Leveraging Social Determinants of Health in Alzheimer's Research Using LLM-Augmented Literature Mining and Knowledge Graphs

Growing evidence suggests that social determinants of health (SDoH), a set of nonmedical factors, affect individuals' risks of developing Alzheimer's disease (AD) and related dementias. Nevertheless, the etiological mechanisms underlying such relationships remain largely unclear, mainly due to difficulties in collecting relevant information. This study presents a novel, automated framework that leverages recent advancements of large language model (LLM) and natural language processing techniques to mine SDoH knowledge from extensive literature and integrate it with AD-related biological entities extracted from the general-purpose knowledge graph PrimeKG. Utilizing graph neural networks, we performed link prediction tasks to evaluate the resultant SDoH-augmented knowledge graph. Our framework shows promise for enhancing knowledge discovery in AD and can be generalized to other SDoH-related research areas, offering a new tool for exploring the impact of social determinants on health outcomes. Our code is available at: https://github.com/hwq0726/SDoHenPKG

Lexicase Selection Parameter Analysis: Varying Population Size and Test Case Redundancy with Diagnostic Metrics

Lexicase selection is a successful parent selection method in genetic programming that has outperformed other methods across multiple benchmark suites. Unlike other selection methods that require explicit parameters to function, such as tournament size in tournament selection, lexicase selection does not. However, if evolutionary parameters like population size and number of generations affect the effectiveness of a selection method, then lexicase's performance may also be impacted by these `hidden' parameters. Here, we study how these hidden parameters affect lexicase's ability to exploit gradients and maintain specialists using diagnostic metrics. By varying the population size with a fixed evaluation budget, we show that smaller populations tend to have greater exploitation capabilities, whereas larger populations tend to maintain more specialists. We also consider the effect redundant test cases have on specialist maintenance, and find that high redundancy may hinder the ability to optimize and maintain specialists, even for larger populations. Ultimately, we highlight that population size, evaluation budget, and test cases must be carefully considered for the characteristics of the problem being solved.

A review of feature selection strategies utilizing graph data structures and knowledge graphs

Feature selection in Knowledge Graphs (KGs) are increasingly utilized in diverse domains, including biomedical research, Natural Language Processing (NLP), and personalized recommendation systems. This paper delves into the methodologies for feature selection within KGs, emphasizing their roles in enhancing machine learning (ML) model efficacy, hypothesis generation, and interpretability. Through this comprehensive review, we aim to catalyze further innovation in feature selection for KGs, paving the way for more insightful, efficient, and interpretable analytical models across various domains. Our exploration reveals the critical importance of scalability, accuracy, and interpretability in feature selection techniques, advocating for the integration of domain knowledge to refine the selection process. We highlight the burgeoning potential of multi-objective optimization and interdisciplinary collaboration in advancing KG feature selection, underscoring the transformative impact of such methodologies on precision medicine, among other fields. The paper concludes by charting future directions, including the development of scalable, dynamic feature selection algorithms and the integration of explainable AI principles to foster transparency and trust in KG-driven models.

Lexidate: Model Evaluation and Selection with Lexicase

Automated machine learning streamlines the task of finding effective machine learning pipelines by automating model training, evaluation, and selection. Traditional evaluation strategies, like cross-validation (CV), generate one value that averages the accuracy of a pipeline's predictions. This single value, however, may not fully describe the generalizability of the pipeline. Here, we present Lexicase-based Validation (lexidate), a method that uses multiple, independent prediction values for selection. Lexidate splits training data into a learning set and a selection set. Pipelines are trained on the learning set and make predictions on the selection set. The predictions are graded for correctness and used by lexicase selection to identify parent pipelines. Compared to 10-fold CV, lexicase reduces the training time. We test the effectiveness of three lexidate configurations within the Tree-based Pipeline Optimization Tool 2 (TPOT2) package on six OpenML classification tasks. In one configuration, we detected no difference in the accuracy of the final model returned from TPOT2 on most tasks compared to 10-fold CV. All configurations studied here returned similar or less complex final pipelines compared to 10-fold CV.

Unleashing the Power of Multi-Task Learning: A Comprehensive Survey Spanning Traditional, Deep, and Pretrained Foundation Model Eras

MTL is a learning paradigm that effectively leverages both task-specific and shared information to address multiple related tasks simultaneously. In contrast to STL, MTL offers a suite of benefits that enhance both the training process and the inference efficiency. MTL's key advantages encompass streamlined model architecture, performance enhancement, and cross-domain generalizability. Over the past twenty years, MTL has become widely recognized as a flexible and effective approach in various fields, including CV, NLP, recommendation systems, disease prognosis and diagnosis, and robotics. This survey provides a comprehensive overview of the evolution of MTL, encompassing the technical aspects of cutting-edge methods from traditional approaches to deep learning and the latest trend of pretrained foundation models. Our survey methodically categorizes MTL techniques into five key areas: regularization, relationship learning, feature propagation, optimization, and pre-training. This categorization not only chronologically outlines the development of MTL but also dives into various specialized strategies within each category. Furthermore, the survey reveals how the MTL evolves from handling a fixed set of tasks to embracing a more flexible approach free from task or modality constraints. It explores the concepts of task-promptable and -agnostic training, along with the capacity for ZSL, which unleashes the untapped potential of this historically coveted learning paradigm. Overall, we hope this survey provides the research community with a comprehensive overview of the advancements in MTL from its inception in 1997 to the present in 2023. We address present challenges and look ahead to future possibilities, shedding light on the opportunities and potential avenues for MTL research in a broad manner. This project is publicly available at https://github.com/junfish/Awesome-Multitask-Learning.

Genetic Programming Theory and Practice: A Fifteen-Year Trajectory

The GPTP workshop series, which began in 2003, has served over the years as a focal meeting for genetic programming (GP) researchers. As such, we think it provides an excellent source for studying the development of GP over the past fifteen years. We thus present herein a trajectory of the thematic developments in the field of GP.

Coevolving Artistic Images Using OMNIREP

We have recently developed OMNIREP, a coevolutionary algorithm to discover both a representation and an interpreter that solve a particular problem of interest. Herein, we demonstrate that the OMNIREP framework can be successfully applied within the field of evolutionary art. Specifically, we coevolve representations that encode image position, alongside interpreters that transform these positions into one of three pre-defined shapes (chunks, polygons, or circles) of varying size, shape, and color. We showcase a sampling of the unique image variations produced by this approach.

New Pathways in Coevolutionary Computation

The simultaneous evolution of two or more species with coupled fitness -- coevolution -- has been put to good use in the field of evolutionary computation. Herein, we present two new forms of coevolutionary algorithms, which we have recently designed and applied with success. OMNIREP is a cooperative coevolutionary algorithm that discovers both a representation and an encoding for solving a particular problem of interest. SAFE is a commensalistic coevolutionary algorithm that maintains two coevolving populations: a population of candidate solutions and a population of candidate objective functions needed to measure solution quality during evolution.

Faster Convergence with Lexicase Selection in Tree-based Automated Machine Learning

In many evolutionary computation systems, parent selection methods can affect, among other things, convergence to a solution. In this paper, we present a study comparing the role of two commonly used parent selection methods in evolving machine learning pipelines in an automated machine learning system called Tree-based Pipeline Optimization Tool (TPOT). Specifically, we demonstrate, using experiments on multiple datasets, that lexicase selection leads to significantly faster convergence as compared to NSGA-II in TPOT. We also compare the exploration of parts of the search space by these selection methods using a trie data structure that contains information about the pipelines explored in a particular run.

Benchmarking AutoML algorithms on a collection of synthetic classification problems

Automated machine learning (AutoML) algorithms have grown in popularity due to their high performance and flexibility to adapt to different problems and data sets. With the increasing number of AutoML algorithms, deciding which would best suit a given problem becomes increasingly more work. Therefore, it is essential to use complex and challenging benchmarks which would be able to differentiate the AutoML algorithms from each other. This paper compares the performance of four different AutoML algorithms: Tree-based Pipeline Optimization Tool (TPOT), Auto-Sklearn, Auto-Sklearn 2, and H2O AutoML. We use the Diverse and Generative ML benchmark (DIGEN), a diverse set of synthetic datasets derived from generative functions designed to highlight the strengths and weaknesses of the performance of common machine learning algorithms. We confirm that AutoML can identify pipelines that perform well on all included datasets. Most AutoML algorithms performed similarly without much room for improvement; however, some were more consistent than others at finding high-performing solutions for some datasets.