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Nov 4

MedAlign: A Clinician-Generated Dataset for Instruction Following with Electronic Medical Records

The ability of large language models (LLMs) to follow natural language instructions with human-level fluency suggests many opportunities in healthcare to reduce administrative burden and improve quality of care. However, evaluating LLMs on realistic text generation tasks for healthcare remains challenging. Existing question answering datasets for electronic health record (EHR) data fail to capture the complexity of information needs and documentation burdens experienced by clinicians. To address these challenges, we introduce MedAlign, a benchmark dataset of 983 natural language instructions for EHR data. MedAlign is curated by 15 clinicians (7 specialities), includes clinician-written reference responses for 303 instructions, and provides 276 longitudinal EHRs for grounding instruction-response pairs. We used MedAlign to evaluate 6 general domain LLMs, having clinicians rank the accuracy and quality of each LLM response. We found high error rates, ranging from 35% (GPT-4) to 68% (MPT-7B-Instruct), and an 8.3% drop in accuracy moving from 32k to 2k context lengths for GPT-4. Finally, we report correlations between clinician rankings and automated natural language generation metrics as a way to rank LLMs without human review. We make MedAlign available under a research data use agreement to enable LLM evaluations on tasks aligned with clinician needs and preferences.

  • 30 authors
·
Aug 27, 2023 4

PET2Rep: Towards Vision-Language Model-Drived Automated Radiology Report Generation for Positron Emission Tomography

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficiency metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications.

  • 15 authors
·
Aug 5

PersianLLaMA: Towards Building First Persian Large Language Model

Despite the widespread use of the Persian language by millions globally, limited efforts have been made in natural language processing for this language. The use of large language models as effective tools in various natural language processing tasks typically requires extensive textual data and robust hardware resources. Consequently, the scarcity of Persian textual data and the unavailability of powerful hardware resources have hindered the development of large language models for Persian. This paper introduces the first large Persian language model, named PersianLLaMA, trained on a collection of Persian texts and datasets. This foundational model comes in two versions, with 7 and 13 billion parameters, trained on formal and colloquial Persian texts using two different approaches. PersianLLaMA has been evaluated for natural language generation tasks based on the latest evaluation methods, namely using larger language models, and for natural language understanding tasks based on automated machine metrics. The results indicate that PersianLLaMA significantly outperforms its competitors in both understanding and generating Persian text. PersianLLaMA marks an important step in the development of Persian natural language processing and can be a valuable resource for the Persian-speaking community. This large language model can be used for various natural language processing tasks, especially text generation like chatbots, question-answering, machine translation, and text summarization

  • 5 authors
·
Dec 25, 2023

Logical Natural Language Generation from Open-Domain Tables

Neural natural language generation (NLG) models have recently shown remarkable progress in fluency and coherence. However, existing studies on neural NLG are primarily focused on surface-level realizations with limited emphasis on logical inference, an important aspect of human thinking and language. In this paper, we suggest a new NLG task where a model is tasked with generating natural language statements that can be logically entailed by the facts in an open-domain semi-structured table. To facilitate the study of the proposed logical NLG problem, we use the existing TabFact dataset chen2019tabfact featured with a wide range of logical/symbolic inferences as our testbed, and propose new automatic metrics to evaluate the fidelity of generation models w.r.t.\ logical inference. The new task poses challenges to the existing monotonic generation frameworks due to the mismatch between sequence order and logical order. In our experiments, we comprehensively survey different generation architectures (LSTM, Transformer, Pre-Trained LM) trained with different algorithms (RL, Adversarial Training, Coarse-to-Fine) on the dataset and made following observations: 1) Pre-Trained LM can significantly boost both the fluency and logical fidelity metrics, 2) RL and Adversarial Training are trading fluency for fidelity, 3) Coarse-to-Fine generation can help partially alleviate the fidelity issue while maintaining high language fluency. The code and data are available at https://github.com/wenhuchen/LogicNLG.

  • 5 authors
·
Apr 22, 2020

A Survey of Evaluation Metrics Used for NLG Systems

The success of Deep Learning has created a surge in interest in a wide a range of Natural Language Generation (NLG) tasks. Deep Learning has not only pushed the state of the art in several existing NLG tasks but has also facilitated researchers to explore various newer NLG tasks such as image captioning. Such rapid progress in NLG has necessitated the development of accurate automatic evaluation metrics that would allow us to track the progress in the field of NLG. However, unlike classification tasks, automatically evaluating NLG systems in itself is a huge challenge. Several works have shown that early heuristic-based metrics such as BLEU, ROUGE are inadequate for capturing the nuances in the different NLG tasks. The expanding number of NLG models and the shortcomings of the current metrics has led to a rapid surge in the number of evaluation metrics proposed since 2014. Moreover, various evaluation metrics have shifted from using pre-determined heuristic-based formulae to trained transformer models. This rapid change in a relatively short time has led to the need for a survey of the existing NLG metrics to help existing and new researchers to quickly come up to speed with the developments that have happened in NLG evaluation in the last few years. Through this survey, we first wish to highlight the challenges and difficulties in automatically evaluating NLG systems. Then, we provide a coherent taxonomy of the evaluation metrics to organize the existing metrics and to better understand the developments in the field. We also describe the different metrics in detail and highlight their key contributions. Later, we discuss the main shortcomings identified in the existing metrics and describe the methodology used to evaluate evaluation metrics. Finally, we discuss our suggestions and recommendations on the next steps forward to improve the automatic evaluation metrics.

  • 3 authors
·
Aug 27, 2020

TIGERScore: Towards Building Explainable Metric for All Text Generation Tasks

We present TIGERScore, a Trained metric that follows Instruction Guidance to perform Explainable, and Reference-free evaluation over a wide spectrum of text generation tasks. Different from other automatic evaluation methods that only provide arcane scores, TIGERScore is guided by the natural language instruction to provide error analysis to pinpoint the mistakes in the generated text. Our metric is based on LLaMA, trained on our meticulously curated instruction-tuning dataset MetricInstruct which covers 6 text generation tasks and 23 text generation datasets. The dataset consists of 48K quadruple in the form of (instruction, input, system output rightarrow error analysis). We collected the `system outputs' through diverse channels to cover different types of errors. To quantitatively assess our metric, we evaluate its correlation with human ratings on 5 held-in datasets, 2 held-out datasets and show that TIGERScore can achieve the highest overall Spearman's correlation with human ratings across these datasets and outperforms other metrics significantly. As a reference-free metric, its correlation can even surpass the best existing reference-based metrics. To further qualitatively assess the rationale generated by our metric, we conduct human evaluation on the generated explanations and found that the explanations are 70.8\% accurate. Through these experimental results, we believe TIGERScore demonstrates the possibility of building universal explainable metrics to evaluate any text generation task.

  • 6 authors
·
Oct 1, 2023

LLM Comparative Assessment: Zero-shot NLG Evaluation through Pairwise Comparisons using Large Language Models

Current developments in large language models (LLMs) have enabled impressive zero-shot capabilities across various natural language tasks. An interesting application of these systems is in the automated assessment of natural language generation (NLG), a highly challenging area with great practical benefit. In this paper, we explore two options for exploiting the emergent abilities of LLMs for zero-shot NLG assessment: absolute score prediction, and comparative assessment which uses relative comparisons between pairs of candidates. Though comparative assessment has not been extensively studied in NLG assessment, we note that humans often find it more intuitive to compare two options rather than scoring each one independently. This work examines comparative assessment from multiple perspectives: performance compared to absolute grading; positional biases in the prompt; and efficient ranking in terms of the number of comparisons. We illustrate that LLM comparative assessment is a simple, general and effective approach for NLG assessment. For moderate-sized open-source LLMs, such as FlanT5 and Llama2-chat, comparative assessment is superior to prompt scoring, and in many cases can achieve performance competitive with state-of-the-art methods. Additionally, we demonstrate that LLMs often exhibit strong positional biases when making pairwise comparisons, and we propose debiasing methods that can further improve performance.

  • 3 authors
·
Jul 15, 2023