Leon Weber

Jason Alan Fries, Leon Weber, Natasha Seelam et al. · stanford, utoronto

Training and evaluating language models increasingly requires the construction of meta-datasets --diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization by transforming existing, supervised datasets into a diversity of novel pretraining tasks, highlighting the benefits of meta-dataset curation. While successful in general-domain text, translating these data-centric approaches to biomedical language modeling remains challenging, as labeled biomedical datasets are significantly underrepresented in popular data hubs. To address this challenge, we introduce BigBIO a community library of 126+ biomedical NLP datasets, currently covering 12 task categories and 10+ languages. BigBIO facilitates reproducible meta-dataset curation via programmatic access to datasets and their metadata, and is compatible with current platforms for prompt engineering and end-to-end few/zero shot language model evaluation. We discuss our process for task schema harmonization, data auditing, contribution guidelines, and outline two illustrative use cases: zero-shot evaluation of biomedical prompts and large-scale, multi-task learning. BigBIO is an ongoing community effort and is available at https://github.com/bigscience-workshop/biomedical

Hugo Laurençon, Lucile Saulnier, Thomas Wang et al. · huggingface

As language models grow ever larger, the need for large-scale high-quality text datasets has never been more pressing, especially in multilingual settings. The BigScience workshop, a 1-year international and multidisciplinary initiative, was formed with the goal of researching and training large language models as a values-driven undertaking, putting issues of ethics, harm, and governance in the foreground. This paper documents the data creation and curation efforts undertaken by BigScience to assemble the Responsible Open-science Open-collaboration Text Sources (ROOTS) corpus, a 1.6TB dataset spanning 59 languages that was used to train the 176-billion-parameter BigScience Large Open-science Open-access Multilingual (BLOOM) language model. We further release a large initial subset of the corpus and analyses thereof, and hope to empower large-scale monolingual and multilingual modeling projects with both the data and the processing tools, as well as stimulate research around this large multilingual corpus.

Samuele Garda, Leon Weber-Genzel, Robert Martin et al.

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base. It plays a vital role in information extraction pipelines for the life sciences literature. We review recent work in the field and find that, as the task is absent from existing benchmarks for biomedical text mining, different studies adopt different experimental setups making comparisons based on published numbers problematic. Furthermore, neural systems are tested primarily on instances linked to the broad coverage knowledge base UMLS, leaving their performance to more specialized ones, e.g. genes or variants, understudied. We therefore developed BELB, a Biomedical Entity Linking Benchmark, providing access in a unified format to 11 corpora linked to 7 knowledge bases and spanning six entity types: gene, disease, chemical, species, cell line and variant. BELB greatly reduces preprocessing overhead in testing BEL systems on multiple corpora offering a standardized testbed for reproducible experiments. Using BELB we perform an extensive evaluation of six rule-based entity-specific systems and three recent neural approaches leveraging pre-trained language models. Our results reveal a mixed picture showing that neural approaches fail to perform consistently across entity types, highlighting the need of further studies towards entity-agnostic models.

Leon Weber-Genzel, Robert Litschko, Ekaterina Artemova et al.

Instruction tuning has become an integral part of training pipelines for Large Language Models (LLMs) and has been shown to yield strong performance gains. In an orthogonal line of research, Annotation Error Detection (AED) has emerged as a tool for detecting quality problems in gold standard labels. So far, however, the application of AED methods has been limited to classification tasks. It is an open question how well AED methods generalize to language generation settings, which are becoming more widespread via LLMs. In this paper, we present a first and novel benchmark for AED on instruction tuning data: DONKII. It comprises three instruction-tuning datasets enriched with error annotations by experts and semi-automatic methods. We also provide a novel taxonomy of error types for instruction-tuning data. We find that all three datasets contain clear errors, which sometimes propagate directly into instruction-tuned LLMs. We propose four AED baselines for the generative setting and evaluate them extensively on the newly introduced dataset. Our results show that the choice of the right AED method and model size is indeed crucial and derive practical recommendations for how to use AED methods to clean instruction-tuning data.

Robert Litschko, Max Müller-Eberstein, Rob van der Goot et al.

Language understanding is a multi-faceted cognitive capability, which the Natural Language Processing (NLP) community has striven to model computationally for decades. Traditionally, facets of linguistic intelligence have been compartmentalized into tasks with specialized model architectures and corresponding evaluation protocols. With the advent of large language models (LLMs) the community has witnessed a dramatic shift towards general purpose, task-agnostic approaches powered by generative models. As a consequence, the traditional compartmentalized notion of language tasks is breaking down, followed by an increasing challenge for evaluation and analysis. At the same time, LLMs are being deployed in more real-world scenarios, including previously unforeseen zero-shot setups, increasing the need for trustworthy and reliable systems. Therefore, we argue that it is time to rethink what constitutes tasks and model evaluation in NLP, and pursue a more holistic view on language, placing trustworthiness at the center. Towards this goal, we review existing compartmentalized approaches for understanding the origins of a model's functional capacity, and provide recommendations for more multi-faceted evaluation protocols.

Leon Weber, Mario Sänger, Jannes Münchmeyer et al.

Summary: Named Entity Recognition (NER) is an important step in biomedical information extraction pipelines. Tools for NER should be easy to use, cover multiple entity types, highly accurate, and robust towards variations in text genre and style. To this end, we propose HunFlair, an NER tagger covering multiple entity types integrated into the widely used NLP framework Flair. HunFlair outperforms other state-of-the-art standalone NER tools with an average gain of 7.26 pp over the next best tool, can be installed with a single command and is applied with only four lines of code. Availability: HunFlair is freely available through the Flair framework under an MIT license: https://github.com/flairNLP/flair and is compatible with all major operating systems. Contact:{weberple,saengema,alan.akbik}@informatik.hu-berlin.de

Xinpeng Wang, Bolei Ma, Chengzhi Hu et al.

The open-ended nature of language generation makes the evaluation of autoregressive large language models (LLMs) challenging. One common evaluation approach uses multiple-choice questions (MCQ) to limit the response space. The model is then evaluated by ranking the candidate answers by the log probability of the first token prediction. However, first-tokens may not consistently reflect the final response output, due to model's diverse response styles such as starting with "Sure" or refusing to answer. Consequently, MCQ evaluation is not indicative of model behaviour when interacting with users. But by how much? We evaluate how aligned first-token evaluation is with the text output along several dimensions, namely final option choice, refusal rate, choice distribution and robustness under prompt perturbation. Our results show that the two approaches are severely misaligned on all dimensions, reaching mismatch rates over 60%. Models heavily fine-tuned on conversational or safety data are especially impacted. Crucially, models remain misaligned even when we increasingly constrain prompts, i.e., force them to start with an option letter or example template. Our findings i) underscore the importance of inspecting the text output as well and ii) caution against relying solely on first-token evaluation.

Leon Weber-Genzel, Siyao Peng, Marie-Catherine de Marneffe et al.

Human label variation arises when annotators assign different labels to the same item for valid reasons, while annotation errors occur when labels are assigned for invalid reasons. These two issues are prevalent in NLP benchmarks, yet existing research has studied them in isolation. To the best of our knowledge, there exists no prior work that focuses on teasing apart error from signal, especially in cases where signal is beyond black-and-white. To fill this gap, we introduce a systematic methodology and a new dataset, VariErr (variation versus error), focusing on the NLI task in English. We propose a 2-round annotation procedure with annotators explaining each label and subsequently judging the validity of label-explanation pairs. VariErr contains 7,732 validity judgments on 1,933 explanations for 500 re-annotated MNLI items. We assess the effectiveness of various automatic error detection (AED) methods and GPTs in uncovering errors versus human label variation. We find that state-of-the-art AED methods significantly underperform GPTs and humans. While GPT-4 is the best system, it still falls short of human performance. Our methodology is applicable beyond NLI, offering fertile ground for future research on error versus plausible variation, which in turn can yield better and more trustworthy NLP systems.

Mario Sänger, Samuele Garda, Xing David Wang et al.

With the exponential growth of the life science literature, biomedical text mining (BTM) has become an essential technology for accelerating the extraction of insights from publications. Identifying named entities (e.g., diseases, drugs, or genes) in texts and their linkage to reference knowledge bases are crucial steps in BTM pipelines to enable information aggregation from different documents. However, tools for these two steps are rarely applied in the same context in which they were developed. Instead, they are applied in the wild, i.e., on application-dependent text collections different from those used for the tools' training, varying, e.g., in focus, genre, style, and text type. This raises the question of whether the reported performance of BTM tools can be trusted for downstream applications. Here, we report on the results of a carefully designed cross-corpus benchmark for named entity extraction, where tools were applied systematically to corpora not used during their training. Based on a survey of 28 published systems, we selected five for an in-depth analysis on three publicly available corpora encompassing four different entity types. Comparison between tools results in a mixed picture and shows that, in a cross-corpus setting, the performance is significantly lower than the one reported in an in-corpus setting. HunFlair2 showed the best performance on average, being closely followed by PubTator. Our results indicate that users of BTM tools should expect diminishing performances when applying them in the wild compared to original publications and show that further research is necessary to make BTM tools more robust.

Leon Weber, Barbara Plank

Manually annotated datasets are crucial for training and evaluating Natural Language Processing models. However, recent work has discovered that even widely-used benchmark datasets contain a substantial number of erroneous annotations. This problem has been addressed with Annotation Error Detection (AED) models, which can flag such errors for human re-annotation. However, even though many of these AED methods assume a final curation step in which a human annotator decides whether the annotation is erroneous, they have been developed as static models without any human-in-the-loop component. In this work, we propose ActiveAED, an AED method that can detect errors more accurately by repeatedly querying a human for error corrections in its prediction loop. We evaluate ActiveAED on eight datasets spanning five different tasks and find that it leads to improvements over the state of the art on seven of them, with gains of up to six percentage points in average precision.

Leon Weber, Pasquale Minervini, Jannes Münchmeyer et al.

Rule-based models are attractive for various tasks because they inherently lead to interpretable and explainable decisions and can easily incorporate prior knowledge. However, such systems are difficult to apply to problems involving natural language, due to its linguistic variability. In contrast, neural models can cope very well with ambiguity by learning distributed representations of words and their composition from data, but lead to models that are difficult to interpret. In this paper, we describe a model combining neural networks with logic programming in a novel manner for solving multi-hop reasoning tasks over natural language. Specifically, we propose to use a Prolog prover which we extend to utilize a similarity function over pretrained sentence encoders. We fine-tune the representations for the similarity function via backpropagation. This leads to a system that can apply rule-based reasoning to natural language, and induce domain-specific rules from training data. We evaluate the proposed system on two different question answering tasks, showing that it outperforms two baselines -- BIDAF (Seo et al., 2016a) and FAST QA (Weissenborn et al., 2017b) on a subset of the WikiHop corpus and achieves competitive results on the MedHop data set (Welbl et al., 2017).