arXiv subjects

David L. Bentley

Publications and source records attributed to David L. Bentley.

4 recordsLinked to original sources

arXiv2026

SeqMaestro: From nucleotide sequences to biological hypotheses through interpretable machine learning

Nucleotide sequence analysis is central to problems spanning regulatory genomics, evolutionary biology, and phenotype prediction. Classical bioinformatics methods extract interpretable sequence properties such as motifs and k-mer composition, but their flexibility is limited. In contrast, modern deep learning models can learn powerful predictive representations directly from raw sequences, yet their internal representations and decision mechanisms are difficult to inspect. Interpretable machine learning methods (e.g., sparse linear models and decision trees) provide human-understandable representations of predictive relationships but are not designed to operate directly on nucleotide sequences. Here, we introduce SeqMaestro, a machine learning framework that proposes biological hypotheses from nucleotide sequences using interpretable models. Our solution is centered around a two-layer interface that connects nucleotide sequences with the broader ecosystem of interpretable machine learning. SeqMaestro uses this interface to fit diverse combinations of interpretable models, feature representations, and extraction strategies, leveraging variability across transparent models to identify robust biological signals and richer predictive relationships than feature importance alone can provide. The system also supports data transformation and cleaning, model fitting, hyperparameter tuning, reliability analysis, and synthesis of results into a contextualized written report. By providing these capabilities through a no-code workflow, SeqMaestro is designed to make interpretable sequence analysis accessible to researchers without requiring extensive programming or machine learning expertise. SeqMaestro thereby provides an accessible route from nucleotide sequences to biological hypotheses.

cs.LG↗

arXiv2026

CellBRIDGE: Learning Cellular Trajectories via Interaction-Aware Alignment

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.

cs.LG↗

arXiv2026

Influence-Guided Symbolic Regression: Scientific Discovery via LLM-Driven Equation Search with Granular Feedback

Large Language Models (LLMs) offer a promising avenue for scientific discovery, yet their application to symbolic regression is often constrained by inefficient search strategies and coarse feedback signals. Current methods typically guide LLMs using scalar metrics (e.g., global Mean Squared Error), which fail to identify which components of a proposed equation are driving performance or causing error. We introduce \textit{Influence-Guided Symbolic Regression} (IGSR), a method that frames equation discovery as an iterative two-step process combining diverse term generation with rigorous selection: an LLM generates candidate basis functions $ψ_j(\mathbf{x})$ for a linear model, which are then evaluated using granular influence scores $Δ_j$. These scores quantify each term's marginal contribution to generalization accuracy, enabling an influence-guided pruning process that systematically refines the model structure. Integrating this mechanism into a Monte Carlo Tree Search (MCTS) enables navigating the combinatorial search space while balancing exploration of novel functional forms with exploitation of high-influence components. We demonstrate IGSR's effectiveness on a diverse suite of benchmarks, including LLM-SRBench, pharmacological PKPD models, an epidemiological simulation, and real-world genomic data. Notably, we validate the framework's capacity for genuine discovery in a case study using a high-dimensional biological dataset, in which IGSR identified a novel relationship between DNA methylation and RNA Polymerase II pausing; a hypothesis that was subsequently supported via wet-lab experimentation.

cs.LG↗

arXiv2025

Hypothesis Hunting with Evolving Networks of Autonomous Scientific Agents

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.

cs.AI↗