The surge in black-box AI models has prompted the need to explain the internal mechanism and justify their reliability, especially in high-stakes applications, such as healthcare and autonomous driving. Due to the lack of a rigorous definition of explainable AI (XAI), a plethora of research related to explainability, interpretability, and transparency has been developed to explain and analyze the model from various perspectives. Consequently, with an exhaustive list of papers, it becomes challenging to have a comprehensive overview of XAI research from all aspects. Considering the popularity of neural networks in AI research, we narrow our focus to a specific area of XAI research: gradient based explanations, which can be directly adopted for neural network models. In this review, we systematically explore gradient based explanation methods to date and introduce a novel taxonomy to categorize them into four distinct classes. Then, we present the essence of technique details in chronological order and underscore the evolution of algorithms. Next, we introduce both human and quantitative evaluations to measure algorithm performance. More importantly, we demonstrate the general challenges in XAI and specific challenges in gradient based explanations. We hope that this survey can help researchers understand state-of-the-art progress and their corresponding disadvantages, which could spark their interest in addressing these issues in future work.

In Precision Agriculture, the utilization of management zones (MZs) that take into account within-field variability facilitates effective fertilizer management. This approach enables the optimization of nitrogen (N) rates to maximize crop yield production and enhance agronomic use efficiency. However, existing works often neglect the consideration of responsivity to fertilizer as a factor influencing MZ determination. In response to this gap, we present a MZ clustering method based on fertilizer responsivity. We build upon the statement that the responsivity of a given site to the fertilizer rate is described by the shape of its corresponding N fertilizer-yield response (N-response) curve. Thus, we generate N-response curves for all sites within the field using a convolutional neural network (CNN). The shape of the approximated N-response curves is then characterized using functional principal component analysis. Subsequently, a counterfactual explanation (CFE) method is applied to discern the impact of various variables on MZ membership. The genetic algorithm-based CFE solves a multi-objective optimization problem and aims to identify the minimum combination of features needed to alter a site's cluster assignment. Results from two yield prediction datasets indicate that the features with the greatest influence on MZ membership are associated with terrain characteristics that either facilitate or impede fertilizer runoff, such as terrain slope or topographic aspect.

Machine learning techniques for cybersecurity-related software engineering tasks are becoming increasingly popular. The representation of source code is a key portion of the technique that can impact the way the model is able to learn the features of the source code. With an increasing number of these techniques being developed, it is valuable to see the current state of the field to better understand what exists and what's not there yet. This paper presents a study of these existing ML-based approaches and demonstrates what type of representations were used for different cybersecurity tasks and programming languages. Additionally, we study what types of models are used with different representations. We have found that graph-based representations are the most popular category of representation, and Tokenizers and Abstract Syntax Trees (ASTs) are the two most popular representations overall. We also found that the most popular cybersecurity task is vulnerability detection, and the language that is covered by the most techniques is C. Finally, we found that sequence-based models are the most popular category of models, and Support Vector Machines (SVMs) are the most popular model overall.

Structure-based drug design aims at generating high affinity ligands with prior knowledge of 3D target structures. Existing methods either use conditional generative model to learn the distribution of 3D ligands given target binding sites, or iteratively modify molecules to optimize a structure-based activity estimator. The former is highly constrained by data quantity and quality, which leaves optimization-based approaches more promising in practical scenario. However, existing optimization-based approaches choose to edit molecules in 2D space, and use molecular docking to estimate the activity using docking predicted 3D target-ligand complexes. The misalignment between the action space and the objective hinders the performance of these models, especially for those employ deep learning for acceleration. In this work, we propose MolEdit3D to combine 3D molecular generation with optimization frameworks. We develop a novel 3D graph editing model to generate molecules using fragments, and pre-train this model on abundant 3D ligands for learning target-independent properties. Then we employ a target-guided self-learning strategy to improve target-related properties using self-sampled molecules. MolEdit3D achieves state-of-the-art performance on majority of the evaluation metrics, and demonstrate strong capability of capturing both target-dependent and -independent properties.

The pretraining-finetuning paradigm has gained widespread adoption in vision tasks and other fields, yet it faces the significant challenge of high sample annotation costs. To mitigate this, the concept of active finetuning has emerged, aiming to select the most appropriate samples for model finetuning within a limited budget. Traditional active learning methods often struggle in this setting due to their inherent bias in batch selection. Furthermore, the recent active finetuning approach has primarily concentrated on aligning the distribution of selected subsets with the overall data pool, focusing solely on diversity. In this paper, we propose a Bi-Level Active Finetuning framework to select the samples for annotation in one shot, which includes two stages: core sample selection for diversity, and boundary sample selection for uncertainty. The process begins with the identification of pseudo-class centers, followed by an innovative denoising method and an iterative strategy for boundary sample selection in the high-dimensional feature space, all without relying on ground-truth labels. Our comprehensive experiments provide both qualitative and quantitative evidence of our method's efficacy, outperforming all the existing baselines.

Station-keeping tasks for high-altitude balloons show promise in areas such as ecological surveys, atmospheric analysis, and communication relays. However, identifying the optimal time and position to launch a latex high-altitude balloon is still a challenging and multifaceted problem. For example, tasks such as forest fire tracking place geometric constraints on the launch location of the balloon. Furthermore, identifying the most optimal location also heavily depends on atmospheric conditions. We first illustrate how reinforcement learning-based controllers, frequently used for station-keeping tasks, can exploit the environment. This exploitation can degrade performance on unseen weather patterns and affect station-keeping performance when identifying an optimal launch configuration. Valuing all states equally in the region, the agent exploits the region's geometry by flying near the edge, leading to risky behaviours. We propose a modification which compensates for this exploitation and finds this leads to, on average, higher steps within the target region on unseen data. Then, we illustrate how Bayesian Optimisation (BO) can identify the optimal launch location to perform station-keeping tasks, maximising the expected undiscounted return from a given rollout. We show BO can find this launch location in fewer steps compared to other optimisation methods. Results indicate that, surprisingly, the most optimal location to launch from is not commonly within the target region. Please find further information about our project at https://sites.google.com/view/bo-lauch-balloon/.

In recent work, the authors have developed a generic methodology for calibrating the noise in fluid dynamics stochastic partial differential equations where the stochasticity was introduced to parametrize subgrid-scale processes. The stochastic parameterization of sub-grid scale processes is required in the estimation of uncertainty in weather and climate predictions, to represent systematic model errors arising from subgrid-scale fluctuations. The previous methodology used a principal component analysis (PCA) technique based on the ansatz that the increments of the stochastic parametrization are normally distributed. In this paper, the PCA technique is replaced by a generative model technique. This enables us to avoid imposing additional constraints on the increments. The methodology is tested on a stochastic rotating shallow water model with the elevation variable of the model used as input data. The numerical simulations show that the noise is indeed non-Gaussian. The generative modelling technology gives good RMSE, CRPS score and forecast rank histogram results.

We developed a common algorithmic solution addressing the problem of resource-constrained outreach encountered by social change organizations with different missions and operations: Breaking Ground -- an organization that helps individuals experiencing homelessness in New York transition to permanent housing and Leket -- the national food bank of Israel that rescues food from farms and elsewhere to feed the hungry. Specifically, we developed an estimation and optimization approach for partially-observed episodic restless bandits under $k$-step transitions. The results show that our Thompson sampling with Markov chain recovery (via Stein variational gradient descent) algorithm significantly outperforms baselines for the problems of both organizations. We carried out this work in a prospective manner with the express goal of devising a flexible-enough but also useful-enough solution that can help overcome a lack of sustainable impact in data science for social good.

For training an encoder network to perform amortized variational inference, the Kullback-Leibler (KL) divergence from the exact posterior to its approximation, known as the inclusive or forward KL, is an increasingly popular choice of variational objective due to the mass-covering property of its minimizer. However, minimizing this objective is challenging. A popular existing approach, Reweighted Wake-Sleep (RWS), suffers from heavily biased gradients and a circular pathology that results in highly concentrated variational distributions. As an alternative, we propose SMC-Wake, a procedure for fitting an amortized variational approximation that uses likelihood-tempered sequential Monte Carlo samplers to estimate the gradient of the inclusive KL divergence. We propose three gradient estimators, all of which are asymptotically unbiased in the number of iterations and two of which are strongly consistent. Our method interleaves stochastic gradient updates, SMC samplers, and iterative improvement to an estimate of the normalizing constant to reduce bias from self-normalization. In experiments with both simulated and real datasets, SMC-Wake fits variational distributions that approximate the posterior more accurately than existing methods.

Combining empirical risk minimization with capacity control is a classical strategy in machine learning when trying to control the generalization gap and avoid overfitting, as the model class capacity gets larger. Yet, in modern deep learning practice, very large over-parameterized models (e.g. neural networks) are optimized to fit perfectly the training data and still obtain great generalization performance. Past the interpolation point, increasing model complexity seems to actually lower the test error. In this tutorial, we explain the concept of double descent and its mechanisms. The first section sets the classical statistical learning framework and introduces the double descent phenomenon. By looking at a number of examples, section 2 introduces inductive biases that appear to have a key role in double descent by selecting, among the multiple interpolating solutions, a smooth empirical risk minimizer. Finally, section 3 explores the double descent with two linear models, and gives other points of view from recent related works.