Jeremy Goldwasser

Rui Yang, Qingcheng Zeng, Keen You et al.

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.

Irene Li, Keen You, Yujie Qiao et al.

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.

Jeremy Goldwasser, Giles Hooker

Shapley values are among the most popular tools for explaining predictions of blackbox machine learning models. However, their high computational cost motivates the use of sampling approximations, inducing a considerable degree of uncertainty. To stabilize these model explanations, we propose ControlSHAP, an approach based on the Monte Carlo technique of control variates. Our methodology is applicable to any machine learning model and requires virtually no extra computation or modeling effort. On several high-dimensional datasets, we find it can produce dramatic reductions in the Monte Carlo variability of Shapley estimates.

Jeremy Goldwasser, Giles Hooker

Feature importance scores are ubiquitous tools for understanding the predictions of machine learning models. However, many popular attribution methods suffer from high instability due to random sampling. Leveraging novel ideas from hypothesis testing, we devise techniques that ensure the most important features are correct with high-probability guarantees. These assess the set of $K$ top-ranked features, as well as the order of its elements. Given a set of local or global importance scores, we demonstrate how to retrospectively verify the stability of the highest ranks. We then introduce two efficient sampling algorithms that identify the $K$ most important features, perhaps in order, with probability exceeding $1-α$. The theoretical justification for these procedures is validated empirically on SHAP and LIME.

Jeremy Goldwasser, Giles Hooker

Counterfactuals are a popular framework for interpreting machine learning predictions. These what if explanations are notoriously challenging to create for computer vision models: standard gradient-based methods are prone to produce adversarial examples, in which imperceptible modifications to image pixels provoke large changes in predictions. We introduce a new, easy-to-implement framework for counterfactual images that can flexibly adapt to contemporary advances in generative modeling. Our method, Counterfactual Attacks, resembles an adversarial attack on the representation of the image along a low-dimensional manifold. In addition, given an auxiliary dataset of image descriptors, we show how to accompany counterfactuals with feature attribution that quantify the changes between the original and counterfactual images. These importance scores can be aggregated into global counterfactual explanations that highlight the overall features driving model predictions. While this unification is possible for any counterfactual method, it has particular computational efficiency for ours. We demonstrate the efficacy of our approach with the MNIST and CelebA datasets.

Irene Li, Jessica Pan, Jeremy Goldwasser et al.

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.

Zhanlin Chen, Jeremy Goldwasser, Philip Tuckman et al.

In the era of single-cell sequencing, there is a growing need to extract insights from data with clustering methods. Here, we introduce Forest Fire Clustering, an efficient and interpretable method for cell-type discovery from single-cell data. Forest Fire Clustering makes minimal prior assumptions and, different from current approaches, calculates a non-parametric posterior probability that each cell is assigned a cell-type label. These posterior distributions allow for the evaluation of a label confidence for each cell and enable the computation of "label entropies," highlighting transitions along developmental trajectories. Furthermore, we show that Forest Fire Clustering can make robust, inductive inferences in an online-learning context and can readily scale to millions of cells. Finally, we demonstrate that our method outperforms state-of-the-art clustering approaches on diverse benchmarks of simulated and experimental data. Overall, Forest Fire Clustering is a useful tool for rare cell type discovery in large-scale single-cell analysis.