Graph neural networks (GNNs) have shown high potential for a variety of real-world, challenging applications, but one of the major obstacles in GNN research is the lack of large-scale flexible datasets. Most existing public datasets for GNNs are relatively small, which limits the ability of GNNs to generalize to unseen data. The few existing large-scale graph datasets provide very limited labeled data. This makes it difficult to determine if the GNN model's low accuracy for unseen data is inherently due to insufficient training data or if the model failed to generalize. Additionally, datasets used to train GNNs need to offer flexibility to enable a thorough study of the impact of various factors while training GNN models. In this work, we introduce the Illinois Graph Benchmark (IGB), a research dataset tool that the developers can use to train, scrutinize and systematically evaluate GNN models with high fidelity. IGB includes both homogeneous and heterogeneous academic graphs of enormous sizes, with more than 40% of their nodes labeled. Compared to the largest graph datasets publicly available, the IGB provides over 162X more labeled data for deep learning practitioners and developers to create and evaluate models with higher accuracy. The IGB dataset is a collection of academic graphs designed to be flexible, enabling the study of various GNN architectures, embedding generation techniques, and analyzing system performance issues for node classification tasks. IGB is open-sourced, supports DGL and PyG frameworks, and comes with releases of the raw text that we believe foster emerging language models and GNN research projects. An early public version of IGB is available at https://github.com/IllinoisGraphBenchmark/IGB-Datasets.

A directed acyclic graph (DAG) provides valuable prior knowledge that is often discarded in regression tasks in machine learning. We show that the independences arising from the presence of collider structures in DAGs provide meaningful inductive biases, which constrain the regression hypothesis space and improve predictive performance. We introduce collider regression, a framework to incorporate probabilistic causal knowledge from a collider in a regression problem. When the hypothesis space is a reproducing kernel Hilbert space, we prove a strictly positive generalisation benefit under mild assumptions and provide closed-form estimators of the empirical risk minimiser. Experiments on synthetic and climate model data demonstrate performance gains of the proposed methodology.

Obesity is a serious issue in the modern society and is often associated to significantly reduced quality of life. Current research conducted to explore obesity-related neurological evidences using electroencephalography (EEG) data are limited to traditional approaches. In this study, we developed a novel machine learning model to identify brain networks of obese females using alpha band functional connectivity features derived from EEG data. An overall classification accuracy of 0.937 is achieved. Our finding suggests that the obese brain is characterized by a dysfunctional network in which the areas that responsible for processing self-referential information and environmental context information are impaired.

We propose DeepIPC, an end-to-end autonomous driving model that handles both perception and control tasks in driving a vehicle. The model consists of two main parts, perception and controller modules. The perception module takes an RGBD image to perform semantic segmentation and bird's eye view (BEV) semantic mapping along with providing their encoded features. Meanwhile, the controller module processes these features with the measurement of GNSS locations and angular speed to estimate waypoints that come with latent features. Then, two different agents are used to translate waypoints and latent features into a set of navigational controls to drive the vehicle. The model is evaluated by predicting driving records and performing automated driving under various conditions in real environments. The experimental results show that DeepIPC achieves the best drivability and multi-task performance even with fewer parameters compared to the other models. Codes will be published at https://github.com/oskarnatan/DeepIPC.

Sampling schemes are fundamental tools in statistics, survey design, and algorithm design. For example, they are used in social science research to conduct surveys on a random sample of a target population. They are also used in machine learning to improve the efficiency and accuracy of algorithms on large datasets. In many of these applications, however, the datasets are sensitive and privacy is a concern. Intuition suggests that (sub)sampling a dataset before analysing it provides additional privacy, since it gives individuals plausible deniability about whether their data was included or not. This intuition has been formalized for some types of sampling schemes (such as simple random sampling with and without replacement and Poisson sampling) in a series of papers in the differential privacy literature [23, 34, 11, 32]. Such privacy amplification by subsampling results can provide tight privacy accounting when analysing algorithms that incorporate subsampling, e.g., [33, 1, 21, 28, 19]. However, in practice, sampling designs are often more complex than the simple, data independent sampling schemes that are addressed in prior work.

Data preparation, also called data wrangling, is considered one of the most expensive and time-consuming steps when performing analytics or building machine learning models. Preparing data typically involves collecting and merging data from complex heterogeneous, and often large-scale data sources, such as data lakes. In this paper, we introduce a novel approach toward automatic data wrangling in an attempt to alleviate the effort of end-users, e.g. data analysts, in structuring dynamic views from data lakes in the form of tabular data. We aim to address table augmentation tasks, including row/column population and data imputation. Given a corpus of tables, we propose a retrieval augmented self-trained transformer model. Our self-learning strategy consists in randomly ablating tables from the corpus and training the retrieval-based model to reconstruct the original values or headers given the partial tables as input. We adopt this strategy to first train the dense neural retrieval model encoding table-parts to vectors, and then the end-to-end model trained to perform table augmentation tasks. We test on EntiTables, the standard benchmark for table augmentation, as well as introduce a new benchmark to advance further research: WebTables. Our model consistently and substantially outperforms both supervised statistical methods and the current state-of-the-art transformer-based models.

One of the fundamental challenges in causal inference is to estimate the causal effect of a treatment on its outcome of interest from observational data. However, causal effect estimation often suffers from the impacts of confounding bias caused by unmeasured confounders that affect both the treatment and the outcome. The instrumental variable (IV) approach is a powerful way to eliminate the confounding bias from latent confounders. However, the existing IV-based estimators require a nominated IV, and for a conditional IV (CIV) the corresponding conditioning set too, for causal effect estimation. This limits the application of IV-based estimators. In this paper, by leveraging the advantage of disentangled representation learning, we propose a novel method, named DVAE.CIV, for learning and disentangling the representations of CIV and the representations of its conditioning set for causal effect estimations from data with latent confounders. Extensive experimental results on both synthetic and real-world datasets demonstrate the superiority of the proposed DVAE.CIV method against the existing causal effect estimators.

The absence of transparency and explainability hinders the clinical adoption of Machine learning (ML) algorithms. Although various methods of explainable artificial intelligence (XAI) have been suggested, there is a lack of literature that delves into their practicality and assesses them based on criteria that could foster trust in clinical environments. To address this gap this study evaluates two popular XAI methods used for explaining predictive models in the healthcare context in terms of whether they (i) generate domain-appropriate representation, i.e. coherent with respect to the application task, (ii) impact clinical workflow and (iii) are consistent. To that end, explanations generated at the cohort and patient levels were analysed. The paper reports the first benchmarking of the XAI methods applied to risk prediction models obtained by evaluating the concordance between generated explanations and the trigger of a future clinical deterioration episode recorded by the data collection system. We carried out an analysis using two Electronic Medical Records (EMR) datasets sourced from Australian major hospitals. The findings underscore the limitations of state-of-the-art XAI methods in the clinical context and their potential benefits. We discuss these limitations and contribute to the theoretical development of trustworthy XAI solutions where clinical decision support guides the choice of intervention by suggesting the pattern or drivers for clinical deterioration in the future.

Varying conditions between the data seen at training and at application time remain a major challenge for machine learning. We study this problem in the context of Acoustic Scene Classification (ASC) with mismatching recording devices. Previous works successfully employed frequency-wise normalization of inputs and hidden layer activations in convolutional neural networks to reduce the recording device discrepancy. The main objective of this work was to adopt frequency-wise normalization for Audio Spectrogram Transformers (ASTs), which have recently become the dominant model architecture in ASC. To this end, we first investigate how recording device characteristics are encoded in the hidden layer activations of ASTs. We find that recording device information is initially encoded in the frequency dimension; however, after the first self-attention block, it is largely transformed into the token dimension. Based on this observation, we conjecture that suppressing recording device characteristics in the input spectrogram is the most effective. We propose a frequency-centering operation for spectrograms that improves the ASC performance on unseen recording devices on average by up to 18.2 percentage points.

Objectives: Graph representation learning (GRL) has emerged as a pivotal field that has contributed significantly to breakthroughs in various fields, including biomedicine. The objective of this survey is to review the latest advancements in GRL methods and their applications in the biomedical field. We also highlight key challenges currently faced by GRL and outline potential directions for future research. Methods: We conducted a comprehensive search of multiple databases, including PubMed, Web of Science, IEEE Xplore, and Google Scholar, to collect relevant publications from the past two years (2021-2022). The studies selected for review were based on their relevance to the topic and the publication quality.