arXiv subjects

Benjamin Rosand

Publications and source records attributed to Benjamin Rosand.

4 recordsLinked to original sources

arXiv2023

Ascle: A Python Natural Language Processing Toolkit for Medical Text Generation

This study introduces Ascle, a pioneering natural language processing (NLP) toolkit designed for medical text generation. Ascle is tailored for biomedical researchers and healthcare professionals with an easy-to-use, all-in-one solution that requires minimal programming expertise. For the first time, Ascle evaluates and provides interfaces for the latest pre-trained language models, encompassing four advanced and challenging generative functions: question-answering, text summarization, text simplification, and machine translation. In addition, Ascle integrates 12 essential NLP functions, along with query and search capabilities for clinical databases. The toolkit, its models, and associated data are publicly available via https://github.com/Yale-LILY/MedGen.

cs.CL↗

arXiv2023

EHRKit: A Python Natural Language Processing Toolkit for Electronic Health Record Texts

The Electronic Health Record (EHR) is an essential part of the modern medical system and impacts healthcare delivery, operations, and research. Unstructured text is attracting much attention despite structured information in the EHRs and has become an exciting research field. The success of the recent neural Natural Language Processing (NLP) method has led to a new direction for processing unstructured clinical notes. In this work, we create a python library for clinical texts, EHRKit. This library contains two main parts: MIMIC-III-specific functions and tasks specific functions. The first part introduces a list of interfaces for accessing MIMIC-III NOTEEVENTS data, including basic search, information retrieval, and information extraction. The second part integrates many third-party libraries for up to 12 off-shelf NLP tasks such as named entity recognition, summarization, machine translation, etc.

cs.CL↗

arXiv2023

Algorithms for perturbative analysis and simulation of quantum dynamics

We develop general purpose algorithms for computing and utilizing both the Dyson series and Magnus expansion, with the goal of facilitating numerical perturbative studies of quantum dynamics. To enable broad applications to models with multiple parameters, we phrase our algorithms in terms of multivariable sensitivity analysis, for either the solution or the time-averaged generator of the evolution over a fixed time-interval. These tools simultaneously compute a collection of terms up to arbitrary order, and are general in the sense that the model can depend on the parameters in an arbitrary time-dependent way. We implement the algorithms in the open source software package \qiskitdynamics{}, utilizing the JAX array library to enable just-in-time compilation, automatic differentiation, and GPU execution of all computations. Using a model of a single transmon, we demonstrate how to use these tools to approximate fidelity in a region of model parameter space, as well as construct perturbative robust control objectives. We also derive and implement Dyson and Magnus-based variations of the recently introduced Dysolve algorithm [Shillito et al., Physical Review Research, 3(3):033266] for simulating linear matrix differential equations. We show how the pre-computation step can be phrased as a multivariable expansion computation problem with fewer terms than in the original method. When simulating a two-transmon entangling gate on a GPU, we find the Dyson and Magnus-based solvers provide a speedup over traditional ODE solvers, ranging from roughly $2\times$ to $4\times$ for a solution and $10\times$ to $60\times$ for a gradient, depending on solution accuracy.

quant-ph↗

arXiv2021

Neural Natural Language Processing for Unstructured Data in Electronic Health Records: a Review

Electronic health records (EHRs), digital collections of patient healthcare events and observations, are ubiquitous in medicine and critical to healthcare delivery, operations, and research. Despite this central role, EHRs are notoriously difficult to process automatically. Well over half of the information stored within EHRs is in the form of unstructured text (e.g. provider notes, operation reports) and remains largely untapped for secondary use. Recently, however, newer neural network and deep learning approaches to Natural Language Processing (NLP) have made considerable advances, outperforming traditional statistical and rule-based systems on a variety of tasks. In this survey paper, we summarize current neural NLP methods for EHR applications. We focus on a broad scope of tasks, namely, classification and prediction, word embeddings, extraction, generation, and other topics such as question answering, phenotyping, knowledge graphs, medical dialogue, multilinguality, interpretability, etc.

cs.CL↗