Limitoy

	{
	"File Number": "1024",
	"Title": "Toward Expanding the Scope of Radiology Report Summarization to Multiple Anatomies and Modalities",
	"Limitation": "Did you describe the limitations of your work? On Page 5. 3 A2. Did you discuss any potential risks of your work? On Page 5. 3 A3. Do the abstract and introduction summarize the paper’s main claims? On Pages 1 and 4. 7 A4. Have you used AI writing assistants when working on this paper? Left blank. B 3 Did you use or create scientific artifacts? Section 2. 3 B1. Did you cite the creators of artifacts you used? Section 2. 3 B2. Did you discuss the license or terms for use and / or distribution of any artifacts? On Page 5. 3 B3. Did you discuss if your use of existing artifact(s) was consistent with their intended use, provided that it was specified? For the artifacts you create, do you specify intended use and whether that is compatible with the original access conditions (in particular, derivatives of data accessed for research purposes should not be used outside of research contexts)? Section 2. 3 B4. Did you discuss the steps taken to check whether the data that was collected / used contains any information that names or uniquely identifies individual people or offensive content, and the steps taken to protect / anonymize it? Section 2. 3 B5. Did you provide documentation of the artifacts, e.g., coverage of domains, languages, and linguistic phenomena, demographic groups represented, etc.? Section 2. 3 B6. Did you report relevant statistics like the number of examples, details of train / test / dev splits, etc. for the data that you used / created? Even for commonly-used benchmark datasets, include the number of examples in train / validation / test splits, as these provide necessary context for a reader to understand experimental results. For example, small differences in accuracy on large test sets may be significant, while on small test sets they may not be. Section 2. C 3 Did you run computational experiments? Section 3. C1. Did you report the number of parameters in the models used, the total computational budget (e.g., GPU hours), and computing infrastructure used? Not applicable. We use the common pre-trained models in our experiments. The Responsible NLP Checklist used at ACL 2023 is adopted from NAACL 2022, with the addition of a question on AI writing assistance. 3 C2. Did you discuss the experimental setup, including hyperparameter search and best-found hyperparameter values? Section 3. 3 C3. Did you report descriptive statistics about your results (e.g., error bars around results, summary statistics from sets of experiments), and is it transparent whether you are reporting the max, mean, etc. or just a single run? Section 3. 3 C4. If you used existing packages (e.g., for preprocessing, for normalization, or for evaluation), did you report the implementation, model, and parameter settings used (e.g., NLTK, Spacy, ROUGE, etc.)? Section 3. D 3 Did you use human annotators (e.g., crowdworkers) or research with human participants? Sections 2 and 3. 3 D1. Did you report the full text of instructions given to participants, including e.g., screenshots, disclaimers of any risks to participants or annotators, etc.? Section 2. 3 D2. Did you report information about how you recruited (e.g., crowdsourcing platform, students) and paid participants, and discuss if such payment is adequate given the participants’ demographic (e.g., country of residence)? Section 2. 3 D3. Did you discuss whether and how consent was obtained from people whose data you’re using/curating? For example, if you collected data via crowdsourcing, did your instructions to crowdworkers explain how the data would be used? Section 2. 3 D4. Was the data collection protocol approved (or determined exempt) by an ethics review board? Section 2 and Page 5. 3 D5. Did you report the basic demographic and geographic characteristics of the annotator population that is the source of the data? Section 2.",
	"abstractText": "Radiology report summarization (RRS) is a growing area of research. Given the Findings section of a radiology report, the goal is to generate a summary (called an Impression section) that highlights the key observations and conclusions of the radiology study. However, RRS currently faces essential limitations. First, many prior studies conduct experiments on private datasets, preventing the reproduction of results and fair comparisons across different systems and solutions. Second, most prior approaches are evaluated solely on chest Xrays. To address these limitations, we propose a dataset (MIMIC-RRS) involving three new modalities and seven new anatomies based on the MIMIC-III and MIMIC-CXR datasets. We then conduct extensive experiments to evaluate the performance of models both within and across modality-anatomy pairs in MIMIC-RRS. In addition, we evaluate their clinical efficacy via RadGraph, a factual correctness metric.",
	"1 Introduction": "A radiology report is a document that provides information about the results of a radiology study. It usually includes a Findings section with key observations from the study and an Impression section with the radiologist’s overall conclusions. The latter is the most critical part of the report and is typically based on both the findings and the patient’s condition. It can be helpful to automate the process of generating the impression section because it can be time-consuming and prone to errors when done manually (Bhargavan et al., 2009; Alexander et al., 2022). Recently, substantial progress has been made towards research on automated radiology report summarization (RRS) (Zhang et al., 2020; Ben Abacha et al., 2021; Hu et al., 2022). However, the field of RRS faces several key limitations. First, the experimental results of many\n*Equal Contribution.\nprior studies (Zhang et al., 2018, 2020) are reported on private datasets, making it difficult to replicate results or compare approaches. Second, existing studies are mainly limited to a single modality (i.e., X-ray) and a single anatomy (i.e., chest) (Zhang et al., 2020; Ben Abacha et al., 2021; Hu et al., 2021). In some cases, researchers omit to disclose the modality and anatomy of the radiology reports used for their experiments (Karn et al., 2022). Finally, recent models (Karn et al., 2022; Hu et al., 2022) present an increased complexity in architecture that offers only marginal improvements on the existing evaluation metrics for summarization. This further makes the replication of studies more difficult. To address the aforementioned limitations, we construct a brand-new open-source dataset (named MIMIC-RRS) for radiology report summarization involving three modalities (X-ray, MRI, and CT) and seven anatomies (chest, head, neck, sinus, spine, abdomen, and pelvis). MIMIC-RRS is based on the MIMIC-CXR (Johnson et al., 2019) and MIMIC-III (Johnson et al., 2016) datasets and introduces data from 12 new modality-anatomy pairs. As a result, we introduce a new setting for evaluating the generalization capabilities of RRS models across different modalities and anatomies. In addition, we benchmark various pre-trained language models on MIMIC-RRS. Through extensive experiments within and across modality-anatomy pairs, we show that adopting an appropriate pretrained model can achieve promising results comparable to previous studies. We also introduce a metric to evaluate factual correctness of generated summaries for any modality-anatomy pair.",
	"2 Dataset Construction": "In this section, we present the new MIMIC-RRS dataset designed for radiology report summarization across multiple modalities and anatomies. Comparisons with existing datasets are shown in\n469\nTable 1. We detail the collection process and the dataset statistics in the following subsections.",
	"2.1 Data Collection": "MIMIC-III One of our main contributions is to generate RRS data from MIMIC-II involving distinct combinations of modalities (i.e., medical imaging techniques) and anatomies (i.e., body parts). To this end, we first select five of the most frequently-occurring modality-anatomy pairs in the pool of MIMIC-III reports: “CT Head”, “CT Spine”, “CT Chest”, “CT Abdomen-Pelvis” and “MR Head”. Note that we discard chest X-rays as they are included in the MIMIC-CXR dataset. In addition, we pick six modality-anatomy pairs that occur infrequently in MIMIC-III to serve as out-ofdomain (OOD) test sets: “CT Neck”, “CT Sinus”, “MR Pelvis”, “MR Neck”, “MR Abdomen”, “MR Spine”. This set of pairs represents two types of OOD cases: (1) the modality has not been seen during training (one could train on CT neck and test on MR Neck), and (2) the anatomy has not been seen during training (for example, CT Sinus is the only “sinus” dataset). For each report, we extract the findings and impression section. However, the findings section is not always clearly labeled as “findings\". With the help of a board-certified radiologist, we identify alternate section headers that reference findings for each modality-anatomy pair. As an example, for CT head, findings may be referenced in reports with the section headings “non-contrast head ct\", “ct head\", “ct head without contrast\", “ct head without iv contrast\", “head ct\", “head ct without iv contrast\", or “cta head\". We identify 537 candidate section headers that reference findings across our dataset. We also discarded reports where multiple studies are pooled in the same radiology report, leading to multiple intricate observations in the impression",
	"230 253 128,003": "section1. Our resulting dataset consists of 79,779 selected reports across 11 modality-anatomy pairs.\nMIMIC-CXR MIMIC-CXR studies are chest Xray examinations. We follow preprocessing steps reported in previous work (Delbrouck et al., 2022b), and we only include reports with both a Findings and an Impression section. This yields 128,003 reports.",
	"2.2 Data statistics": "In total, there are 207,782 samples in the MIMICRRS dataset. The number of examples for each modality and anatomy is provided in Table 2. To further analyze this dataset, we report in Figure 1 the text lengths and vocabulary sizes associated with reports from each modality-anatomy pair. We find that for all modality-anatomy pairs, the findings section is significantly longer than the impression section (up to +315% for MR abdomen). Additionally, the findings sections of chest X-ray reports, which average only 49 words, are much shorter than reports from other modality-anatomy\n1We release our candidate section headers as well as code to recreate the dataset from scratch (Appendix B).\npairs. In contrast, MR Abdomen and MR Pelvis reports including findings sections that average 205 and 174 words, respectively. We see that CT Chest, CT Head, and CT Abdomen-Pelvis reports have a relatively large vocabulary size (given their sample size) with 20,909, 19,813, and 18,933 words. Surprisingly, the CT Abdomen-Pelvis impressions include a larger vocabulary than the findings. On the other hand, MR pelvis and MR abdomen impressions contain 36% and 37% fewer words than their corresponding findings, respectively. We assign reports from the following modalityanatomy pairs to training, validation, and test sets due to their large sample sizes: “CT abdomen/pelvis”, “CT Chest”, “CT Neck”, “CT Spine”, “CT Head”, “MR Head”, and “X-ray Chest”. The remaining reports (i.e., “MR Pelvis”, “MR Spine”, “MR Neck”, “MR Abdomen”, and “CT Sinus”) are used for OOD test sets2.",
	"3 Algorithmic Analysis": "In this section, we conduct experiments to analyze the performance of different models on MIMICRRS. We provide three categories of analyses: inmodality-anatomy, cross-modality-anatomy, and clinical efficacy.",
	"3.1 In-modality-anatomy": "To benchmark the performance of different models on the proposed MIMIC-RRS dataset, we conduct experiments within each modality-anatomy pair (i.e., the training and test procedures are performed using only one modality-anatomy pair). We evaluate three types of pre-trained sequence-tosequence models, namely T5 (Raffel et al., 2020), BART (Lewis et al., 2020), BioBART (Yuan et al., 2022), and their variants.3 Results are reported in\n2We release data splits publicly so that future work can fairly compare new results.\n3We do not evaluate several pre-trained models (e.g., ClinicalBERT (Alsentzer et al., 2019), BioClinicalBERT (Alsentzer\nTable 3. Several observations can be drawn from these experiments. First, simply adopting pretrained sequence-to-sequence language models can achieve results comparable to previous state-of-theart approaches designed for radiology summarization. Indeed, using BART-L as a backbone achieves the best performance, confirming the necessity of exploiting appropriate pre-trained language models. Secondly, the performances across different model types vary (i.e., BART-L/BART-B, BioBART-L/ BioBART-B). Yet, we notice that the number of training parameters matters; large models report the best results. According to our evaluations, the BART models achieve better results across all modality-anatomy pairs. Surprisingly, it is worth noting that the BioBART models do not achieve better results than BART, although BioBART is pre-trained on a biomedical corpus. One explanation could be that BioBART models are pre-trained on abstracts from PubMed, which are not within the same domain as radiology reports. In summary, we note several key findings for future studies: (i) “Less is more”: starting from an appropriate backbone instead of designing complicated modules; (ii) the model size matters; (iii) the pretraining domain matters: knowledge from clinical notes or medical literature does not easily translate to radiology reports.",
	"3.2 Cross-modality-anatomy": "In this section, we conduct experiments across modality-anatomy pairs (i.e., models are trained on reports from a subset of modality-anatomy pairs and then evaluated on all pairs, including the OOD test sets). We report the cross-modality-anatomy scores in Figure 2. A few interesting observations can be made. First, there are some associations between different anatomies and modalities. For example, the model trained on “CT Head” can also achieve promising results on the “MR Head” set. Secondly, training the model with all the modalityanatomy pairs (denoted as ALL) achieves the best generalization, obtaining the best results across all modalities and anatomies including the OOD test sets. We leave further exploration of crossmodality-anatomy associations and zero-shot OOD\net al., 2019), and Clinical-T5 (Lu et al., 2022)) that specialize in the clinical text since they were trained on the text from MIMIC-III, which overlaps with our dataset. The MIMICRRS test set is included in their pre-training data. Thus, we do not adopt them in our experiments to avoid potential data leakage and ensure a fair comparison.\ntransfer for future work.",
	"3.3 Clinical-Efficacy": "In addition to evaluating our systems using the ROUGE-1, ROUGE-2, and ROUGE-L metrics (Lin, 2004), we use a factual correctness metric to analyze clinical efficacy. Most prior works (Zhang et al., 2020; Smit et al., 2020; Hu et al., 2022) mainly use the F1CheXbert metric, an F1-score that evaluates the factual correctness of the generated impressions using 14 chest radio-\ngraphic observations. Unfortunately, this metric is unsuitable for MIMIC-RRS, which contains reports from other modality-anatomy pairs beyond chest X-rays. For this reason, instead of using F1CheXbert, we propose to use RadGraph (Jain et al., 2021) to evaluate the clinical correctness of the generated impressions. RadGraph is a dataset containing boardcertified radiologist annotations of radiology reports corresponding to 14,579 entities and 10,889 relations (Appendix A.1). We used the released pretrained model to annotate our reports and asked one board-certified radiologist to subjectively validate that the printed entities of the RadGraph model on our data are correct (examples are shown in Table 5). After confirming the effectiveness of the model, we follow Delbrouck et al. (2022a) to compute the F1-RadGraph scores. The score evaluates the correctness of the generated named entities in the hypothesis impression compared to the groundtruth impression. We report these results in Ta-\nble 4. It can be observed that the BART models can achieve the best performance with respect to clinical efficacy. The results are consistent with the ROUGE scores, further confirming the effectiveness of adopting BART as the backbone instead of designing complicated solutions.",
	"4 Related Work": "In this section, we discuss prior research related to the radiology report summarization task. The first attempt at automatic summarization of radiology findings into natural language impression statements was proposed by Zhang et al. (2018). Their contribution was to propose a first baseline on the task, using a bidirectional-LSTM as encoder and decoder. Importantly, they found that about 30% of the summaries generated from neural models contained factual errors. Subsequently, Zhang et al. (2020) proposed the F1CheXbert score to evaluate the factual correctness of the generated impression. They also used reinforcement learning to optimize the F1CheXbert score directly. Finally, both Hu et al. (2021) and Hu et al. (2022) used the Biomedical and Clinical English Model Packages in the Stanza Python NLP Library (Zhang et al., 2021) to extract medical entities. The former study used the entities to construct a Graph Neural Network, which was used as input in their summarization pipeline. In contrast, the latter study used the entities to mask the findings duringcontrastive pre-training.\nWe believe this paper is an original contribution to the aforementioned line of work. As instigated by Zhang et al. (2018), our goal is to release a new summarization corpus and baselines on new modalities and anatomies. We do so by releasing an RRS dataset with data from 11 new modality-anatomy pairs. In addition, we extend the work performed by Zhang et al. (2020) by proposing a new metric to evaluates the factual correctness and completeness of the generated impression, namely the RadGraph score. Finally, we improve on the work of Hu et al. (2021, 2022) in two ways: (1) we use semantic annotations from a pre-trained model trained using annotations from board-certified radiologists, as opposed to Stanza which leverages unsupervised biomedical and clinical text data; (2) we leverage relation annotations between entities, a feature that was not available in prior work.",
	"5 Conclusion and Discussion": "In this paper, we highlight and address several weaknesses associated with the radiology report summarization task. First, from a data perspective, we propose a publicly available dataset named MIMIC-RRS involving data samples from twelve modality-anatomy pairs, with 79,779 samples from MIMIC-III and 128,003 samples from MIMIC-CXR.\nSecond, we conducted more than 40 experiments and over 400 cross-modality-anatomy evaluations to benchmark the performance of different models. We show that instead of designing complicated modules, we can start from an appropriate backbone model such as BART.\nFinally, we proposed an elegant and simple metric, F1-RadGraph, to evaluate the factual correctness of summaries generated for any modality and anatomy. In the future, we hope that our work broadens the scope of the radiology report summarization task and contributes to the development of reliable RRS models that generalize well to new anatomies and modalities.\nLimitations\nWe note two limitations of our paper. First, our work does not extensively evaluate all the available pre-trained models that could be suitable for this task, e.g., ELECTRA (Clark et al., 2020), BioLinkBERT (Yasunaga et al., 2022), GatorTron (Yang et al., 2022), RadBERT (Yan et al., 2022), and PubMedBERT (Gu et al., 2021). The aim of this work is not to report the strongest possible score but rather to address weaknesses of existing radiology report summarization studies (in terms of data and evaluation). Yet, we are confident our proposed solutions report a strong baseline for future work. Second, although F1-RadGraph seems like an appropriate metric to evaluate our new modalities and anatomies (and appears to be consistent with ROUGE scores), it has only been evaluated subjectively and not systematically.",
	"Acknowledgments": "Maya Varma is supported by graduate fellowship awards from the Department of Defense (NDSEG) and the Knight-Hennessy Scholars program at Stanford University.",
	"A Details of RadGraph Scores": "A.1 The Introduction of RadGraph\nTo design our new evaluation metric, we leverage the RadGraph dataset (Jain et al., 2021) containing board-certified radiologist annotations of chest Xray reports, which correspond to 14,579 entities and 10,889 relations. RadGraph has released a PubMedBERT model (Gu et al., 2021) pre-trained on these annotations to annotate new reports. An example of annotation can be seen in Figure 3. Before moving on to the next section, we quickly describe the concept of entities and relations:\nEntities An entity is defined as a continuous span of text that can include one or more adjacent words. Entities in RadGraph center around two concepts: Anatomy and Observation. Three uncertainty levels exist for Observation, leading to four different entities: Anatomy (ANAT-DP), Observation: Definitely Present (OBS-DP), Observation: Uncertain (OBSU), and Observation: Definitely Absent (OBS-DA).\nRelations A relation is defined as a directed edge between two entities. Three levels exist: Suggestive Of (., .), Located At (., .), and Modify (., .).\nA.2 Metric Computation\nUsing the RadGraph annotation scheme and pretrained model, we designed an F-score style reward that measures the factual consistency and completeness of the generated impression (also called hypothesis impression) compared to the reference impression. To do so, we treat the RadGraph annotations of an impression as a graph G(V,E) with the set of nodes V = {v1, v2, . . . , v\|V \|} containing the entities and the set of edges E = {e1, e2, . . . , e\|E\|} the relations between pairs of entities. The graph is directed, meaning that the edge e = (v1, v2) ̸= (v2, v1). An example is depicted in Figure 4. Each node or edge of the graph also has a label, which\nwe denote as viL for an entity i (for example “OBSDP\" or “ANAT\") and eijL for a relation e = (vi, vj) (such as “modified\" or “located at\"). To design our RadGraph score, we focus on the nodes V and whether or not a node has a relation in E. For a hypothesis impression y, we create a new set of triplets Ty = {(vi, viL ,R)}i=1:\|V \|. The value R is 1 if (vi, vj)j=1:\|E\|,i ̸=j ∈ E, 0 otherwise. In other words, a triplet contains an entity, the entity label, and whether or not this entity has a relation. We proceed to construct the same set for the reference report ŷ and denote this set Tŷ. Finally, our score is defined as the harmonic mean of precision and recall between the hypothesis set Ty and the reference set Tŷ, giving a value between 0 and 100. As an illustration, the set V , E and T of the graph G in Figure 4 are shown as follows: V = {mild, fluid, overload, overt, pulmonary, edema} E = {(mild,overload), (overload, fluid), (edema, pulmonary)} T = {(mild, obs-dp, 1), (fluid, obs-dp, 0), (overload, obs-dp, 1), (overt, obs-da, 0), (pulmonary, anat-dp, 0), (edema, obs-da, 1)}",
	"B Code and Data Release": "Our research has been carried out using the ViLMedic library (Delbrouck et al., 2022b). Our code is available at https://github.com/jbdel/ vilmedic. This link is anonymized and complies with the double-blind review process. More specifically, we release the code of the RadGraph score as well as the training of our baseline. We also release the script to download, pre-process, and split the radiology reports of the MIMIC-III database\nas per our experiments. To download the MIMICIII database, researchers are required to formally request access via a process documented on the MIMIC website. There are two key steps that must be completed before access is granted: (i) the researcher must complete a recognized course in protecting human research participants, including Health Insurance Portability and Accountability Act (HIPAA) requirements. (ii) the researcher must sign a data use agreement, which outlines appropriate data usage and security standards, and forbids efforts to identify individual patients.",
	"C More Results": "We present the results (including four metrics, i.e., ROUGE-1, ROUGE-2, ROUGE-L, and RadGraph scores) of all the experiments on Figure 5-9 for further research in this field. We also show the output of RadGraph (for entities) on a few samples of our new dataset in Table 5.",
	"D Ethics Statement": "The MIMIC-CXR and MIMIC-III datasets are deidentified to satisfy the US Health Insurance Portability and Accountability Act of 1996 (HIPAA) Safe Harbor requirements. Protected health information (PHI) has been removed. Therefore, the ethical approval statement and the need for informed consent were waived for the studies on this database, which was approved by the Massachusetts Institute of Technology (Cambridge, MA) and Beth Israel Deaconess Medical Center (Boston, MA). This research was conducted in accordance with the Declaration of Helsinki, describing the ethical principles of medical research involving human subjects.\nACL 2023 Responsible NLP Checklist",
	"A For every submission:": "3 A1. Did you describe the limitations of your work?\nOn Page 5.\n3 A2. Did you discuss any potential risks of your work? On Page 5.\n3 A3. Do the abstract and introduction summarize the paper’s main claims? On Pages 1 and 4.\n7 A4. Have you used AI writing assistants when working on this paper? Left blank.\nB 3 Did you use or create scientific artifacts? Section 2.\n3 B1. Did you cite the creators of artifacts you used? Section 2.\n3 B2. Did you discuss the license or terms for use and / or distribution of any artifacts? On Page 5.\n3 B3. Did you discuss if your use of existing artifact(s) was consistent with their intended use, provided that it was specified? For the artifacts you create, do you specify intended use and whether that is compatible with the original access conditions (in particular, derivatives of data accessed for research purposes should not be used outside of research contexts)? Section 2.\n3 B4. Did you discuss the steps taken to check whether the data that was collected / used contains any information that names or uniquely identifies individual people or offensive content, and the steps taken to protect / anonymize it? Section 2.\n3 B5. Did you provide documentation of the artifacts, e.g., coverage of domains, languages, and linguistic phenomena, demographic groups represented, etc.? Section 2.\n3 B6. Did you report relevant statistics like the number of examples, details of train / test / dev splits, etc. for the data that you used / created? Even for commonly-used benchmark datasets, include the number of examples in train / validation / test splits, as these provide necessary context for a reader to understand experimental results. For example, small differences in accuracy on large test sets may be significant, while on small test sets they may not be. Section 2.\nC 3 Did you run computational experiments? Section 3.\nC1. Did you report the number of parameters in the models used, the total computational budget (e.g., GPU hours), and computing infrastructure used? Not applicable. We use the common pre-trained models in our experiments.\nThe Responsible NLP Checklist used at ACL 2023 is adopted from NAACL 2022, with the addition of a question on AI writing assistance.\n3 C2. Did you discuss the experimental setup, including hyperparameter search and best-found hyperparameter values? Section 3.\n3 C3. Did you report descriptive statistics about your results (e.g., error bars around results, summary statistics from sets of experiments), and is it transparent whether you are reporting the max, mean, etc. or just a single run? Section 3.\n3 C4. If you used existing packages (e.g., for preprocessing, for normalization, or for evaluation), did you report the implementation, model, and parameter settings used (e.g., NLTK, Spacy, ROUGE, etc.)? Section 3.\nD 3 Did you use human annotators (e.g., crowdworkers) or research with human participants? Sections 2 and 3.\n3 D1. Did you report the full text of instructions given to participants, including e.g., screenshots, disclaimers of any risks to participants or annotators, etc.? Section 2.\n3 D2. Did you report information about how you recruited (e.g., crowdsourcing platform, students) and paid participants, and discuss if such payment is adequate given the participants’ demographic (e.g., country of residence)? Section 2.\n3 D3. Did you discuss whether and how consent was obtained from people whose data you’re using/curating? For example, if you collected data via crowdsourcing, did your instructions to crowdworkers explain how the data would be used? Section 2.\n3 D4. Was the data collection protocol approved (or determined exempt) by an ethics review board? Section 2 and Page 5.\n3 D5. Did you report the basic demographic and geographic characteristics of the annotator population that is the source of the data? Section 2."
	}