a network. However, there is still a practical challenge of not having all devices (and hence their traffic) available during the training of a model. This essentially means, during the operational phase, we need to classify new devices not seen in the training phase. To address this challenge, we propose ZEST -- a ZSL (zero-shot learning) framework based on self-attention for classifying both seen and unseen devices. ZEST consists of i) a self-attention based network feature extractor, termed SANE, for extracting latent space representations of IoT traffic, ii) a generative model that trains a decoder using latent features to generate pseudo data, and iii) a supervised model that is trained on the generated pseudo data for classifying devices. We carry out extensive experiments on real IoT traffic data; our experiments demonstrate i) ZEST achieves significant improvement (in terms of accuracy) over the baselines; ii) SANE is able to better extract meaningful representations than LSTM which has been commonly used for modeling network traffic.

Exemplar-free class-incremental learning (CIL) poses several challenges since it prohibits the rehearsal of data from previous tasks and thus suffers from catastrophic forgetting. Recent approaches to incrementally learning the classifier by freezing the feature extractor after the first task have gained much attention. In this paper, we explore prototypical networks for CIL, which generate new class prototypes using the frozen feature extractor and classify the features based on the Euclidean distance to the prototypes. In an analysis of the feature distributions of classes, we show that classification based on Euclidean metrics is successful for jointly trained features. However, when learning from non-stationary data, we observe that the Euclidean metric is suboptimal and that feature distributions are heterogeneous. To address this challenge, we revisit the anisotropic Mahalanobis distance for CIL. In addition, we empirically show that modeling the feature covariance relations is better than previous attempts at sampling features from normal distributions and training a linear classifier.

End-to-end neural Natural Language Processing (NLP) models are notoriously difficult to understand. This has given rise to numerous efforts towards model explainability in recent years. One desideratum of model explanation is faithfulness, i.e. an explanation should accurately represent the reasoning process behind the model's prediction. In this survey, we review over 110 model explanation methods in NLP through the lens of faithfulness. We first discuss the definition and evaluation of faithfulness, as well as its significance for explainability. We then introduce recent advances in faithful explanation, grouping existing approaches into five categories: similarity-based methods, analysis of model-internal structures, backpropagation-based methods, counterfactual intervention, and self-explanatory models. For each category, we synthesize its representative studies, strengths, and weaknesses. Finally, we summarize their common virtues and remaining challenges, and reflect on future work directions towards faithful explainability in NLP.

The goal of this paper is to debunk and dispel the magic behind black-box optimizers and stochastic optimizers. It aims to build a solid foundation on how and why the techniques work. This manuscript crystallizes this knowledge by deriving from simple intuitions, the mathematics behind the strategies. This tutorial doesn't shy away from addressing both the formal and informal aspects of gradient descent and stochastic optimization methods. By doing so, it hopes to provide readers with a deeper understanding of these techniques as well as the when, the how and the why of applying these algorithms. Gradient descent is one of the most popular algorithms to perform optimization and by far the most common way to optimize machine learning tasks. Its stochastic version receives attention in recent years, and this is particularly true for optimizing deep neural networks. In deep neural networks, the gradient followed by a single sample or a batch of samples is employed to save computational resources and escape from saddle points. In 1951, Robbins and Monro published \textit{A stochastic approximation method}, one of the first modern treatments on stochastic optimization that estimates local gradients with a new batch of samples. And now, stochastic optimization has become a core technology in machine learning, largely due to the development of the back propagation algorithm in fitting a neural network. The sole aim of this article is to give a self-contained introduction to concepts and mathematical tools in gradient descent and stochastic optimization.

The parametric constant false alarm rate (CFAR) detection algorithms which are based on various statistical distributions, such as Gaussian, Gamma, Weibull, log-normal, G0 distribution, alpha-stable distribution, etc, are most widely used to detect the ship targets in SAR image at present. However, the clutter background in SAR images is complicated and variable. When the actual clutter background deviates from the assumed statistical distribution, the performance of the parametric CFAR detector will deteriorate. In addition to the parametric CFAR schemes, there is another class of nonparametric CFAR detectors which can maintain a constant false alarm rate for the target detection without the assumption of a known clutter distribution. In this work, the Wilcoxon nonparametric CFAR scheme for ship detection in SAR image is proposed and analyzed, and a closed form of the false alarm rate for the Wilcoxon nonparametric detector to determine the decision threshold is presented. By comparison with several typical parametric CFAR schemes on Radarsat-2, ICEYE-X6 and Gaofen-3 SAR images, the robustness of the Wilcoxon nonparametric detector to maintain a good false alarm performance in different detection backgrounds is revealed, and its detection performance for the weak ship in rough sea surface is improved to some extent. Moreover, the Wilcoxon nonparametric detector can suppress the false alarms resulting from the sidelobes at some degree and its detection speed is fast.

When implementing hierarchical federated learning over wireless networks, scalability assurance and the ability to handle both interference and device data heterogeneity are crucial. This work introduces a new two-level learning method designed to address these challenges, along with a scalable over-the-air aggregation scheme for the uplink and a bandwidth-limited broadcast scheme for the downlink that efficiently use a single wireless resource. To provide resistance against data heterogeneity, we employ gradient aggregations. Meanwhile, the impact of uplink and downlink interference is minimized through optimized receiver normalizing factors. We present a comprehensive mathematical approach to derive the convergence bound for the proposed algorithm, applicable to a multi-cluster wireless network encompassing any count of collaborating clusters, and provide special cases and design remarks. As a key step to enable a tractable analysis, we develop a spatial model for the setup by modeling devices as a Poisson cluster process over the edge servers and rigorously quantify uplink and downlink error terms due to the interference. Finally, we show that despite the interference and data heterogeneity, the proposed algorithm not only achieves high learning accuracy for a variety of parameters but also significantly outperforms the conventional hierarchical learning algorithm.