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Expanding our knowledge of small molecules beyond what is known in nature or designed in wet laboratories promises to significantly advance cheminformatics, drug discovery, biotechnology and material science. In silico molecular design remains challenging, primarily due to the complexity of the chemical space and the non-trivial relationship between chemical structures and biological properties. Deep generative models that learn directly from data are intriguing, but they have yet to demonstrate interpretability in the learned representation, so we can learn more about the relationship between the chemical and biological space. In this article, we advance research on disentangled representation learning for small molecule generation. We build on recent work by us and others on deep graph generative frameworks, which capture atomic interactions via a graph-based representation of a small molecule. The methodological novelty is how we leverage the concept of disentanglement in the graph variational autoencoder framework both to generate biologically relevant small molecules and to enhance model interpretability.

Extensive qualitative and quantitative experimental evaluation in comparison with state-of-the-art models demonstrate the superiority of our disentanglement framework. We believe this work is an important step to address key challenges in small molecule generation with deep generative frameworks.

Training and generated data are made available at https://ieee-dataport.org/documents/dataset-disentangled-representation-learning-interpretable-molecule-generation. All code is made available at https://anonymous.4open.science/r/D-MolVAE-2799/.

Supplementary data are available at Bioinformatics online.

 

Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise experience and intensive human efforts, yet still suffer from the insufficiency of scientific knowledge and low throughput to support effective and efficient data generation. Recently, the advancement of deep learning has created the opportunity for expressive methods to learn the underlying representation and properties of data. Such capability provides new ways of determining the mutual relationship between the structural patterns and functional properties of the data and leveraging such relationships to generate structural data, given the desired properties. This article is a systematic review that explains this promising research area, commonly known as controllable deep data generation. First, the article raises the potential challenges and provides preliminaries. Then the article formally defines controllable deep data generation, proposes a taxonomy on various techniques and summarizes the evaluation metrics in this specific domain. After that, the article introduces exciting applications of controllable deep data generation, experimentally analyzes and compares existing works. Finally, this article highlights the promising future directions of controllable deep data generation and identifies five potential challenges.

 

As the societal impact of Deep Neural Networks (DNNs) grows, the goals for advancing DNNs become more complex and diverse, ranging from improving a conventional model accuracy metric to infusing advanced human virtues such as fairness, accountability, transparency, and unbiasedness. Recently, techniques in Explainable Artificial Intelligence (XAI) have been attracting considerable attention and have tremendously helped Machine Learning (ML) engineers in understand AI models. However, at the same time, we started to witness the emerging need beyond XAI among AI communities; based on the insights learned from XAI, how can we better empower ML engineers in steering their DNNs so that the model’s reasonableness and performance can be improved as intended? This article provides a timely and extensive literature overview of the field Explanation-Guided Learning (EGL), a domain of techniques that steer the DNNs’ reasoning process by adding regularization, supervision, or intervention on model explanations. In doing so, we first provide a formal definition of EGL and its general learning paradigm. Second, an overview of the key factors for EGL evaluation, as well as summarization and categorization of existing evaluation procedures and metrics for EGL are provided. Finally, the current and potential future application areas and directions of EGL are discussed, and an extensive experimental study is presented aiming at providing comprehensive comparative studies among existing EGL models in various popular application domains, such as Computer Vision and Natural Language Processing domains. Additional resources related to event prediction are included in the article website:https://kugaoyang.github.io/EGL/

 

In recent years, analyzing the explanation for the prediction of Graph Neural Networks (GNNs) has attracted increasing attention. Despite this progress, most existing methods do not adequately consider the inherent uncertainties stemming from the randomness of model parameters and graph data, which may lead to overconfidence and misguiding explanations. However, it is challenging for most of GNN explanation methods to quantify these uncertainties since they obtain the prediction explanation in apost-hocand model-agnostic manner without considering the randomness ofgraph dataandmodel parameters. To address the above problems, this paper proposes a novel uncertainty quantification framework for GNN explanations. For mitigating the randomness of graph data in the explanation, our framework accounts for two distinct data uncertainties, allowing for a direct assessment of the uncertainty in GNN explanations. For mitigating the randomness of learned model parameters, our method learns the parameter distribution directly from the data, obviating the need for assumptions about specific distributions. Moreover, the explanation uncertainty within model parameters is also quantified based on the learned parameter distributions. This holistic approach can integrate with anypost-hocGNN explanation methods. Empirical results from our study show that our proposed method sets a new standard for GNN explanation performance across diverse real-world graph benchmarks.

 

The local explanation provides heatmaps on images to explain how Convolutional Neural Networks (CNNs) derive their output. Due to its visual straightforwardness, the method has been one of the most popular explainable AI (XAI) methods for diagnosing CNNs. Through our formative study (S1), however, we captured ML engineers' ambivalent perspective about the local explanation as a valuable and indispensable envision in building CNNs versus the process that exhausts them due to the heuristic nature of detecting vulnerability. Moreover, steering the CNNs based on the vulnerability learned from the diagnosis seemed highly challenging. To mitigate the gap, we designed DeepFuse, the first interactive design that realizes the direct feedback loop between a user and CNNs in diagnosing and revising CNN's vulnerability using local explanations. DeepFuse helps CNN engineers to systemically search unreasonable local explanations and annotate the new boundaries for those identified as unreasonable in a labor-efficient manner. Next, it steers the model based on the given annotation such that the model doesn't introduce similar mistakes. We conducted a two-day study (S2) with 12 experienced CNN engineers. Using DeepFuse, participants made a more accurate and reasonable model than the current state-of-the-art. Also, participants found the way DeepFuse guides case-based reasoning can practically improve their current practice. We provide implications for design that explain how future HCI-driven design can move our practice forward to make XAI-driven insights more actionable.

 

Spatial prediction is to predict the values of the targeted variable, such as PM2.5 values and temperature, at arbitrary locations based on the collected geospatial data. It greatly affects the key research topics in geoscience in terms of obtaining heterogeneous spatial information (e.g., soil conditions, precipitation rates, wheat yields) for geographic modeling and decision-making at local, regional, and global scales. In-situ data, collected by ground-level in-situ sensors, and remote sensing data, collected by satellite or aircraft, are two important data sources for this task. In-situ data are relatively accurate while sparse and unevenly distributed. Remote sensing data cover large spatial areas but are coarse with low spatiotemporal resolution and prone to interference. How to synergize the complementary strength of these two data types is still a grand challenge. Moreover, it is difficult to model the unknown spatial predictive mapping while handling the trade-off between spatial autocorrelation and heterogeneity. Third, representing spatial relations without substantial information loss is also a critical issue. To address these challenges, we propose a novel Heterogeneous Self-supervised Spatial Prediction (HSSP) framework that synergizes multi-source data by minimizing the inconsistency between in-situ and remote sensing observations. We propose a new deep geometric spatial interpolation model as the prediction backbone that automatically interpolates the values of the targeted variable at unknown locations based on existing observations by taking into account both distance and orientation information. Our proposed interpolator is proven to both be the general form of popular interpolation methods and preserve spatial information. The spatial prediction is enhanced by a novel error-compensation framework to capture the prediction inconsistency due to spatial heterogeneity. Extensive experiments have been conducted on real-world datasets and demonstrated our model’s superiority in performance over state-of-the-art models.