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Mar 11

Latent Diffusion Model for Medical Image Standardization and Enhancement

Computed tomography (CT) serves as an effective tool for lung cancer screening, diagnosis, treatment, and prognosis, providing a rich source of features to quantify temporal and spatial tumor changes. Nonetheless, the diversity of CT scanners and customized acquisition protocols can introduce significant inconsistencies in texture features, even when assessing the same patient. This variability poses a fundamental challenge for subsequent research that relies on consistent image features. Existing CT image standardization models predominantly utilize GAN-based supervised or semi-supervised learning, but their performance remains limited. We present DiffusionCT, an innovative score-based DDPM model that operates in the latent space to transform disparate non-standard distributions into a standardized form. The architecture comprises a U-Net-based encoder-decoder, augmented by a DDPM model integrated at the bottleneck position. First, the encoder-decoder is trained independently, without embedding DDPM, to capture the latent representation of the input data. Second, the latent DDPM model is trained while keeping the encoder-decoder parameters fixed. Finally, the decoder uses the transformed latent representation to generate a standardized CT image, providing a more consistent basis for downstream analysis. Empirical tests on patient CT images indicate notable improvements in image standardization using DiffusionCT. Additionally, the model significantly reduces image noise in SPAD images, further validating the effectiveness of DiffusionCT for advanced imaging tasks.

GENIE: Generative Note Information Extraction model for structuring EHR data

Electronic Health Records (EHRs) hold immense potential for advancing healthcare, offering rich, longitudinal data that combines structured information with valuable insights from unstructured clinical notes. However, the unstructured nature of clinical text poses significant challenges for secondary applications. Traditional methods for structuring EHR free-text data, such as rule-based systems and multi-stage pipelines, are often limited by their time-consuming configurations and inability to adapt across clinical notes from diverse healthcare settings. Few systems provide a comprehensive attribute extraction for terminologies. While giant large language models (LLMs) like GPT-4 and LLaMA 405B excel at structuring tasks, they are slow, costly, and impractical for large-scale use. To overcome these limitations, we introduce GENIE, a Generative Note Information Extraction system that leverages LLMs to streamline the structuring of unstructured clinical text into usable data with standardized format. GENIE processes entire paragraphs in a single pass, extracting entities, assertion statuses, locations, modifiers, values, and purposes with high accuracy. Its unified, end-to-end approach simplifies workflows, reduces errors, and eliminates the need for extensive manual intervention. Using a robust data preparation pipeline and fine-tuned small scale LLMs, GENIE achieves competitive performance across multiple information extraction tasks, outperforming traditional tools like cTAKES and MetaMap and can handle extra attributes to be extracted. GENIE strongly enhances real-world applicability and scalability in healthcare systems. By open-sourcing the model and test data, we aim to encourage collaboration and drive further advancements in EHR structurization.

The Dataset Nutrition Label: A Framework To Drive Higher Data Quality Standards

Artificial intelligence (AI) systems built on incomplete or biased data will often exhibit problematic outcomes. Current methods of data analysis, particularly before model development, are costly and not standardized. The Dataset Nutrition Label (the Label) is a diagnostic framework that lowers the barrier to standardized data analysis by providing a distilled yet comprehensive overview of dataset "ingredients" before AI model development. Building a Label that can be applied across domains and data types requires that the framework itself be flexible and adaptable; as such, the Label is comprised of diverse qualitative and quantitative modules generated through multiple statistical and probabilistic modelling backends, but displayed in a standardized format. To demonstrate and advance this concept, we generated and published an open source prototype with seven sample modules on the ProPublica Dollars for Docs dataset. The benefits of the Label are manyfold. For data specialists, the Label will drive more robust data analysis practices, provide an efficient way to select the best dataset for their purposes, and increase the overall quality of AI models as a result of more robust training datasets and the ability to check for issues at the time of model development. For those building and publishing datasets, the Label creates an expectation of explanation, which will drive better data collection practices. We also explore the limitations of the Label, including the challenges of generalizing across diverse datasets, and the risk of using "ground truth" data as a comparison dataset. We discuss ways to move forward given the limitations identified. Lastly, we lay out future directions for the Dataset Nutrition Label project, including research and public policy agendas to further advance consideration of the concept.

LCFO: Long Context and Long Form Output Dataset and Benchmarking

This paper presents the Long Context and Form Output (LCFO) benchmark, a novel evaluation framework for assessing gradual summarization and summary expansion capabilities across diverse domains. LCFO consists of long input documents (5k words average length), each of which comes with three summaries of different lengths (20%, 10%, and 5% of the input text), as well as approximately 15 questions and answers (QA) related to the input content. Notably, LCFO also provides alignments between specific QA pairs and corresponding summaries in 7 domains. The primary motivation behind providing summaries of different lengths is to establish a controllable framework for generating long texts from shorter inputs, i.e. summary expansion. To establish an evaluation metric framework for summarization and summary expansion, we provide human evaluation scores for human-generated outputs, as well as results from various state-of-the-art large language models (LLMs). GPT-4o-mini achieves best human scores among automatic systems in both summarization and summary expansion tasks (~ +10% and +20%, respectively). It even surpasses human output quality in the case of short summaries (~ +7%). Overall automatic metrics achieve low correlations with human evaluation scores (~ 0.4) but moderate correlation on specific evaluation aspects such as fluency and attribution (~ 0.6). The LCFO benchmark offers a standardized platform for evaluating summarization and summary expansion performance, as well as corresponding automatic metrics, thereby providing an important evaluation framework to advance generative AI.

Easy2Hard-Bench: Standardized Difficulty Labels for Profiling LLM Performance and Generalization

While generalization over tasks from easy to hard is crucial to profile language models (LLMs), the datasets with fine-grained difficulty annotations for each problem across a broad range of complexity are still blank. Aiming to address this limitation, we present Easy2Hard-Bench, a consistently formatted collection of 6 benchmark datasets spanning various domains, such as mathematics and programming problems, chess puzzles, and reasoning questions. Each problem within these datasets is annotated with numerical difficulty scores. To systematically estimate problem difficulties, we collect abundant performance data on attempts to each problem by humans in the real world or LLMs on the prominent leaderboard. Leveraging the rich performance data, we apply well-established difficulty ranking systems, such as Item Response Theory (IRT) and Glicko-2 models, to uniformly assign numerical difficulty scores to problems. Moreover, datasets in Easy2Hard-Bench distinguish themselves from previous collections by a higher proportion of challenging problems. Through extensive experiments with six state-of-the-art LLMs, we provide a comprehensive analysis of their performance and generalization capabilities across varying levels of difficulty, with the aim of inspiring future research in LLM generalization. The datasets are available at https://huggingface.co/datasets/furonghuang-lab/Easy2Hard-Bench.

L-Eval: Instituting Standardized Evaluation for Long Context Language Models

Recently, there has been growing interest in extending the context length of instruction-following models in order to effectively process single-turn long input (e.g. summarizing a paper) and conversations with more extensive histories. While proprietary models such as GPT-4 and Claude have demonstrated considerable advancements in handling tens of thousands of tokens of context, open-sourced models are still in the early stages of experimentation. It also remains unclear whether developing these long context models can offer substantial gains on practical downstream tasks over retrieval-based methods or models simply trained on chunked contexts. To address this challenge, we propose to institute standardized evaluation for long context language models. Concretely, we develop L-Eval which contains 411 long documents and over 2,000 query-response pairs manually annotated and checked by the authors encompassing areas such as law, finance, school lectures, lengthy conversations, news, long-form novels, and meetings. L-Eval also adopts diverse evaluation methods and instruction styles, enabling a more reliable assessment of Long Context Language Models (LCLMs). Our findings indicate that while open-source models typically lag behind their commercial counterparts, they still exhibit impressive performance. LLaMA2 achieves the best results (win 45\% vs turbo-16k) on open-ended tasks with only 4k context length and ChatGLM2 achieves the best results on closed-ended tasks with 8k input tokens. We release our new evaluation suite, code, and all generation results including predictions from all open-sourced LCLMs, GPT4-32k, Cluade-100k at {https://github.com/OpenLMLab/LEval}.

ChEF: A Comprehensive Evaluation Framework for Standardized Assessment of Multimodal Large Language Models

Multimodal Large Language Models (MLLMs) have shown impressive abilities in interacting with visual content with myriad potential downstream tasks. However, even though a list of benchmarks has been proposed, the capabilities and limitations of MLLMs are still not comprehensively understood, due to a lack of a standardized and holistic evaluation framework. To this end, we present the first Comprehensive Evaluation Framework (ChEF) that can holistically profile each MLLM and fairly compare different MLLMs. First, we structure ChEF as four modular components, i.e., Scenario as scalable multimodal datasets, Instruction as flexible instruction retrieving formulae, Inferencer as reliable question answering strategies, and Metric as indicative task-specific score functions. Based on them, ChEF facilitates versatile evaluations in a standardized framework, and new evaluations can be built by designing new Recipes (systematic selection of these four components). Notably, current MLLM benchmarks can be readily summarized as recipes of ChEF. Second, we introduce 6 new recipes to quantify competent MLLMs' desired capabilities (or called desiderata, i.e., calibration, in-context learning, instruction following, language performance, hallucination, and robustness) as reliable agents that can perform real-world multimodal interactions. Third, we conduct a large-scale evaluation of 9 prominent MLLMs on 9 scenarios and 6 desiderata. Our evaluation summarized over 20 valuable observations concerning the generalizability of MLLMs across various scenarios and the composite capability of MLLMs required for multimodal interactions. We will publicly release all the detailed implementations for further analysis, as well as an easy-to-use modular toolkit for the integration of new recipes and models, so that ChEF can be a growing evaluation framework for the MLLM community.

TRACE: A Comprehensive Benchmark for Continual Learning in Large Language Models

Aligned large language models (LLMs) demonstrate exceptional capabilities in task-solving, following instructions, and ensuring safety. However, the continual learning aspect of these aligned LLMs has been largely overlooked. Existing continual learning benchmarks lack sufficient challenge for leading aligned LLMs, owing to both their simplicity and the models' potential exposure during instruction tuning. In this paper, we introduce TRACE, a novel benchmark designed to evaluate continual learning in LLMs. TRACE consists of 8 distinct datasets spanning challenging tasks including domain-specific tasks, multilingual capabilities, code generation, and mathematical reasoning. All datasets are standardized into a unified format, allowing for effortless automatic evaluation of LLMs. Our experiments show that after training on TRACE, aligned LLMs exhibit significant declines in both general ability and instruction-following capabilities. For example, the accuracy of llama2-chat 13B on gsm8k dataset declined precipitously from 28.8\% to 2\% after training on our datasets. This highlights the challenge of finding a suitable tradeoff between achieving performance on specific tasks while preserving the original prowess of LLMs. Empirical findings suggest that tasks inherently equipped with reasoning paths contribute significantly to preserving certain capabilities of LLMs against potential declines. Motivated by this, we introduce the Reasoning-augmented Continual Learning (RCL) approach. RCL integrates task-specific cues with meta-rationales, effectively reducing catastrophic forgetting in LLMs while expediting convergence on novel tasks.

Generating Structured Outputs from Language Models: Benchmark and Studies

Reliably generating structured outputs has become a critical capability for modern language model (LM) applications. Constrained decoding has emerged as the dominant technology across sectors for enforcing structured outputs during generation. Despite its growing adoption, little has been done with the systematic evaluation of the behaviors and performance of constrained decoding. Constrained decoding frameworks have standardized around JSON Schema as a structured data format, with most uses guaranteeing constraint compliance given a schema. However, there is poor understanding of the effectiveness of the methods in practice. We present an evaluation framework to assess constrained decoding approaches across three critical dimensions: efficiency in generating constraint-compliant outputs, coverage of diverse constraint types, and quality of the generated outputs. To facilitate this evaluation, we introduce JSONSchemaBench, a benchmark for constrained decoding comprising 10K real-world JSON schemas that encompass a wide range of constraints with varying complexity. We pair the benchmark with the existing official JSON Schema Test Suite and evaluate six state-of-the-art constrained decoding frameworks, including Guidance, Outlines, Llamacpp, XGrammar, OpenAI, and Gemini. Through extensive experiments, we gain insights into the capabilities and limitations of constrained decoding on structured generation with real-world JSON schemas. Our work provides actionable insights for improving constrained decoding frameworks and structured generation tasks, setting a new standard for evaluating constrained decoding and structured generation. We release JSONSchemaBench at https://github.com/guidance-ai/jsonschemabench

LongBench: A Bilingual, Multitask Benchmark for Long Context Understanding

Although large language models (LLMs) demonstrate impressive performance for many language tasks, most of them can only handle texts a few thousand tokens long, limiting their applications on longer sequence inputs, such as books, reports, and codebases. Recent works have proposed methods to improve LLMs' long context capabilities by extending context windows and more sophisticated memory mechanisms. However, comprehensive benchmarks tailored for evaluating long context understanding are lacking. In this paper, we introduce LongBench, the first bilingual, multi-task benchmark for long context understanding, enabling a more rigorous evaluation of long context understanding. LongBench comprises 21 datasets across 6 task categories in both English and Chinese, with an average length of 6,711 words (English) and 13,386 characters (Chinese). These tasks cover key long-text application areas including single-doc QA, multi-doc QA, summarization, few-shot learning, synthetic tasks, and code completion. All datasets in LongBench are standardized into a unified format, allowing for effortless automatic evaluation of LLMs. Upon comprehensive evaluation of 8 LLMs on LongBench, we find that: (1) Commercial model (GPT-3.5-Turbo-16k) outperforms other open-sourced models, but still struggles on longer contexts. (2) Scaled position embedding and fine-tuning on longer sequences lead to substantial improvement on long context understanding. (3) Context compression technique such as retrieval brings improvement for model with weak ability on long contexts, but the performance still lags behind models that have strong long context understanding capability. The code and datasets are available at https://github.com/THUDM/LongBench.

LLM Reasoners: New Evaluation, Library, and Analysis of Step-by-Step Reasoning with Large Language Models

Generating accurate step-by-step reasoning is essential for Large Language Models (LLMs) to address complex problems and enhance robustness and interpretability. Despite the flux of research on developing advanced reasoning approaches, systematically analyzing the diverse LLMs and reasoning strategies in generating reasoning chains remains a significant challenge. The difficulties stem from the lack of two key elements: (1) an automatic method for evaluating the generated reasoning chains on different tasks, and (2) a unified formalism and implementation of the diverse reasoning approaches for systematic comparison. This paper aims to close the gap: (1) We introduce AutoRace for fully automated reasoning chain evaluation. Existing metrics rely on expensive human annotations or pre-defined LLM prompts not adaptable to different tasks. In contrast, AutoRace automatically creates detailed evaluation criteria tailored for each task, and uses GPT-4 for accurate evaluation following the criteria. (2) We develop LLM Reasoners, a library for standardized modular implementation of existing and new reasoning algorithms, under a unified formulation of the search, reward, and world model components. With the new evaluation and library, (3) we conduct extensive study of different reasoning approaches (e.g., CoT, ToT, RAP). The analysis reveals interesting findings about different factors contributing to reasoning, including the reward-guidance, breadth-vs-depth in search, world model, and prompt formats, etc.

GUI Testing Arena: A Unified Benchmark for Advancing Autonomous GUI Testing Agent

Nowadays, research on GUI agents is a hot topic in the AI community. However, current research focuses on GUI task automation, limiting the scope of applications in various GUI scenarios. In this paper, we propose a formalized and comprehensive environment to evaluate the entire process of automated GUI Testing (GTArena), offering a fair, standardized environment for consistent operation of diverse multimodal large language models. We divide the testing process into three key subtasks: test intention generation, test task execution, and GUI defect detection, and construct a benchmark dataset based on these to conduct a comprehensive evaluation. It evaluates the performance of different models using three data types: real mobile applications, mobile applications with artificially injected defects, and synthetic data, thoroughly assessing their capabilities in this relevant task. Additionally, we propose a method that helps researchers explore the correlation between the performance of multimodal language large models in specific scenarios and their general capabilities in standard benchmark tests. Experimental results indicate that even the most advanced models struggle to perform well across all sub-tasks of automated GUI Testing, highlighting a significant gap between the current capabilities of Autonomous GUI Testing and its practical, real-world applicability. This gap provides guidance for the future direction of GUI Agent development. Our code is available at https://github.com/ZJU-ACES-ISE/ChatUITest.

Who Audits the Auditors? Recommendations from a field scan of the algorithmic auditing ecosystem

AI audits are an increasingly popular mechanism for algorithmic accountability; however, they remain poorly defined. Without a clear understanding of audit practices, let alone widely used standards or regulatory guidance, claims that an AI product or system has been audited, whether by first-, second-, or third-party auditors, are difficult to verify and may exacerbate, rather than mitigate, bias and harm. To address this knowledge gap, we provide the first comprehensive field scan of the AI audit ecosystem. We share a catalog of individuals (N=438) and organizations (N=189) who engage in algorithmic audits or whose work is directly relevant to algorithmic audits; conduct an anonymous survey of the group (N=152); and interview industry leaders (N=10). We identify emerging best practices as well as methods and tools that are becoming commonplace, and enumerate common barriers to leveraging algorithmic audits as effective accountability mechanisms. We outline policy recommendations to improve the quality and impact of these audits, and highlight proposals with wide support from algorithmic auditors as well as areas of debate. Our recommendations have implications for lawmakers, regulators, internal company policymakers, and standards-setting bodies, as well as for auditors. They are: 1) require the owners and operators of AI systems to engage in independent algorithmic audits against clearly defined standards; 2) notify individuals when they are subject to algorithmic decision-making systems; 3) mandate disclosure of key components of audit findings for peer review; 4) consider real-world harm in the audit process, including through standardized harm incident reporting and response mechanisms; 5) directly involve the stakeholders most likely to be harmed by AI systems in the algorithmic audit process; and 6) formalize evaluation and, potentially, accreditation of algorithmic auditors.

Reshaping Free-Text Radiology Notes Into Structured Reports With Generative Transformers

BACKGROUND: Radiology reports are typically written in a free-text format, making clinical information difficult to extract and use. Recently the adoption of structured reporting (SR) has been recommended by various medical societies thanks to the advantages it offers, e.g. standardization, completeness and information retrieval. We propose a pipeline to extract information from free-text radiology reports, that fits with the items of the reference SR registry proposed by a national society of interventional and medical radiology, focusing on CT staging of patients with lymphoma. METHODS: Our work aims to leverage the potential of Natural Language Processing (NLP) and Transformer-based models to deal with automatic SR registry filling. With the availability of 174 radiology reports, we investigate a rule-free generative Question Answering approach based on a domain-specific version of T5 (IT5). Two strategies (batch-truncation and ex-post combination) are implemented to comply with the model's context length limitations. Performance is evaluated in terms of strict accuracy, F1, and format accuracy, and compared with the widely used GPT-3.5 Large Language Model. A 5-point Likert scale questionnaire is used to collect human-expert feedback on the similarity between medical annotations and generated answers. RESULTS: The combination of fine-tuning and batch splitting allows IT5 to achieve notable results; it performs on par with GPT-3.5 albeit its size being a thousand times smaller in terms of parameters. Human-based assessment scores show a high correlation (Spearman's correlation coefficients>0.88, p-values<0.001) with AI performance metrics (F1) and confirm the superior ability of LLMs (i.e., GPT-3.5, 175B of parameters) in generating plausible human-like statements.

One Language, Many Gaps: Evaluating Dialect Fairness and Robustness of Large Language Models in Reasoning Tasks

Language is not monolithic. While many benchmarks are used as proxies to systematically estimate Large Language Models' (LLM) performance in real-life tasks, they tend to ignore the nuances of within-language variation and thus fail to model the experience of speakers of minority dialects. Focusing on African American Vernacular English (AAVE), we present the first study on LLMs' fairness and robustness to a dialect in canonical reasoning tasks (algorithm, math, logic, and comprehensive reasoning). We hire AAVE speakers, including experts with computer science backgrounds, to rewrite seven popular benchmarks, such as HumanEval and GSM8K. The result of this effort is ReDial, a dialectal benchmark comprising 1.2K+ parallel query pairs in Standardized English and AAVE. We use ReDial to evaluate state-of-the-art LLMs, including GPT-4o/4/3.5-turbo, LLaMA-3.1/3, Mistral, and Phi-3. We find that, compared to Standardized English, almost all of these widely used models show significant brittleness and unfairness to queries in AAVE. Furthermore, AAVE queries can degrade performance more substantially than misspelled texts in Standardized English, even when LLMs are more familiar with the AAVE queries. Finally, asking models to rephrase questions in Standardized English does not close the performance gap but generally introduces higher costs. Overall, our findings indicate that LLMs provide unfair service to dialect users in complex reasoning tasks. Code can be found at https://github.com/fangru-lin/redial_dialect_robustness_fairness.git.

Named Clinical Entity Recognition Benchmark

This technical report introduces a Named Clinical Entity Recognition Benchmark for evaluating language models in healthcare, addressing the crucial natural language processing (NLP) task of extracting structured information from clinical narratives to support applications like automated coding, clinical trial cohort identification, and clinical decision support. The leaderboard provides a standardized platform for assessing diverse language models, including encoder and decoder architectures, on their ability to identify and classify clinical entities across multiple medical domains. A curated collection of openly available clinical datasets is utilized, encompassing entities such as diseases, symptoms, medications, procedures, and laboratory measurements. Importantly, these entities are standardized according to the Observational Medical Outcomes Partnership (OMOP) Common Data Model, ensuring consistency and interoperability across different healthcare systems and datasets, and a comprehensive evaluation of model performance. Performance of models is primarily assessed using the F1-score, and it is complemented by various assessment modes to provide comprehensive insights into model performance. The report also includes a brief analysis of models evaluated to date, highlighting observed trends and limitations. By establishing this benchmarking framework, the leaderboard aims to promote transparency, facilitate comparative analyses, and drive innovation in clinical entity recognition tasks, addressing the need for robust evaluation methods in healthcare NLP.