Clinical NLP

Foundation Models (FMs) trained on Electronic Health Records (EHRs) have achieved state-of-the-art results on numerous clinical prediction tasks. However, prior EHR FMs typically have context windows of $<$1k tokens, which prevents them from modeling full patient EHRs which can exceed 10k's of events. For making clinical predictions, both model performance and robustness to the unique properties of EHR data are crucial. Recent advancements in subquadratic long-context architectures (e.g. Mamba) offer a promising solution. However, their application to EHR data has not been well-studied. We address this gap by presenting the first systematic evaluation of the effect of context length on modeling EHR data. We find that longer context models improve predictive performance -- our Mamba-based model surpasses the prior state-of-the-art on 9/14 tasks on the EHRSHOT prediction benchmark. Additionally, we measure robustness to three unique, previously underexplored properties of EHR data: (1) the prevalence of ``copy-forwarded" diagnoses which create artificial token repetition in EHR sequences; (2) the irregular time intervals between EHR events which can lead to a wide range of timespans within a context window; and (3) the natural increase in disease complexity over time which makes later tokens in the EHR harder to predict than earlier ones. Stratifying our EHRSHOT results, we find that higher levels of each property correlate negatively with model performance (e.g., a 14% higher Brier loss between the least and most irregular patients), but that longer context models are more robust to more extreme levels of these properties. Our work highlights the potential for using long-context architectures to model EHR data, and offers a case study on how to identify and quantify new challenges in modeling sequential data motivated by domains outside of natural language. We release all of our model checkpoints and code.

Fixed-size learned representations (dense representations, or embeddings) are widely used in many machine learning applications across language, vision or speech modalities. This paper investigates the role of the temperature parameter in contrastive training for text embeddings. We shed light on the impact this parameter has on the intrinsic dimensionality of the embedding spaces obtained, and show that lower intrinsic dimensionality is further correlated with effective compression of embeddings. We still observe a trade-off between absolute performance and effective compression and we propose temperature aggregation methods which reduce embedding size by an order of magnitude with minimal impact on quality.

Synthetic data augmentation via Large Language Models (LLMs) allows researchers to leverage additional training data, thus enhancing the performance of downstream tasks, especially when real-world data is scarce. However, the generated data can deviate from the real-world data, and this misalignment can bring about deficient results while applying the trained model to applications. Therefore, we proposed efficient weighted-loss approaches to align synthetic data with real-world distribution by emphasizing high-quality and diversified data generated by LLMs using merely a tiny amount of real-world data. We empirically assessed the effectiveness of our methods on multiple text classification tasks, and the results showed that leveraging our approaches on a BERT-level model robustly outperformed standard cross-entropy and other data weighting approaches, providing potential solutions to effectively leveraging synthetic data from any suitable data generator.

Large Language Models (LLMs) with the Mixture-of-Experts (MoE) architectures have shown promising performance on various tasks. However, due to the huge model sizes, running them in resource-constrained environments where the GPU memory is not abundant is challenging. Some existing systems propose to use CPU resources to solve that, but they either suffer from the significant overhead of frequently moving data between CPU and GPU, or fail to consider distinct characteristics of CPUs and GPUs. This paper proposes Fiddler, a resource-efficient inference system for MoE models with limited GPU resources. Fiddler strategically utilizes CPU and GPU resources by determining the optimal execution strategy. Our evaluation shows that, unlike state-of-the-art systems that optimize for specific scenarios such as single batch inference or long prefill, Fiddler performs better in all scenarios. Compared against different baselines, Fiddler achieves 1.26 times speed up in single batch inference, 1.30 times in long prefill processing, and 11.57 times in beam search inference. The code of Fiddler is publicly available at https://github.com/efeslab/fiddler.

Tokenization — the practice of converting strings of characters from an alphabet into sequences of tokens over a vocabulary — is a critical step in the NLP pipeline. The use of token representations is widely credited with increased model performance but is also the source of many undesirable behaviors, such as spurious ambiguity or inconsistency. Despite its recognized importance as a standard representation method in NLP, the theoretical underpinnings of tokenization are not yet fully understood. In particular, the impact of tokenization on language model estimation has been investigated primarily through empirical means. The present paper contributes to addressing this theoretical gap by proposing a unified formal framework for representing and analyzing tokenizer models. Based on the category of stochastic maps, this framework enables us to establish general conditions for a principled use of tokenizers and, most importantly, the necessary and sufficient conditions for a tokenizer model to preserve the consistency of statistical estimators. In addition, we discuss statistical and computational concerns crucial for designing and implementing tokenizer models, such as inconsistency, ambiguity, finiteness, and sequentiality. The framework and results advanced in this paper contribute to building robust theoretical foundations for representations in neural language modeling that can inform future theoretical and empirical research.

Bidirectional models are considered essential for strong text embeddings. Recent approaches to adapt autoregressive language models (LMs) into strong text embedding models have largely had the requirement to modify the LM architecture to be bidirectional. We challenge this premise by introducing ``echo embeddings'' which converts autoregressive LMs into high quality text embedding models \emph{without} changing the architecture or requiring fine-tuning. By repeating the input and extracting embeddings from the repeated tokens—which have access to all original tokens—echo embeddings improve over classical LM embeddings by over 5\% in zero-shot settings. Our zero-shot embeddings nearly match those obtained by bidirectionally-converted LMs that undergo additional masked-language modeling training. Echo embeddings are also compatible with supervised fine-tuning, matching or outperforming bidirectionally-converted LMs in an apples-to-apples comparison, even with an identical compute budget during training and inference. Overall, repetition is a simple and effective strategy to circumvent the need for bidirectional attention in embedding models, paving the way towards a unified architecture for all NLP tasks.

Machine learning models are routinely used to support decisions that affect individuals -- be it to screen a patient for a serious illness or to gauge their response to treatment. In these tasks, we are limited to learning models from datasets with noisy labels. In this paper, we study the instance-level impact of learning under label noise. We introduce a notion of regret for this regime, which measures the number of unforeseen mistakes due to noisy labels. We show that standard approaches to learning under label noise can return models that perform well at a population-level while subjecting individuals to a lottery of mistakes. We present a versatile approach to estimate the likelihood of mistakes at the individual-level from a noisy dataset by training models over plausible realizations of datasets without label noise. This is supported by a comprehensive empirical study of label noise in clinical prediction tasks. Our results reveal how failure to anticipate mistakes can compromise model reliability and adoption -- we demonstrate how we can address these challenges by anticipating and avoiding regretful decisions.