Joseph D. Janizek

Jon M. Laurent, Joseph D. Janizek, Michael Ruzo et al.

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and reasoning on textbook-style science questions, but few if any benchmarks are designed to evaluate language model performance on practical tasks required for scientific research, such as literature search, protocol planning, and data analysis. As a step toward building such benchmarks, we introduce the Language Agent Biology Benchmark (LAB-Bench), a broad dataset of over 2,400 multiple choice questions for evaluating AI systems on a range of practical biology research capabilities, including recall and reasoning over literature, interpretation of figures, access and navigation of databases, and comprehension and manipulation of DNA and protein sequences. Importantly, in contrast to previous scientific benchmarks, we expect that an AI system that can achieve consistently high scores on the more difficult LAB-Bench tasks would serve as a useful assistant for researchers in areas such as literature search and molecular cloning. As an initial assessment of the emergent scientific task capabilities of frontier language models, we measure performance of several against our benchmark and report results compared to human expert biology researchers. We will continue to update and expand LAB-Bench over time, and expect it to serve as a useful tool in the development of automated research systems going forward. A public subset of LAB-Bench is available for use at the following URL: https://huggingface.co/datasets/futurehouse/lab-bench

Joseph D. Janizek, Pascal Sturmfels, Su-In Lee

Recent work has shown great promise in explaining neural network behavior. In particular, feature attribution methods explain which features were most important to a model's prediction on a given input. However, for many tasks, simply knowing which features were important to a model's prediction may not provide enough insight to understand model behavior. The interactions between features within the model may better help us understand not only the model, but also why certain features are more important than others. In this work, we present Integrated Hessians, an extension of Integrated Gradients that explains pairwise feature interactions in neural networks. Integrated Hessians overcomes several theoretical limitations of previous methods to explain interactions, and unlike such previous methods is not limited to a specific architecture or class of neural network. Additionally, we find that our method is faster than existing methods when the number of features is large, and outperforms previous methods on existing quantitative benchmarks. Code available at https://github.com/suinleelab/path_explain

Joseph D. Janizek, Gabriel Erion, Alex J. DeGrave et al.

While deep learning has shown promise in the domain of disease classification from medical images, models based on state-of-the-art convolutional neural network architectures often exhibit performance loss due to dataset shift. Models trained using data from one hospital system achieve high predictive performance when tested on data from the same hospital, but perform significantly worse when they are tested in different hospital systems. Furthermore, even within a given hospital system, deep learning models have been shown to depend on hospital- and patient-level confounders rather than meaningful pathology to make classifications. In order for these models to be safely deployed, we would like to ensure that they do not use confounding variables to make their classification, and that they will work well even when tested on images from hospitals that were not included in the training data. We attempt to address this problem in the context of pneumonia classification from chest radiographs. We propose an approach based on adversarial optimization, which allows us to learn more robust models that do not depend on confounders. Specifically, we demonstrate improved out-of-hospital generalization performance of a pneumonia classifier by training a model that is invariant to the view position of chest radiographs (anterior-posterior vs. posterior-anterior). Our approach leads to better predictive performance on external hospital data than both a standard baseline and previously proposed methods to handle confounding, and also suggests a method for identifying models that may rely on confounders. Code available at https://github.com/suinleelab/cxr_adv.

Joseph D. Janizek, Sonnet Xu, Junayd Lateef et al.

Ensuring the reliability of machine learning models in safety-critical domains such as healthcare requires auditing methods that can uncover model shortcomings. We introduce a method for identifying important visual concepts within large multimodal models (LMMs) and use it to investigate the behaviors these models exhibit when prompted with medical tasks. We primarily focus on the task of classifying malignant skin lesions from clinical dermatology images, with supplemental experiments including both chest radiographs and natural images. After showing how LMMs display unexpected gaps in performance between different demographic subgroups when prompted with demonstrating examples, we apply our method, Visual Concept Ranking (VCR), to these models and prompts. VCR generates hypotheses related to different visual feature dependencies, which we are then able to validate with manual interventions.

Hugh Chen, Joseph D. Janizek, Scott Lundberg et al.

A variety of recent papers discuss the application of Shapley values, a concept for explaining coalitional games, for feature attribution in machine learning. However, the correct way to connect a machine learning model to a coalitional game has been a source of controversy. The two main approaches that have been proposed differ in the way that they condition on known features, using either (1) an interventional or (2) an observational conditional expectation. While previous work has argued that one of the two approaches is preferable in general, we argue that the choice is application dependent. Furthermore, we argue that the choice comes down to whether it is desirable to be true to the model or true to the data. We use linear models to investigate this choice. After deriving an efficient method for calculating observational conditional expectation Shapley values for linear models, we investigate how correlation in simulated data impacts the convergence of observational conditional expectation Shapley values. Finally, we present two real data examples that we consider to be representative of possible use cases for feature attribution -- (1) credit risk modeling and (2) biological discovery. We show how a different choice of value function performs better in each scenario, and how possible attributions are impacted by modeling choices.

Gabriel Erion, Joseph D. Janizek, Pascal Sturmfels et al.

Recent research has demonstrated that feature attribution methods for deep networks can themselves be incorporated into training; these attribution priors optimize for a model whose attributions have certain desirable properties -- most frequently, that particular features are important or unimportant. These attribution priors are often based on attribution methods that are not guaranteed to satisfy desirable interpretability axioms, such as completeness and implementation invariance. Here, we introduce attribution priors to optimize for higher-level properties of explanations, such as smoothness and sparsity, enabled by a fast new attribution method formulation called expected gradients that satisfies many important interpretability axioms. This improves model performance on many real-world tasks where previous attribution priors fail. Our experiments show that the gains from combining higher-level attribution priors with expected gradients attributions are consistent across image, gene expression, and health care data sets. We believe this work motivates and provides the necessary tools to support the widespread adoption of axiomatic attribution priors in many areas of applied machine learning. The implementations and our results have been made freely available to academic communities.