Silas Ruhrberg Estévez

Luca Muscarnera, Silas Ruhrberg Estévez, Yuanzhang Xiao et al.

A central problem in machine learning is that models can achieve near-perfect training performance while generalizing substantially less well to unseen examples. This gap is especially acute in high-dimensional, low-sample regimes, where many interpolating solutions exist and optimization must implicitly select among minima with different generalization properties. Following recent theoretical advances on optimization dynamics near the interpolation threshold, we note that the two-regime structure of risk minimization, with loss minimization followed by complexity minimization, motivates a biphasic optimization schedule. We thus theoretically demonstrate that GROKtimizer, a biphasic strategy that combines rapid convergence to interpolation with Critically Damped Momentum (CDM)-based post-interpolation norm minimization, offers a natural solution for selecting low-norm interpolating solutions. Under a local quadratic model of the post-interpolation basin, GROKtimizer provides a quadratic speedup over classical gradient descent, with provable optimality among first-order optimizers. To showcase the applicability of our method, we evaluate GROKtimizer on several synthetic benchmarks common in the classical grokking literature and on various real-world datasets. Finally, we reconcile our findings with the flat-minima hypothesis, highlighting the importance of post-interpolation dynamics in the construction of high-quality, generalizing models.

Silas Ruhrberg Estévez, Nicolas Huynh, Tennison Liu et al.

Inferring dynamics from population snapshots is a fundamental challenge in machine learning and biology. In scRNA-sequencing (scRNA-seq), destructive measurements preclude direct tracking of individual cells across time, making trajectory inference underdetermined. Optimal Transport (OT) provides a principled framework for snapshot alignment, but a long-standing modeling question is which cost functions yield biologically meaningful couplings. Standard OT approaches rely on gene-expression distances, implicitly treating cells as independent points and neglecting structured cell-cell communication mediated by ligand-receptor signaling. We introduce CellBRIDGE (Cell-Based Regularized Interaction-Driven Gene Expression), which augments feature-based OT with a directed, typed interaction cost derived from ligand-receptor activity. By explicitly modeling cell-cell communication, CellBRIDGE improves cross-snapshot couplings and downstream trajectory estimates across synthetic and real scRNA-seq datasets relative to feature-only baselines. Notably, CellBRIDGE enables mechanistically interpretable in silico perturbations: on lung cancer data, silencing specific ligand-receptor pairs induces trajectory shifts that recapitulate expected effects of targeted pathway inhibition.

Luca Muscarnera, Silas Ruhrberg Estévez, Samuel Holt et al.

Recovering governing equations from data is central to scientific discovery, yet existing methods often break down under noisy, partial observations, or rely on black-box latent dynamics that obscure mechanism. We introduce MAAT (Model Aware Approximation of Trajectories), a framework for symbolic discovery built on knowledge-informed Kernel State Reconstruction. MAAT formulates state reconstruction in a reproducing kernel Hilbert space and directly incorporates structural and semantic priors such as non-negativity, conservation laws, and domain-specific observation models into the reconstruction objective, while accommodating heterogeneous sampling and measurement granularity. This yields smooth, physically consistent state estimates with analytic time derivatives, providing a principled interface between fragmented sensor data and symbolic regression. Across twelve diverse scientific benchmarks and multiple noise regimes, MAAT substantially reduces state-estimation MSE for trajectories and derivatives used by downstream symbolic regression relative to strong baselines.

Silas Ruhrberg Estévez, Christopher Chiu, Mihaela van der Schaar

Modern clinical practice relies on evidence-based guidelines implemented as compact scoring systems composed of a small number of interpretable decision rules. While machine-learning models achieve strong performance, many fail to translate into routine clinical use due to misalignment with workflow constraints such as memorability, auditability, and bedside execution. We argue that this gap arises not from insufficient predictive power, but from optimizing over model classes that are incompatible with guideline deployment. Deployable guidelines often take the form of unit-weighted clinical checklists, formed by thresholding the sum of binary rules, but learning such scores requires searching an exponentially large discrete space of possible rule sets. We introduce AgentScore, which performs semantically guided optimization in this space by using LLMs to propose candidate rules and a deterministic, data-grounded verification-and-selection loop to enforce statistical validity and deployability constraints. Across eight clinical prediction tasks, AgentScore outperforms existing score-generation methods and achieves AUC comparable to more flexible interpretable models despite operating under stronger structural constraints. On two additional externally validated tasks, AgentScore achieves higher discrimination than established guideline-based scores.

Silas Ruhrberg Estévez, Nicolás Astorga, Mihaela van der Schaar

There is growing interest in using machine learning (ML) to support clinical diagnosis, but most approaches rely on static, fully observed datasets and fail to reflect the sequential, resource-aware reasoning clinicians use in practice. Diagnosis remains complex and error prone, especially in high-pressure or resource-limited settings, underscoring the need for frameworks that help clinicians make timely and cost-effective decisions. We propose ACTMED (Adaptive Clinical Test selection via Model-based Experimental Design), a diagnostic framework that integrates Bayesian Experimental Design (BED) with large language models (LLMs) to better emulate real-world diagnostic reasoning. At each step, ACTMED selects the test expected to yield the greatest reduction in diagnostic uncertainty for a given patient. LLMs act as flexible simulators, generating plausible patient state distributions and supporting belief updates without requiring structured, task-specific training data. Clinicians can remain in the loop; reviewing test suggestions, interpreting intermediate outputs, and applying clinical judgment throughout. We evaluate ACTMED on real-world datasets and show it can optimize test selection to improve diagnostic accuracy, interpretability, and resource use. This represents a step toward transparent, adaptive, and clinician-aligned diagnostic systems that generalize across settings with reduced reliance on domain-specific data.

Tennison Liu, Silas Ruhrberg Estévez, David L. Bentley et al.

Large-scale scientific datasets -- spanning health biobanks, cell atlases, Earth reanalyses, and more -- create opportunities for exploratory discovery unconstrained by specific research questions. We term this process hypothesis hunting: the cumulative search for insight through sustained exploration across vast and complex hypothesis spaces. To support it, we introduce AScience, a framework modeling discovery as the interaction of agents, networks, and evaluation norms, and implement it as ASCollab, a distributed system of LLM-based research agents with heterogeneous behaviors. These agents self-organize into evolving networks, continually producing and peer-reviewing findings under shared standards of evaluation. Experiments show that such social dynamics enable the accumulation of expert-rated results along the diversity-quality-novelty frontier, including rediscoveries of established biomarkers, extensions of known pathways, and proposals of new therapeutic targets. While wet-lab validation remains indispensable, our experiments on cancer cohorts demonstrate that socially structured, agentic networks can sustain exploratory hypothesis hunting at scale.

Silas Ruhrberg Estévez, Josée Mallah, Dominika Kazieczko et al.

Ankle exoskeletons have garnered considerable interest for their potential to enhance mobility and reduce fall risks, particularly among the aging population. The efficacy of these devices relies on accurate real-time prediction of the user's intended movements through sensor-based inputs. This paper presents a novel motion prediction framework that integrates three Inertial Measurement Units (IMUs) and eight surface Electromyography (sEMG) sensors to capture both kinematic and muscular activity data. A comprehensive set of activities, representative of everyday movements in barrier-free environments, was recorded for the purpose. Our findings reveal that Convolutional Neural Networks (CNNs) slightly outperform Long Short-Term Memory (LSTM) networks on a dataset of five motion tasks, achieving classification accuracies of $96.5 \pm 0.8 \%$ and $87.5 \pm 2.9 \%$, respectively. Furthermore, we demonstrate the system's proficiency in transfer learning, enabling accurate motion classification for new subjects using just ten samples per class for finetuning. The robustness of the model is demonstrated by its resilience to sensor failures resulting in absent signals, maintaining reliable performance in real-world scenarios. These results underscore the potential of deep learning algorithms to enhance the functionality and safety of ankle exoskeletons, ultimately improving their usability in daily life.