Automatic medical coding has the potential to ease documentation and billing processes. For this task, transparency plays an important role for medical coders and regulatory bodies, which can be achieved using explainability methods. However, the evaluation of these approaches has been mostly limited to short text and binary settings due to a scarcity of annotated data. Recent efforts by Cheng et al. (2023) have introduced the MDACE dataset, which provides a valuable resource containing code evidence in clinical records. In this work, we conduct an in-depth analysis of the MDACE dataset and perform plausibility evaluation of current explainable medical coding systems from an applied perspective. With this, we contribute to a deeper understanding of automatic medical coding and evidence extraction. Our findings reveal that ground truth evidence aligns with code descriptions to a certain degree. An investigation into state-of-the-art approaches shows a high overlap with ground truth evidence. We propose match measures and highlight success and failure cases. Based on our findings, we provide recommendations for developing and evaluating explainable medical coding systems.

Artificial Intelligence (AI) is making a major impact on healthcare, particularly through its application in natural language processing (NLP) and predictive analytics. The healthcare sector has increasingly adopted AI for tasks such as clinical data analysis and medical code assignment. However, searching for clinical information in large and often unorganized datasets remains a manual and error-prone process. Assisting this process with automations can help physicians improve their operational productivity significantly. In this paper, we present a generative AI approach, coined SearchAI, to enhance the accuracy and efficiency of searching clinical data. Unlike traditional code assignment, which is a one-to-one problem, clinical data search is a one-to-many problem, i.e., a given search query can map to a family of codes. Healthcare professionals typically search for groups of related diseases, drugs, or conditions that map to many codes, and therefore, they need search tools that can handle keyword synonyms, semantic variants, and broad open-ended queries. SearchAI employs a hierarchical model that respects the coding hierarchy and improves the traversal of relationships from parent to child nodes. SearchAI navigates these hierarchies predictively and ensures that all paths are reachable without losing any relevant nodes. To evaluate the effectiveness of SearchAI, we conducted a series of experiments using both public and production datasets. Our results show that SearchAI outperforms default hierarchical traversals across several metrics, including accuracy, robustness, performance, and scalability. SearchAI can help make clinical data more accessible, leading to streamlined workflows, reduced administrative burden, and enhanced coding and diagnostic accuracy.

Understanding code represents a core ability needed for automating software development tasks. While foundation models like LLMs show impressive results across many software engineering challenges, the extent of their true semantic understanding beyond simple token recognition remains unclear. This research uses code obfuscation as a structured testing framework to evaluate LLMs' semantic understanding capabilities. We methodically apply controlled obfuscation changes to source code and measure comprehension through two complementary tasks: generating accurate descriptions of obfuscated code and performing deobfuscation, a skill with important implications for reverse engineering applications. Our testing approach includes 13 cutting-edge models, covering both code-specialized (e.g., StarCoder2) and general-purpose (e.g., GPT-4o) architectures, evaluated on a benchmark created from CodeNet and consisting of filtered 250 Java programming problems and their solutions. Findings show a statistically significant performance decline as obfuscation complexity increases, with unexpected resilience shown by general-purpose models compared to their code-focused counterparts. While some models successfully identify obfuscation techniques, their ability to reconstruct the underlying program logic remains constrained, suggesting limitations in their semantic representation mechanisms. This research introduces a new evaluation approach for assessing code comprehension in language models and establishes empirical baselines for advancing research in security-critical code analysis applications such as reverse engineering and adversarial code analysis.

ICD(International Classification of Diseases) coding involves assigning ICD codes to patients visit based on their medical notes. ICD coding is a challenging multilabel text classification problem due to noisy medical document inputs. Recent advancements in automated ICD coding have enhanced performance by integrating additional data and knowledge bases with the encoding of medical notes and codes. However, most of them ignore the code hierarchy, leading to improper code assignments. To address these problems, we propose a novel framework based on associated and hierarchical code description distillation (AHDD) for better code representation learning and avoidance of improper code assignment.we utilize the code description and the hierarchical structure inherent to the ICD codes. Therefore, in this paper, we leverage the code description and the hierarchical structure inherent to the ICD codes. The code description is also applied to aware the attention layer and output layer. Experimental results on the benchmark dataset show the superiority of the proposed framework over several state-of-the-art baselines.

Qualitative coding, or content analysis, extracts meaning from text to discern quantitative patterns across a corpus of texts. Recently, advances in the interpretive abilities of large language models (LLMs) offer potential for automating the coding process (applying category labels to texts), thereby enabling human researchers to concentrate on more creative research aspects, while delegating these interpretive tasks to AI. Our case study comprises a set of socio-historical codes on dense, paragraph-long passages representative of a humanistic study. We show that GPT-4 is capable of human-equivalent interpretations, whereas GPT-3.5 is not. Compared to our human-derived gold standard, GPT-4 delivers excellent intercoder reliability (Cohen's $\kappa \geq 0.79$) for 3 of 9 codes, and substantial reliability ($\kappa \geq 0.6$) for 8 of 9 codes. In contrast, GPT-3.5 greatly underperforms for all codes ($mean(\kappa) = 0.34$; $max(\kappa) = 0.55$). Importantly, we find that coding fidelity improves considerably when the LLM is prompted to give rationale justifying its coding decisions (chain-of-thought reasoning). We present these and other findings along with a set of best practices for adapting traditional codebooks for LLMs. Our results indicate that for certain codebooks, state-of-the-art LLMs are already adept at large-scale content analysis. Furthermore, they suggest the next generation of models will likely render AI coding a viable option for a majority of codebooks.

The increasing use of tools and solutions based on Large Language Models (LLMs) for various tasks in the medical domain has become a prominent trend. Their use in this highly critical and sensitive domain has thus raised important questions about their robustness, especially in response to variations in input, and the reliability of the generated outputs. This study addresses these questions by constructing a textual dataset based on the ICD-10-CM code descriptions, widely used in US hospitals and containing many clinical terms, and their easily reproducible rephrasing. We then benchmarked existing embedding models, either generalist or specialized in the clinical domain, in a semantic search task where the goal was to correctly match the rephrased text to the original description. Our results showed that generalist models performed better than clinical models, suggesting that existing clinical specialized models are more sensitive to small changes in input that confuse them. The highlighted problem of specialized models may be due to the fact that they have not been trained on sufficient data, and in particular on datasets that are not diverse enough to have a reliable global language understanding, which is still necessary for accurate handling of medical documents.

The task of assigning diagnostic ICD codes to patient hospital admissions is typically performed by expert human coders. Efforts towards automated ICD coding are dominated by supervised deep learning models. However, difficulties in learning to predict the large number of rare codes remain a barrier to adoption in clinical practice. In this work, we leverage off-the-shelf pre-trained generative large language models (LLMs) to develop a practical solution that is suitable for zero-shot and few-shot code assignment, with no need for further task-specific training. Unsupervised pre-training alone does not guarantee precise knowledge of the ICD ontology and specialist clinical coding task, therefore we frame the task as information extraction, providing a description of each coded concept and asking the model to retrieve related mentions. For efficiency, rather than iterating over all codes, we leverage the hierarchical nature of the ICD ontology to sparsely search for relevant codes.

AI-based code generators have become pivotal in assisting developers in writing software starting from natural language (NL). However, they are trained on large amounts of data, often collected from unsanitized online sources (e.g., GitHub, HuggingFace). As a consequence, AI models become an easy target for data poisoning, i.e., an attack that injects malicious samples into the training data to generate vulnerable code. To address this threat, we investigate the security of AI code generators by devising a targeted data poisoning strategy. We poison the training data by injecting increasing amounts of code containing security vulnerabilities and assess the attack's success on different state-of-the-art models for code generation. Our study shows that AI code generators are vulnerable to even a small amount of poison. Notably, the attack success strongly depends on the model architecture and poisoning rate, whereas it is not influenced by the type of vulnerabilities. Moreover, since the attack does not impact the correctness of code generated by pre-trained models, it is hard to detect. Lastly, our work offers practical insights into understanding and potentially mitigating this threat.

In this work, we present a method to add perturbations to the code descriptions to create new inputs in natural language (NL) from well-intentioned developers that diverge from the original ones due to the use of new words or because they miss part of them. The goal is to analyze how and to what extent perturbations affect the performance of AI code generators in the context of security-oriented code. First, we show that perturbed descriptions preserve the semantics of the original, non-perturbed ones. Then, we use the method to assess the robustness of three state-of-the-art code generators against the newly perturbed inputs, showing that the performance of these AI-based solutions is highly affected by perturbations in the NL descriptions. To enhance their robustness, we use the method to perform data augmentation, i.e., to increase the variability and diversity of the NL descriptions in the training data, proving its effectiveness against both perturbed and non-perturbed code descriptions.

Automatic International Classification of Diseases (ICD) coding aims to assign multiple ICD codes to a medical note with an average of 3,000+ tokens. This task is challenging due to the high-dimensional space of multi-label assignment (155,000+ ICD code candidates) and the long-tail challenge - Many ICD codes are infrequently assigned yet infrequent ICD codes are important clinically. This study addresses the long-tail challenge by transforming this multi-label classification task into an autoregressive generation task. Specifically, we first introduce a novel pretraining objective to generate free text diagnoses and procedure using the SOAP structure, the medical logic physicians use for note documentation. Second, instead of directly predicting the high dimensional space of ICD codes, our model generates the lower dimension of text descriptions, which then infer ICD codes. Third, we designed a novel prompt template for multi-label classification. We evaluate our Generation with Prompt model with the benchmark of all code assignment (MIMIC-III-full) and few shot ICD code assignment evaluation benchmark (MIMIC-III-few). Experiments on MIMIC-III-few show that our model performs with a marco F1 30.2, which substantially outperforms the previous MIMIC-III-full SOTA model (marco F1 4.3) and the model specifically designed for few/zero shot setting (marco F1 18.7). Finally, we design a novel ensemble learner, a cross attention reranker with prompts, to integrate previous SOTA and our best few-shot coding predictions. Experiments on MIMIC-III-full show that our ensemble learner substantially improves both macro and micro F1, from 10.4 to 14.6 and from 58.2 to 59.1, respectively.