Foundation models (FMs), such as GPT-4 and AlphaFold, are reshaping the landscape of scientific research. Beyond accelerating tasks such as hypothesis generation, experimental design, and result interpretation, they prompt a more fundamental question: Are FMs merely enhancing existing scientific methodologies, or are they redefining the way science is conducted? In this paper, we argue that FMs are catalyzing a transition toward a new scientific paradigm. We introduce a three-stage framework to describe this evolution: (1) Meta-Scientific Integration, where FMs enhance workflows within traditional paradigms; (2) Hybrid Human-AI Co-Creation, where FMs become active collaborators in problem formulation, reasoning, and discovery; and (3) Autonomous Scientific Discovery, where FMs operate as independent agents capable of generating new scientific knowledge with minimal human intervention. Through this lens, we review current applications and emerging capabilities of FMs across existing scientific paradigms. We further identify risks and future directions for FM-enabled scientific discovery. This position paper aims to support the scientific community in understanding the transformative role of FMs and to foster reflection on the future of scientific discovery.

Factorization machines (FMs) are a supervised learning approach that can use second-order feature combinations even when the data is very high-dimensional. Unfortunately, despite increasing interest in FMs, there exists to date no efficient training algorithm for higher-order FMs (HOFMs). In this paper, we present the first generic yet efficient algorithms for training arbitrary-order HOFMs. We also present new variants of HOFMs with shared parameters, which greatly reduce model size and prediction times while maintaining similar accuracy. We demonstrate the proposed approaches on four different link prediction tasks.

The advent of foundation models (FMs) in healthcare offers unprecedented opportunities to enhance medical diagnostics through automated classification and segmentation tasks. However, these models also raise significant concerns about their fairness, especially when applied to diverse and underrepresented populations in healthcare applications. Currently, there is a lack of comprehensive benchmarks, standardized pipelines, and easily adaptable libraries to evaluate and understand the fairness performance of FMs in medical imaging, leading to considerable challenges in formulating and implementing solutions that ensure equitable outcomes across diverse patient populations. To fill this gap, we introduce FairMedFM, a fairness benchmark for FM research in medical imaging.

Factorization machines (FMs) are a supervised learning approach that can use second-order feature combinations even when the data is very high-dimensional. Unfortunately, despite increasing interest in FMs, there exists to date no efficient training algorithm for higher-order FMs (HOFMs). In this paper, we present the first generic yet efficient algorithms for training arbitrary-order HOFMs. We also present new variants of HOFMs with shared parameters, which greatly reduce model size and prediction times while maintaining similar accuracy. We demonstrate the proposed approaches on four different link prediction tasks.

We help address these challenges through three contributions. First, we publish a new dataset, EHRSHOT, which contains de-identified structured data from the electronic health records (EHRs) of 6,739 patients from Stanford Medicine.

This underlines the necessity to explicitly evaluate and finetune FMs on such expert tasks, arguably ones that appear the most in practical real-world applications.

Factorisation-based Models (FMs), such as DistMult, have enjoyed enduring success for Knowledge Graph Completion (KGC) tasks, often outperforming Graph Neural Networks (GNNs). However, unlike GNNs, FMs struggle to incorporate node features and generalise to unseen nodes in inductive settings.