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Accurate prediction of compound potency accelerates early-stage drug discovery by prioritizing candidates for experimental testing. However, many Quantitative Structure-Activity Relationship (QSAR) approaches for this prediction are…

Stacking (or stacked generalization) is an ensemble learning method with one main distinctiveness from the rest: even though several base models are trained on the original data set, their predictions are further used as input data for one…

We present Connection-Aware Motif Sequencing (CamS), a graph-to-sequence representation that enables decoder-only Transformers to learn molecular graphs via standard next-token prediction (NTP). For molecular property prediction,…

Machine learning methods can detect complex relationships between variables, but usually do not exploit domain knowledge. This is a limitation because in many scientific disciplines, such as systems biology, domain knowledge is available in…

In this work, we propose a simple transformer-based baseline for multimodal molecular representation learning, integrating three distinct modalities: SMILES strings, 2D graph representations, and 3D conformers of molecules. A key aspect of…

A variety of statistical and machine learning methods are used to model crash frequency on specific roadways with machine learning methods generally having a higher prediction accuracy. Recently, heterogeneous ensemble methods (HEM),…

Variable selection for structured covariates lying on an underlying known graph is a problem motivated by practical applications, and has been a topic of increasing interest. However, most of the existing methods may not be scalable to high…

The quest for accurate prediction of drug molecule properties poses a fundamental challenge in the realm of Artificial Intelligence Drug Discovery (AIDD). An effective representation of drug molecules emerges as a pivotal component in this…

Stacking, a potent ensemble learning method, leverages a meta-model to harness the strengths of multiple base models, thereby enhancing prediction accuracy. Traditional stacking techniques typically utilize established learning models, such…

In many applications, data can be heterogeneous in the sense of spanning latent groups with different underlying distributions. When predictive models are applied to such data the heterogeneity can affect both predictive performance and…

Synthesis planning and reaction outcome prediction are two fundamental problems in computer-aided organic chemistry for which a variety of data-driven approaches have emerged. Natural language approaches that model each problem as a…

It is increasingly common to encounter prediction tasks in the biomedical sciences for which multiple datasets are available for model training. Common approaches such as pooling datasets and applying standard statistical learning methods…

Multimodal pathology-genomic analysis is critical for cancer survival prediction. However, existing approaches predominantly integrate formalin-fixed paraffin-embedded (FFPE) slides with genomic data, while neglecting the availability of…

Spread through air spaces (STAS) represents a newly identified aggressive pattern in lung cancer, which is known to be associated with adverse prognostic factors and complex pathological features. Pathologists currently rely on time…

Cancer is a heterogeneous disease with different combinations of genetic and epigenetic alterations driving the development of cancer in different individuals. While these alterations are believed to converge on genes in key cellular…

Graphical models are commonly used to discover associations within gene or protein networks for complex diseases such as cancer. Most existing methods estimate a single graph for a population, while in many cases, researchers are interested…

The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case…

Multiple Sclerosis (MS) is a chronic autoimmune disease of the central nervous system whose molecular mechanisms remain incompletely understood. In this study, we developed an end-to-end machine learning pipeline to analyze transcriptomic…

SMILES is a linear representation of chemical structures which encodes the connection table, and the stereochemistry of a molecule as a line of text with a grammar structure denoting atoms, bonds, rings and chains, and this information can…

Traffic flow prediction plays a critical role in the intelligent transportation system, and it is also a challenging task because of the underlying complex Spatio-temporal patterns and heterogeneities evolving across time. However, most…