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Researcher profile

Jacob R. Gardner

Jacob R. Gardner contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine Learningmath.NANumerical Analysis

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Published work

4 published item(s)

preprint2026arXiv

Self-Driving Datasets: From 20 Million Papers to Nuanced Biomedical Knowledge at Scale

Manually curated biomedical repositories -- spanning bioactivity, genomics, and chemistry -- are expensive to maintain, lag behind primary literature, and discard experimental context, obscuring nuances needed to assess data correctness and coverage. We show that PubMed itself can be autonomously and cost-effectively turned into structured datasets that are larger, more nuanced, and more accurate than the curated databases they replace. We present three coupled contributions: (1) an LLM-based entity-tagging pipeline, grounded in nine biomedical ontologies, that tags 4.5B entities across 19 categories in a 22.5M-paper, 2.5T-token PubMed corpus; (2) hybrid sparse-dense retrieval supporting entity-filtered semantic queries over the tagged corpus; and (3) Starling, a multi-agent deep research system that, given only a natural-language task description, designs precision- and recall-targeted retrieval filters, induces an extraction schema, and emits structured records with nuance-rich fields and supporting passages. Across six tasks -- blood-brain barrier permeability, oral bioavailability, acute toxicity (LD50), gene-disease associations, protein subcellular localization, and chemical reactions -- Starling produces ~6.3M records (91K-3M per task); several are, to our knowledge, the largest public datasets for their property. Frontier-model rejection of our extractions is 0.6-7.7% across tasks, far below error rates we measure on widely used curated counterparts (e.g., 16.5% on BBB_Martins, 7.3% on Bioavailability_Ma). Beyond scale and accuracy, the supporting passages carry nuance tabular databases discard -- e.g., oral bioavailability may depend on fed vs. fasted state. Together, the corpus, retrieval, and agent establish a foundation for AI-driven therapeutic design. Code and datasets: https://github.com/starling-labs/starling.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Local Bayesian optimization via maximizing probability of descent

Local optimization presents a promising approach to expensive, high-dimensional black-box optimization by sidestepping the need to globally explore the search space. For objective functions whose gradient cannot be evaluated directly, Bayesian optimization offers one solution -- we construct a probabilistic model of the objective, design a policy to learn about the gradient at the current location, and use the resulting information to navigate the objective landscape. Previous work has realized this scheme by minimizing the variance in the estimate of the gradient, then moving in the direction of the expected gradient. In this paper, we re-examine and refine this approach. We demonstrate that, surprisingly, the expected value of the gradient is not always the direction maximizing the probability of descent, and in fact, these directions may be nearly orthogonal. This observation then inspires an elegant optimization scheme seeking to maximize the probability of descent while moving in the direction of most-probable descent. Experiments on both synthetic and real-world objectives show that our method outperforms previous realizations of this optimization scheme and is competitive against other, significantly more complicated baselines.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Preconditioning for Scalable Gaussian Process Hyperparameter Optimization

Gaussian process hyperparameter optimization requires linear solves with, and log-determinants of, large kernel matrices. Iterative numerical techniques are becoming popular to scale to larger datasets, relying on the conjugate gradient method (CG) for the linear solves and stochastic trace estimation for the log-determinant. This work introduces new algorithmic and theoretical insights for preconditioning these computations. While preconditioning is well understood in the context of CG, we demonstrate that it can also accelerate convergence and reduce variance of the estimates for the log-determinant and its derivative. We prove general probabilistic error bounds for the preconditioned computation of the log-determinant, log-marginal likelihood and its derivatives. Additionally, we derive specific rates for a range of kernel-preconditioner combinations, showing that up to exponential convergence can be achieved. Our theoretical results enable provably efficient optimization of kernel hyperparameters, which we validate empirically on large-scale benchmark problems. There our approach accelerates training by up to an order of magnitude.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Efficient Nonmyopic Bayesian Optimization via One-Shot Multi-Step Trees

Bayesian optimization is a sequential decision making framework for optimizing expensive-to-evaluate black-box functions. Computing a full lookahead policy amounts to solving a highly intractable stochastic dynamic program. Myopic approaches, such as expected improvement, are often adopted in practice, but they ignore the long-term impact of the immediate decision. Existing nonmyopic approaches are mostly heuristic and/or computationally expensive. In this paper, we provide the first efficient implementation of general multi-step lookahead Bayesian optimization, formulated as a sequence of nested optimization problems within a multi-step scenario tree. Instead of solving these problems in a nested way, we equivalently optimize all decision variables in the full tree jointly, in a ``one-shot'' fashion. Combining this with an efficient method for implementing multi-step Gaussian process ``fantasization,'' we demonstrate that multi-step expected improvement is computationally tractable and exhibits performance superior to existing methods on a wide range of benchmarks.

0 citations0 reviewsNo code linkedOpen access