Clinical Reasoning over Tabular Data and Text with Bayesian Networks

Bayesian networks are well-suited for clinical reasoning on tabular data, but are less compatible with natural language data, for which neural networks provide a successful framework. This paper compares and discusses strategies to augment Bayesian networks with neural text representations, both in a generative and discriminative manner. This is illustrated with simulation results for a primary care use case (diagnosis of pneumonia) and discussed in a broader clinical context.

In-Context Learning for Extreme Multi-Label Classification

Multi-label classification problems with thousands of classes are hard to solve with in-context learning alone, as language models (LMs) might lack prior knowledge about the precise classes or how to assign them, and it is generally infeasible to demonstrate every class in a prompt. We propose a general program, $\texttt{Infer--Retrieve--Rank}$, that defines multi-step interactions between LMs and retrievers to efficiently tackle such problems. We implement this program using the $\texttt{DSPy}$ programming model, which specifies in-context systems in a declarative manner, and use $\texttt{DSPy}$ optimizers to tune it towards specific datasets by bootstrapping only tens of few-shot examples. Our primary extreme classification program, optimized separately for each task, attains state-of-the-art results across three benchmarks (HOUSE, TECH, TECHWOLF). We apply the same program to a benchmark with vastly different characteristics and attain competitive performance as well (BioDEX). Unlike prior work, our proposed solution requires no finetuning, is easily applicable to new tasks, alleviates prompt engineering, and requires only tens of labeled examples. Our code is public at https://github.com/KarelDO/xmc.dspy.

Synthetic Data: Can We Trust Statistical Estimators?

The increasing interest in data sharing makes synthetic data appealing. However, the analysis of synthetic data raises a unique set of methodological challenges. In this work, we highlight the importance of inferential utility and provide empirical evidence against naive inference from synthetic data (that handles these as if they were really observed). We argue that the rate of false-positive findings (type 1 error) will be unacceptably high, even when the estimates are unbiased. One of the reasons is the underestimation of the true standard error, which may even progressively increase with larger sample sizes due to slower convergence. This is especially problematic for deep generative models. Before publishing synthetic data, it is essential to develop statistical inference tools for such data.

Exploring the Temperature-Dependent Phase Transition in Modern Hopfield Networks

The recent discovery of a connection between Transformers and Modern Hopfield Networks (MHNs) has reignited the study of neural networks from a physical energy-based perspective. This paper focuses on the pivotal effect of the inverse temperature hyperparameter $\beta$ on the distribution of energy minima of the MHN. To achieve this, the distribution of energy minima is tracked in a simplified MHN in which equidistant normalised patterns are stored. This network demonstrates a phase transition at a critical temperature $\beta_{\text{c}}$, from a single global attractor towards highly pattern specific minima as $\beta$ is increased. Importantly, the dynamics are not solely governed by the hyperparameter $\beta$ but are instead determined by an effective inverse temperature $\beta_{\text{eff}}$ which also depends on the distribution and size of the stored patterns. Recognizing the role of hyperparameters in the MHN could, in the future, aid researchers in the domain of Transformers to optimise their initial choices, potentially reducing the necessity for time and energy expensive hyperparameter fine-tuning.

BioLORD-2023: Semantic Textual Representations Fusing LLM and Clinical Knowledge Graph Insights

In this study, we investigate the potential of Large Language Models to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains. Drawing on the wealth of the UMLS knowledge graph and harnessing cutting-edge Large Language Models, we propose a new state-of-the-art approach for obtaining high-fidelity representations of biomedical concepts and sentences, consisting of three steps: an improved contrastive learning phase, a novel self-distillation phase, and a weight averaging phase. Through rigorous evaluations via the extensive BioLORD testing suite and diverse downstream tasks, we demonstrate consistent and substantial performance improvements over the previous state of the art (e.g. +2pts on MedSTS, +2.5pts on MedNLI-S, +6.1pts on EHR-Rel-B). Besides our new state-of-the-art biomedical model for English, we also distill and release a multilingual model compatible with 50+ languages and finetuned on 7 European languages. Many clinical pipelines can benefit from our latest models. Our new multilingual model enables a range of languages to benefit from our advancements in biomedical semantic representation learning, opening a new avenue for bioinformatics researchers around the world. As a result, we hope to see BioLORD-2023 becoming a precious tool for future biomedical applications.

Accelerating Hierarchical Associative Memory: A Deep Equilibrium Approach

Hierarchical Associative Memory models have recently been proposed as a versatile extension of continuous Hopfield networks. In order to facilitate future research on such models, especially at scale, we focus on increasing their simulation efficiency on digital hardware. In particular, we propose two strategies to speed up memory retrieval in these models, which corresponds to their use at inference, but is equally important during training. First, we show how they can be cast as Deep Equilibrium Models, which allows using faster and more stable solvers. Second, inspired by earlier work, we show that alternating optimization of the even and odd layers accelerates memory retrieval by a factor close to two. Combined, these two techniques allow for a much faster energy minimization, as shown in our proof-of-concept experimental results. The code is available at https://github.com/cgoemaere/hamdeq

Training a Hopfield Variational Autoencoder with Equilibrium Propagation

On dedicated analog hardware, equilibrium propagation is an energy-efficient alternative to backpropagation. In spite of its theoretical guarantees, its application in the AI domain remains limited to the discriminative setting. Meanwhile, despite its high computational demands, generative AI is on the rise. In this paper, we demonstrate the application of Equilibrium Propagation in training a variational autoencoder (VAE) for generative modeling. Leveraging the symmetric nature of Hopfield networks, we propose using a single model to serve as both the encoder and decoder which could effectively halve the required chip size for VAE implementations, paving the way for more efficient analog hardware configurations.

Flexible Model Interpretability through Natural Language Model Editing

Model interpretability and model editing are crucial goals in the age of large language models. Interestingly, there exists a link between these two goals: if a method is able to systematically edit model behavior with regard to a human concept of interest, this editor method can help make internal representations more interpretable by pointing towards relevant representations and systematically manipulating them.

Zero-Shot Cross-Lingual Sentiment Classification under Distribution Shift: an Exploratory Study

The brittleness of finetuned language model performance on out-of-distribution (OOD) test samples in unseen domains has been well-studied for English, yet is unexplored for multi-lingual models. Therefore, we study generalization to OOD test data specifically in zero-shot cross-lingual transfer settings, analyzing performance impacts of both language and domain shifts between train and test data. We further assess the effectiveness of counterfactually augmented data (CAD) in improving OOD generalization for the cross-lingual setting, since CAD has been shown to benefit in a monolingual English setting. Finally, we propose two new approaches for OOD generalization that avoid the costly annotation process associated with CAD, by exploiting the power of recent large language models (LLMs). We experiment with 3 multilingual models, LaBSE, mBERT, and XLM-R trained on English IMDb movie reviews, and evaluate on OOD test sets in 13 languages: Amazon product reviews, Tweets, and Restaurant reviews. Results echo the OOD performance decline observed in the monolingual English setting. Further, (i) counterfactuals from the original high-resource language do improve OOD generalization in the low-resource language, and (ii) our newly proposed cost-effective approaches reach similar or up to +3.1% better accuracy than CAD for Amazon and Restaurant reviews.