Clinical document classification is essential for converting unstructured medical texts into standardised ICD-10 diagnoses, yet it faces challenges due to complex medical language, privacy constraints, and limited annotated datasets. Large Language Models (LLMs) offer promising improvements in accuracy and efficiency for this task. This study evaluates the performance and consistency of eight LLMs; four reasoning (Qwen QWQ, Deepseek Reasoner, GPT o3 Mini, Gemini 2.0 Flash Thinking) and four non-reasoning (Llama 3.3, GPT 4o Mini, Gemini 2.0 Flash, Deepseek Chat); in classifying clinical discharge summaries using the MIMIC-IV dataset. Using cTAKES to structure clinical narratives, models were assessed across three experimental runs, with majority voting determining final predictions. Results showed that reasoning models outperformed non-reasoning models in accuracy (71% vs 68%) and F1 score (67% vs 60%), with Gemini 2.0 Flash Thinking achieving the highest accuracy (75%) and F1 score (76%). However, non-reasoning models demonstrated greater stability (91% vs 84% consistency). Performance varied across ICD-10 codes, with reasoning models excelling in complex cases but struggling with abstract categories. Findings indicate a trade-off between accuracy and consistency, suggesting that a hybrid approach could optimise clinical coding. Future research should explore multi-label classification, domain-specific fine-tuning, and ensemble methods to enhance model reliability in real-world applications.
Urban systems are managed using complex textual documentation that need coding and analysis to set requirements and evaluate built environment performance. This paper contributes to the study of applying large-language models (LLM) to qualitative coding activities to reduce resource requirements while maintaining comparable reliability to humans. Qualitative coding and assessment face challenges like resource limitations and bias, accuracy, and consistency between human evaluators. Here we report the application of LLMs to deductively code 10 case documents on the presence of 17 digital twin characteristics for the management of urban systems. We utilize two prompting methods to compare the semantic processing of LLMs with human coding efforts: whole text analysis and text chunk analysis using OpenAI's GPT-4o, GPT-4o-mini, and o1-mini models. We found similar trends of internal variability between methods and results indicate that LLMs may perform on par with human coders when initialized with specific deductive coding contexts. GPT-4o, o1-mini and GPT-4o-mini showed significant agreement with human raters when employed using a chunking method. The application of both GPT-4o and GPT-4o-mini as an additional rater with three manual raters showed statistically significant agreement across all raters, indicating that the analysis of textual documents is benefited by LLMs. Our findings reveal nuanced sub-themes of LLM application suggesting LLMs follow human memory coding processes where whole-text analysis may introduce multiple meanings. The novel contributions of this paper lie in assessing the performance of OpenAI GPT models and introduces the chunk-based prompting approach, which addresses context aggregation biases by preserving localized context.
Negative sampling has emerged as an effective technique that enables deep learning models to learn better representations by introducing the paradigm of learn-to-compare. The goal of this approach is to add robustness to deep learning models to learn better representation by comparing the positive samples against the negative ones. Despite its numerous demonstrations in various areas of computer vision and natural language processing, a comprehensive study of the effect of negative sampling in an unsupervised domain like topic modeling has not been well explored. In this paper, we present a comprehensive analysis of the impact of different negative sampling strategies on neural topic models. We compare the performance of several popular neural topic models by incorporating a negative sampling technique in the decoder of variational autoencoder-based neural topic models. Experiments on four publicly available datasets demonstrate that integrating negative sampling into topic models results in significant enhancements across multiple aspects, including improved topic coherence, richer topic diversity, and more accurate document classification. Manual evaluations also indicate that the inclusion of negative sampling into neural topic models enhances the quality of the generated topics. These findings highlight the potential of negative sampling as a valuable tool for advancing the effectiveness of neural topic models.
Recent advances in deep learning have established Transformer architectures as the predominant modeling paradigm. Central to the success of Transformers is the self-attention mechanism, which scores the similarity between query and key matrices to modulate a value matrix. This operation bears striking similarities to digraph convolution, prompting an investigation into whether digraph convolution could serve as an alternative to self-attention. In this study, we formalize this concept by introducing a synthetic unitary digraph convolution based on the digraph Fourier transform. The resulting model, which we term Converter, effectively converts a Transformer into a Directed Graph Neural Network (DGNN) form. We have tested Converter on Long-Range Arena benchmark, long document classification, and DNA sequence-based taxonomy classification. Our experimental results demonstrate that Converter achieves superior performance while maintaining computational efficiency and architectural simplicity, which establishes it as a lightweight yet powerful Transformer variant.
Black-box textual adversarial attacks are challenging due to the lack of model information and the discrete, non-differentiable nature of text. Existing methods often lack versatility for attacking different models, suffer from limited attacking performance due to the inefficient optimization with word saliency ranking, and frequently sacrifice semantic integrity to achieve better attack outcomes. This paper introduces a novel approach to textual adversarial attacks, which we call Cross-Entropy Attacks (CEA), that uses Cross-Entropy optimization to address the above issues. Our CEA approach defines adversarial objectives for both soft-label and hard-label settings and employs CE optimization to identify optimal replacements. Through extensive experiments on document classification and language translation problems, we demonstrate that our attack method excels in terms of attacking performance, imperceptibility, and sentence quality.
Self-supervised graph representation learning (SSGRL) is a representation learning paradigm used to reduce or avoid manual labeling. An essential part of SSGRL is graph data augmentation. Existing methods usually rely on heuristics commonly identified through trial and error and are effective only within some application domains. Also, it is not clear why one heuristic is better than another. Moreover, recent studies have argued against some techniques (e.g., dropout: that can change the properties of molecular graphs or destroy relevant signals for graph-based document classification tasks). In this study, we propose a novel data-driven SSGRL approach that automatically learns a suitable graph augmentation from the signal encoded in the graph (i.e., the nodes' predictive feature and topological information). We propose two complementary approaches that produce learnable feature and topological augmentations. The former learns multi-view augmentation of node features, and the latter learns a high-order view of the topology. Moreover, the augmentations are jointly learned with the representation. Our approach is general that it can be applied to homogeneous and heterogeneous graphs. We perform extensive experiments on node classification (using nine homogeneous and heterogeneous datasets) and graph property prediction (using another eight datasets). The results show that the proposed method matches or outperforms the SOTA SSGRL baselines and performs similarly to semi-supervised methods. The anonymised source code is available at https://github.com/AhmedESamy/dsgrl/
Tobacco3482 is a widely used document classification benchmark dataset. However, our manual inspection of the entire dataset uncovers widespread ontological issues, especially large amounts of annotation label problems in the dataset. We establish data label guidelines and find that 11.7% of the dataset is improperly annotated and should either have an unknown label or a corrected label, and 16.7% of samples in the dataset have multiple valid labels. We then analyze the mistakes of a top-performing model and find that 35% of the model's mistakes can be directly attributed to these label issues, highlighting the inherent problems with using a noisily labeled dataset as a benchmark. Supplementary material, including dataset annotations and code, is available at https://github.com/gordon-lim/tobacco3482-mistakes/.
Retrieval-Augmented Generation (RAG) enhances Large Language Models (LLMs) by integrating external document retrieval to provide domain-specific or up-to-date knowledge. The effectiveness of RAG depends on the relevance of retrieved documents, which is influenced by the semantic alignment of embeddings with the domain's specialized content. Although full fine-tuning can align language models to specific domains, it is computationally intensive and demands substantial data. This paper introduces Hierarchical Embedding Alignment Loss (HEAL), a novel method that leverages hierarchical fuzzy clustering with matrix factorization within contrastive learning to efficiently align LLM embeddings with domain-specific content. HEAL computes level/depth-wise contrastive losses and incorporates hierarchical penalties to align embeddings with the underlying relationships in label hierarchies. This approach enhances retrieval relevance and document classification, effectively reducing hallucinations in LLM outputs. In our experiments, we benchmark and evaluate HEAL across diverse domains, including Healthcare, Material Science, Cyber-security, and Applied Maths.
Orthogonal nonnegative matrix factorization (ONMF) has become a standard approach for clustering. As far as we know, most works on ONMF rely on the Frobenius norm to assess the quality of the approximation. This paper presents a new model and algorithm for ONMF that minimizes the Kullback-Leibler (KL) divergence. As opposed to the Frobenius norm which assumes Gaussian noise, the KL divergence is the maximum likelihood estimator for Poisson-distributed data, which can model better sparse vectors of word counts in document data sets and photo counting processes in imaging. We develop an algorithm based on alternating optimization, KL-ONMF, and show that it performs favorably with the Frobenius-norm based ONMF for document classification and hyperspectral image unmixing.
Scientific document classification is a critical task and often involves many classes. However, collecting human-labeled data for many classes is expensive and usually leads to label-scarce scenarios. Moreover, recent work has shown that sentence embedding model fine-tuning for few-shot classification is efficient, robust, and effective. In this work, we propose FusionSent (Fusion-based Sentence Embedding Fine-tuning), an efficient and prompt-free approach for few-shot classification of scientific documents with many classes. FusionSent uses available training examples and their respective label texts to contrastively fine-tune two different sentence embedding models. Afterward, the parameters of both fine-tuned models are fused to combine the complementary knowledge from the separate fine-tuning steps into a single model. Finally, the resulting sentence embedding model is frozen to embed the training instances, which are then used as input features to train a classification head. Our experiments show that FusionSent significantly outperforms strong baselines by an average of $6.0$ $F_{1}$ points across multiple scientific document classification datasets. In addition, we introduce a new dataset for multi-label classification of scientific documents, which contains 203,961 scientific articles and 130 classes from the arXiv category taxonomy. Code and data are available at https://github.com/sebischair/FusionSent.
The advent of large language models (LLMs) has initiated much research into their various financial applications. However, in applying LLMs on long documents, semantic relations are not explicitly incorporated, and a full or arbitrarily sparse attention operation is employed. In recent years, progress has been made in Abstract Meaning Representation (AMR), which is a graph-based representation of text to preserve its semantic relations. Since AMR can represent semantic relationships at a deeper level, it can be beneficially utilized by graph neural networks (GNNs) for constructing effective document-level graph representations built upon LLM embeddings to predict target metrics in the financial domain. We propose FLAG: Financial Long document classification via AMR-based GNN, an AMR graph based framework to generate document-level embeddings for long financial document classification. We construct document-level graphs from sentence-level AMR graphs, endow them with specialized LLM word embeddings in the financial domain, apply a deep learning mechanism that utilizes a GNN, and examine the efficacy of our AMR-based approach in predicting labeled target data from long financial documents. Extensive experiments are conducted on a dataset of quarterly earnings calls transcripts of companies in various sectors of the economy, as well as on a corpus of more recent earnings calls of companies in the S&P 1500 Composite Index. We find that our AMR-based approach outperforms fine-tuning LLMs directly on text in predicting stock price movement trends at different time horizons in both datasets. Our work also outperforms previous work utilizing document graphs and GNNs for text classification.
NLP datasets may still contain annotation errors, even when they are manually annotated. Researchers have attempted to develop methods to automatically reduce the adverse effect of errors in datasets. However, existing methods are time-consuming because they require many trained models to detect errors. This paper proposes a time-saving method that utilizes a tokenization technique called subword regularization to simulate multiple error detection models for detecting errors. Our proposed method, SubRegWeigh, can perform annotation weighting four to five times faster than the existing method. Additionally, SubRegWeigh improved performance in document classification and named entity recognition tasks. In experiments with pseudo-incorrect labels, SubRegWeigh clearly identifies pseudo-incorrect labels as annotation errors. Our code is available at https://github.com/4ldk/SubRegWeigh .
Detecting out-of-distribution (OOD) data is crucial in machine learning applications to mitigate the risk of model overconfidence, thereby enhancing the reliability and safety of deployed systems. The majority of existing OOD detection methods predominantly address uni-modal inputs, such as images or texts. In the context of multi-modal documents, there is a notable lack of extensive research on the performance of these methods, which have primarily been developed with a focus on computer vision tasks. We propose a novel methodology termed as attention head masking (AHM) for multi-modal OOD tasks in document classification systems. Our empirical results demonstrate that the proposed AHM method outperforms all state-of-the-art approaches and significantly decreases the false positive rate (FPR) compared to existing solutions up to 7.5\%. This methodology generalizes well to multi-modal data, such as documents, where visual and textual information are modeled under the same Transformer architecture. To address the scarcity of high-quality publicly available document datasets and encourage further research on OOD detection for documents, we introduce FinanceDocs, a new document AI dataset. Our code and dataset are publicly available.
Large semantic knowledge bases are grounded in factual knowledge. However, recent approaches to dense text representations (i.e. embeddings) do not efficiently exploit these resources. Dense and robust representations of documents are essential for effectively solving downstream classification and retrieval tasks. This work demonstrates that injecting embedded information from knowledge bases can augment the performance of contemporary Large Language Model (LLM)-based representations for the task of text classification. Further, by considering automated machine learning (AutoML) with the fused representation space, we demonstrate it is possible to improve classification accuracy even if we use low-dimensional projections of the original representation space obtained via efficient matrix factorization. This result shows that significantly faster classifiers can be achieved with minimal or no loss in predictive performance, as demonstrated using five strong LLM baselines on six diverse real-life datasets. The code is freely available at \url{https://github.com/bkolosk1/bablfusion.git}.
Clinical machine learning research and AI driven clinical decision support models rely on clinically accurate labels. Manually extracting these labels with the help of clinical specialists is often time-consuming and expensive. This study tests the feasibility of automatic span- and document-level diagnosis extraction from unstructured Dutch echocardiogram reports. We included 115,692 unstructured echocardiogram reports from the UMCU a large university hospital in the Netherlands. A randomly selected subset was manually annotated for the occurrence and severity of eleven commonly described cardiac characteristics. We developed and tested several automatic labelling techniques at both span and document levels, using weighted and macro F1-score, precision, and recall for performance evaluation. We compared the performance of span labelling against document labelling methods, which included both direct document classifiers and indirect document classifiers that rely on span classification results. The SpanCategorizer and MedRoBERTa$.$nl models outperformed all other span and document classifiers, respectively. The weighted F1-score varied between characteristics, ranging from 0.60 to 0.93 in SpanCategorizer and 0.96 to 0.98 in MedRoBERTa$.$nl. Direct document classification was superior to indirect document classification using span classifiers. SetFit achieved competitive document classification performance using only 10% of the training data. Utilizing a reduced label set yielded near-perfect document classification results. We recommend using our published SpanCategorizer and MedRoBERTa$.$nl models for span- and document-level diagnosis extraction from Dutch echocardiography reports. For settings with limited training data, SetFit may be a promising alternative for document classification.
The task of $\textit{keyword extraction}$ is often an important initial step in unsupervised information extraction, forming the basis for tasks such as topic modeling or document classification. While recent methods have proven to be quite effective in the extraction of keywords, the identification of $\textit{class-specific}$ keywords, or only those pertaining to a predefined class, remains challenging. In this work, we propose an improved method for class-specific keyword extraction, which builds upon the popular $\textbf{KeyBERT}$ library to identify only keywords related to a class described by $\textit{seed keywords}$. We test this method using a dataset of German business registry entries, where the goal is to classify each business according to an economic sector. Our results reveal that our method greatly improves upon previous approaches, setting a new standard for $\textit{class-specific}$ keyword extraction.
Scientific documents record research findings and valuable human knowledge, comprising a vast corpus of high-quality data. Leveraging multi-modality data extracted from these documents and assessing large models' abilities to handle scientific document-oriented tasks is therefore meaningful. Despite promising advancements, large models still perform poorly on multi-page scientific document extraction and understanding tasks, and their capacity to process within-document data formats such as charts and equations remains under-explored. To address these issues, we present DocGenome, a structured document benchmark constructed by annotating 500K scientific documents from 153 disciplines in the arXiv open-access community, using our custom auto-labeling pipeline. DocGenome features four key characteristics: 1) Completeness: It is the first dataset to structure data from all modalities including 13 layout attributes along with their LaTeX source codes. 2) Logicality: It provides 6 logical relationships between different entities within each scientific document. 3) Diversity: It covers various document-oriented tasks, including document classification, visual grounding, document layout detection, document transformation, open-ended single-page QA and multi-page QA. 4) Correctness: It undergoes rigorous quality control checks conducted by a specialized team. We conduct extensive experiments to demonstrate the advantages of DocGenome and objectively evaluate the performance of large models on our benchmark.
Lengthy documents pose a unique challenge to neural language models due to substantial memory consumption. While existing state-of-the-art (SOTA) models segment long texts into equal-length snippets (e.g., 128 tokens per snippet) or deploy sparse attention networks, these methods have new challenges of context fragmentation and generalizability due to sentence boundaries and varying text lengths. For example, our empirical analysis has shown that SOTA models consistently overfit one set of lengthy documents (e.g., 2000 tokens) while performing worse on texts with other lengths (e.g., 1000 or 4000). In this study, we propose a Length-Aware Multi-Kernel Transformer (LAMKIT) to address the new challenges for the long document classification. LAMKIT encodes lengthy documents by diverse transformer-based kernels for bridging context boundaries and vectorizes text length by the kernels to promote model robustness over varying document lengths. Experiments on five standard benchmarks from health and law domains show LAMKIT outperforms SOTA models up to an absolute 10.9% improvement. We conduct extensive ablation analyses to examine model robustness and effectiveness over varying document lengths.
Document understanding models have recently demonstrated remarkable performance by leveraging extensive collections of user documents. However, since documents often contain large amounts of personal data, their usage can pose a threat to user privacy and weaken the bonds of trust between humans and AI services. In response to these concerns, legislation advocating ``the right to be forgotten" has recently been proposed, allowing users to request the removal of private information from computer systems and neural network models. A novel approach, known as machine unlearning, has emerged to make AI models forget about a particular class of data. In our research, we explore machine unlearning for document classification problems, representing, to the best of our knowledge, the first investigation into this area. Specifically, we consider a realistic scenario where a remote server houses a well-trained model and possesses only a small portion of training data. This setup is designed for efficient forgetting manipulation. This work represents a pioneering step towards the development of machine unlearning methods aimed at addressing privacy concerns in document analysis applications. Our code is publicly available at \url{https://github.com/leitro/MachineUnlearning-DocClassification}.
The availability of text or topic classification datasets in the low-resource Marathi language is limited, typically consisting of fewer than 4 target labels, with some achieving nearly perfect accuracy. In this work, we introduce L3Cube-MahaNews, a Marathi text classification corpus that focuses on News headlines and articles. This corpus stands out as the largest supervised Marathi Corpus, containing over 1.05L records classified into a diverse range of 12 categories. To accommodate different document lengths, MahaNews comprises three supervised datasets specifically designed for short text, long documents, and medium paragraphs. The consistent labeling across these datasets facilitates document length-based analysis. We provide detailed data statistics and baseline results on these datasets using state-of-the-art pre-trained BERT models. We conduct a comparative analysis between monolingual and multilingual BERT models, including MahaBERT, IndicBERT, and MuRIL. The monolingual MahaBERT model outperforms all others on every dataset. These resources also serve as Marathi topic classification datasets or models and are publicly available at https://github.com/l3cube-pune/MarathiNLP .