arXiv subjects

Seth Blumberg

Publications and source records attributed to Seth Blumberg.

3 recordsLinked to original sources

arXiv2026

abx_amr_simulator: A simulation environment for antibiotic prescribing policy optimization under antimicrobial resistance

Antimicrobial resistance (AMR) poses a global health threat, reducing the effectiveness of antibiotics and complicating clinical decision-making. To address this challenge, we introduce abx_amr_simulator, a Python-based simulation package designed to model antibiotic prescribing and AMR dynamics within a controlled, reinforcement learning (RL)-compatible environment. The simulator allows users to specify patient populations, antibiotic-specific AMR response curves, and reward functions that balance immedi- ate clinical benefit against long-term resistance management. Key features include a modular design for configuring patient attributes, antibiotic resistance dynamics modeled via a leaky-balloon abstraction, and tools to explore partial observability through noise, bias, and delay in observations. The package is compatible with the Gymnasium RL API, enabling users to train and test RL agents under diverse clinical scenarios. From an ML perspective, the package provides a configurable benchmark environment for sequential decision-making under uncertainty, including partial observability induced by noisy, biased, and delayed observations. By providing a customizable and extensible framework, abx_amr_simulator offers a valuable tool for studying AMR dynamics and optimizing antibiotic stewardship strategies under realistic uncertainty.

cs.LG↗

arXiv2024

Can Language Models Use Forecasting Strategies?

Advances in deep learning systems have allowed large models to match or surpass human accuracy on a number of skills such as image classification, basic programming, and standardized test taking. As the performance of the most capable models begin to saturate on tasks where humans already achieve high accuracy, it becomes necessary to benchmark models on increasingly complex abilities. One such task is forecasting the future outcome of events. In this work we describe experiments using a novel dataset of real world events and associated human predictions, an evaluation metric to measure forecasting ability, and the accuracy of a number of different LLM based forecasting designs on the provided dataset. Additionally, we analyze the performance of the LLM forecasters against human predictions and find that models still struggle to make accurate predictions about the future. Our follow-up experiments indicate this is likely due to models' tendency to guess that most events are unlikely to occur (which tends to be true for many prediction datasets, but does not reflect actual forecasting abilities). We reflect on next steps for developing a systematic and reliable approach to studying LLM forecasting.

cs.LG↗

arXiv2008

Concentration and Length Dependence of DNA Looping in Transcriptional Regulation

In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least) two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the J-factor for looping.

q-bio.BM↗