arXiv subjects

Ramakanth Kavuluru

Publications and source records attributed to Ramakanth Kavuluru.

At least 19 recordsLinked to original sources

arXiv2025

Large Language Models for Drug Overdose Prediction from Longitudinal Medical Records

The ability to predict drug overdose risk from a patient's medical records is crucial for timely intervention and prevention. Traditional machine learning models have shown promise in analyzing longitudinal medical records for this task. However, recent advancements in large language models (LLMs) offer an opportunity to enhance prediction performance by leveraging their ability to process long textual data and their inherent prior knowledge across diverse tasks. In this study, we assess the effectiveness of Open AI's GPT-4o LLM in predicting drug overdose events using patients' longitudinal insurance claims records. We evaluate its performance in both fine-tuned and zero-shot settings, comparing them to strong traditional machine learning methods as baselines. Our results show that LLMs not only outperform traditional models in certain settings but can also predict overdose risk in a zero-shot setting without task-specific training. These findings highlight the potential of LLMs in clinical decision support, particularly for drug overdose risk prediction.

cs.AI↗

arXiv2025

A Benchmark for End-to-End Zero-Shot Biomedical Relation Extraction with LLMs: Experiments with OpenAI Models

Extracting relations from scientific literature is a fundamental task in biomedical NLP because entities and relations among them drive hypothesis generation and knowledge discovery. As literature grows rapidly, relation extraction (RE) is indispensable to curate knowledge graphs to be used as computable structured and symbolic representations. With the rise of LLMs, it is pertinent to examine if it is better to skip tailoring supervised RE methods, save annotation burden, and just use zero shot RE (ZSRE) via LLM API calls. In this paper, we propose a benchmark with seven biomedical RE datasets with interesting characteristics and evaluate three Open AI models (GPT-4, o1, and GPT-OSS-120B) for end-to-end ZSRE. We show that LLM-based ZSRE is inching closer to supervised methods in performances on some datasets but still struggles on complex inputs expressing multiple relations with different predicates. Our error analysis reveals scope for improvements.

cs.CL↗

arXiv2025

Do LLMs Surpass Encoders for Biomedical NER?

Recognizing spans of biomedical concepts and their types (e.g., drug or gene) in free text, often called biomedical named entity recognition (NER), is a basic component of information extraction (IE) pipelines. Without a strong NER component, other applications, such as knowledge discovery and information retrieval, are not practical. State-of-the-art in NER shifted from traditional ML models to deep neural networks with transformer-based encoder models (e.g., BERT) emerging as the current standard. However, decoder models (also called large language models or LLMs) are gaining traction in IE. But LLM-driven NER often ignores positional information due to the generative nature of decoder models. Furthermore, they are computationally very expensive (both in inference time and hardware needs). Hence, it is worth exploring if they actually excel at biomedical NER and assess any associated trade-offs (performance vs efficiency). This is exactly what we do in this effort employing the same BIO entity tagging scheme (that retains positional information) using five different datasets with varying proportions of longer entities. Our results show that the LLMs chosen (Mistral and Llama: 8B range) often outperform best encoder models (BERT-(un)cased, BiomedBERT, and DeBERTav3: 300M range) by 2-8% in F-scores except for one dataset, where they equal encoder performance. This gain is more prominent among longer entities of length >= 3 tokens. However, LLMs are one to two orders of magnitude more expensive at inference time and may need cost prohibitive hardware. Thus, when performance differences are small or real time user feedback is needed, encoder models might still be more suitable than LLMs.

cs.CL↗

arXiv2025

Relation Extraction with Instance-Adapted Predicate Descriptions

Relation extraction (RE) is a standard information extraction task playing a major role in downstream applications such as knowledge discovery and question answering. Although decoder-only large language models are excelling in generative tasks, smaller encoder models are still the go to architecture for RE. In this paper, we revisit fine-tuning such smaller models using a novel dual-encoder architecture with a joint contrastive and cross-entropy loss. Unlike previous methods that employ a fixed linear layer for predicate representations, our approach uses a second encoder to compute instance-specific predicate representations by infusing them with real entity spans from corresponding input instances. We conducted experiments on two biomedical RE datasets and two general domain datasets. Our approach achieved F1 score improvements ranging from 1% to 2% over state-of-the-art methods with a simple but elegant formulation. Ablation studies justify the importance of various components built into the proposed architecture.

cs.CL↗

arXiv2024

Clinical Reading Comprehension with Encoder-Decoder Models Enhanced by Direct Preference Optimization

Extractive question answering over clinical text is a crucial need to help deal with the deluge of clinical text generated in hospitals. While encoder models (e.g., BERT) have been popular for this reading comprehension task, recently encoder-decoder models (e.g., T5) are on the rise. There is also the emergence of preference optimization techniques to align decoder-only LLMs with human preferences. In this paper, we combine encoder-decoder models with the direct preference optimization (DPO) method to improve over prior state of the art for the RadQA radiology question answering task by 12-15 F1 points. To the best of our knowledge, this effort is the first to show that DPO method also works for reading comprehension via novel heuristics to generate preference data without human inputs.

cs.IR↗

arXiv2024

Knowledge-Driven Cross-Document Relation Extraction

Relation extraction (RE) is a well-known NLP application often treated as a sentence- or document-level task. However, a handful of recent efforts explore it across documents or in the cross-document setting (CrossDocRE). This is distinct from the single document case because different documents often focus on disparate themes, while text within a document tends to have a single goal. Linking findings from disparate documents to identify new relationships is at the core of the popular literature-based knowledge discovery paradigm in biomedicine and other domains. Current CrossDocRE efforts do not consider domain knowledge, which are often assumed to be known to the reader when documents are authored. Here, we propose a novel approach, KXDocRE, that embed domain knowledge of entities with input text for cross-document RE. Our proposed framework has three main benefits over baselines: 1) it incorporates domain knowledge of entities along with documents' text; 2) it offers interpretability by producing explanatory text for predicted relations between entities 3) it improves performance over the prior methods.

cs.CL↗

arXiv2024

How Important is Domain Specificity in Language Models and Instruction Finetuning for Biomedical Relation Extraction?

Cutting edge techniques developed in the general NLP domain are often subsequently applied to the high-value, data-rich biomedical domain. The past few years have seen generative language models (LMs), instruction finetuning, and few-shot learning become foci of NLP research. As such, generative LMs pretrained on biomedical corpora have proliferated and biomedical instruction finetuning has been attempted as well, all with the hope that domain specificity improves performance on downstream tasks. Given the nontrivial effort in training such models, we investigate what, if any, benefits they have in the key biomedical NLP task of relation extraction. Specifically, we address two questions: (1) Do LMs trained on biomedical corpora outperform those trained on general domain corpora? (2) Do models instruction finetuned on biomedical datasets outperform those finetuned on assorted datasets or those simply pretrained? We tackle these questions using existing LMs, testing across four datasets. In a surprising result, general-domain models typically outperformed biomedical-domain models. However, biomedical instruction finetuning improved performance to a similar degree as general instruction finetuning, despite having orders of magnitude fewer instructions. Our findings suggest it may be more fruitful to focus research effort on larger-scale biomedical instruction finetuning of general LMs over building domain-specific biomedical LMs

cs.CL↗

arXiv2024

Revisiting Document-Level Relation Extraction with Context-Guided Link Prediction

Document-level relation extraction (DocRE) poses the challenge of identifying relationships between entities within a document as opposed to the traditional RE setting where a single sentence is input. Existing approaches rely on logical reasoning or contextual cues from entities. This paper reframes document-level RE as link prediction over a knowledge graph with distinct benefits: 1) Our approach combines entity context with document-derived logical reasoning, enhancing link prediction quality. 2) Predicted links between entities offer interpretability, elucidating employed reasoning. We evaluate our approach on three benchmark datasets: DocRED, ReDocRED, and DWIE. The results indicate that our proposed method outperforms the state-of-the-art models and suggests that incorporating context-based link prediction techniques can enhance the performance of document-level relation extraction models.

cs.IR↗

arXiv2023

Comparison of pipeline, sequence-to-sequence, and GPT models for end-to-end relation extraction: experiments with the rare disease use-case

End-to-end relation extraction (E2ERE) is an important and realistic application of natural language processing (NLP) in biomedicine. In this paper, we aim to compare three prevailing paradigms for E2ERE using a complex dataset focused on rare diseases involving discontinuous and nested entities. We use the RareDis information extraction dataset to evaluate three competing approaches (for E2ERE): NER $\rightarrow$ RE pipelines, joint sequence to sequence models, and generative pre-trained transformer (GPT) models. We use comparable state-of-the-art models and best practices for each of these approaches and conduct error analyses to assess their failure modes. Our findings reveal that pipeline models are still the best, while sequence-to-sequence models are not far behind; GPT models with eight times as many parameters are worse than even sequence-to-sequence models and lose to pipeline models by over 10 F1 points. Partial matches and discontinuous entities caused many NER errors contributing to lower overall E2E performances. We also verify these findings on a second E2ERE dataset for chemical-protein interactions. Although generative LM-based methods are more suitable for zero-shot settings, when training data is available, our results show that it is better to work with more conventional models trained and tailored for E2ERE. More innovative methods are needed to marry the best of the both worlds from smaller encoder-decoder pipeline models and the larger GPT models to improve E2ERE. As of now, we see that well designed pipeline models offer substantial performance gains at a lower cost and carbon footprint for E2ERE. Our contribution is also the first to conduct E2ERE for the RareDis dataset.

cs.CL↗

arXiv2023

End-to-End Models for Chemical-Protein Interaction Extraction: Better Tokenization and Span-Based Pipeline Strategies

End-to-end relation extraction (E2ERE) is an important task in information extraction, more so for biomedicine as scientific literature continues to grow exponentially. E2ERE typically involves identifying entities (or named entity recognition (NER)) and associated relations, while most RE tasks simply assume that the entities are provided upfront and end up performing relation classification. E2ERE is inherently more difficult than RE alone given the potential snowball effect of errors from NER leading to more errors in RE. A complex dataset in biomedical E2ERE is the ChemProt dataset (BioCreative VI, 2017) that identifies relations between chemical compounds and genes/proteins in scientific literature. ChemProt is included in all recent biomedical natural language processing benchmarks including BLUE, BLURB, and BigBio. However, its treatment in these benchmarks and in other separate efforts is typically not end-to-end, with few exceptions. In this effort, we employ a span-based pipeline approach to produce a new state-of-the-art E2ERE performance on the ChemProt dataset, resulting in $> 4\%$ improvement in F1-score over the prior best effort. Our results indicate that a straightforward fine-grained tokenization scheme helps span-based approaches excel in E2ERE, especially with regards to handling complex named entities. Our error analysis also identifies a few key failure modes in E2ERE for ChemProt.

cs.CL↗

arXiv2023

End-to-End $n$-ary Relation Extraction for Combination Drug Therapies

Combination drug therapies are treatment regimens that involve two or more drugs, administered more commonly for patients with cancer, HIV, malaria, or tuberculosis. Currently there are over 350K articles in PubMed that use the "combination drug therapy" MeSH heading with at least 10K articles published per year over the past two decades. Extracting combination therapies from scientific literature inherently constitutes an $n$-ary relation extraction problem. Unlike in the general $n$-ary setting where $n$ is fixed (e.g., drug-gene-mutation relations where $n=3$), extracting combination therapies is a special setting where $n \geq 2$ is dynamic, depending on each instance. Recently, Tiktinsky et al. (NAACL 2022) introduced a first of its kind dataset, CombDrugExt, for extracting such therapies from literature. Here, we use a sequence-to-sequence style end-to-end extraction method to achieve an F1-Score of $66.7\%$ on the CombDrugExt test set for positive (or effective) combinations. This is an absolute $\approx 5\%$ F1-score improvement even over the prior best relation classification score with spotted drug entities (hence, not end-to-end). Thus our effort introduces a state-of-the-art first model for end-to-end extraction that is already superior to the best prior non end-to-end model for this task. Our model seamlessly extracts all drug entities and relations in a single pass and is highly suitable for dynamic $n$-ary extraction scenarios.

cs.CL↗

arXiv2023

COVID-19 event extraction from Twitter via extractive question answering with continuous prompts

As COVID-19 ravages the world, social media analytics could augment traditional surveys in assessing how the pandemic evolves and capturing consumer chatter that could help healthcare agencies in addressing it. This typically involves mining disclosure events that mention testing positive for the disease or discussions surrounding perceptions and beliefs in preventative or treatment options. The 2020 shared task on COVID-19 event extraction (conducted as part of the W-NUT workshop during the EMNLP conference) introduced a new Twitter dataset for benchmarking event extraction from COVID-19 tweets. In this paper, we cast the problem of event extraction as extractive question answering using recent advances in continuous prompting in language models. On the shared task test dataset, our approach leads to over 5% absolute micro-averaged F1-score improvement over prior best results, across all COVID-19 event slots. Our ablation study shows that continuous prompts have a major impact on the eventual performance.

cs.CL↗

arXiv2022

Deep neural networks for fine-grained surveillance of overdose mortality

Surveillance of drug overdose deaths relies on death certificates for identification of the substances that caused death. Drugs and drug classes can be identified through the International Classification of Diseases, 10th Revision (ICD-10) codes present on death certificates. However, ICD-10 codes do not always provide high levels of specificity in drug identification. To achieve more fine-grained identification of substances on a death certificate, the free-text cause of death section, completed by the medical certifier, must be analyzed. Current methods for analyzing free-text death certificates rely solely on look-up tables for identifying specific substances, which must be frequently updated and maintained. To improve identification of drugs on death certificates, a deep learning named-entity recognition model was developed, which achieved an F1-score of 99.13%. This model can identify new drug misspellings and novel substances that are not present on current surveillance look-up tables, enhancing the surveillance of drug overdose deaths.

cs.CL↗

arXiv2022

An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C)

While we pay attention to the latest advances in clinical natural language processing (NLP), we can notice some resistance in the clinical and translational research community to adopt NLP models due to limited transparency, interpretability, and usability. In this study, we proposed an open natural language processing development framework. We evaluated it through the implementation of NLP algorithms for the National COVID Cohort Collaborative (N3C). Based on the interests in information extraction from COVID-19 related clinical notes, our work includes 1) an open data annotation process using COVID-19 signs and symptoms as the use case, 2) a community-driven ruleset composing platform, and 3) a synthetic text data generation workflow to generate texts for information extraction tasks without involving human subjects. The corpora were derived from texts from three different institutions (Mayo Clinic, University of Kentucky, University of Minnesota). The gold standard annotations were tested with a single institution's (Mayo) ruleset. This resulted in performances of 0.876, 0.706, and 0.694 in F-scores for Mayo, Minnesota, and Kentucky test datasets, respectively. The study as a consortium effort of the N3C NLP subgroup demonstrates the feasibility of creating a federated NLP algorithm development and benchmarking platform to enhance multi-institution clinical NLP study and adoption. Although we use COVID-19 as a use case in this effort, our framework is general enough to be applied to other domains of interest in clinical NLP.

cs.CL↗

arXiv2021

Contrastive Cross-Modal Pre-Training: A General Strategy for Small Sample Medical Imaging

A key challenge in training neural networks for a given medical imaging task is often the difficulty of obtaining a sufficient number of manually labeled examples. In contrast, textual imaging reports, which are often readily available in medical records, contain rich but unstructured interpretations written by experts as part of standard clinical practice. We propose using these textual reports as a form of weak supervision to improve the image interpretation performance of a neural network without requiring additional manually labeled examples. We use an image-text matching task to train a feature extractor and then fine-tune it in a transfer learning setting for a supervised task using a small labeled dataset. The end result is a neural network that automatically interprets imagery without requiring textual reports during inference. This approach can be applied to any task for which text-image pairs are readily available. We evaluate our method on three classification tasks and find consistent performance improvements, reducing the need for labeled data by 67%-98%.

cs.LG↗

arXiv2021

Improved Biomedical Word Embeddings in the Transformer Era

Biomedical word embeddings are usually pre-trained on free text corpora with neural methods that capture local and global distributional properties. They are leveraged in downstream tasks using various neural architectures that are designed to optimize task-specific objectives that might further tune such embeddings. Since 2018, however, there is a marked shift from these static embeddings to contextual embeddings motivated by language models (e.g., ELMo, transformers such as BERT, and ULMFiT). These dynamic embeddings have the added benefit of being able to distinguish homonyms and acronyms given their context. However, static embeddings are still relevant in low resource settings (e.g., smart devices, IoT elements) and to study lexical semantics from a computational linguistics perspective. In this paper, we jointly learn word and concept embeddings by first using the skip-gram method and further fine-tuning them with correlational information manifesting in co-occurring Medical Subject Heading (MeSH) concepts in biomedical citations. This fine-tuning is accomplished with the BERT transformer architecture in the two-sentence input mode with a classification objective that captures MeSH pair co-occurrence. In essence, we repurpose a transformer architecture (typically used to generate dynamic embeddings) to improve static embeddings using concept correlations. We conduct evaluations of these tuned static embeddings using multiple datasets for word relatedness developed by previous efforts. Without selectively culling concepts and terms (as was pursued by previous efforts), we believe we offer the most exhaustive evaluation of static embeddings to date with clear performance improvements across the board. We provide our code and embeddings for public use for downstream applications and research endeavors: https://github.com/bionlproc/BERT-CRel-Embeddings

cs.CL↗

arXiv2021

Predicting Opioid Use Disorder from Longitudinal Healthcare Data using Multi-stream Transformer

Opioid Use Disorder (OUD) is a public health crisis costing the US billions of dollars annually in healthcare, lost workplace productivity, and crime. Analyzing longitudinal healthcare data is critical in addressing many real-world problems in healthcare. Leveraging the real-world longitudinal healthcare data, we propose a novel multi-stream transformer model called MUPOD for OUD identification. MUPOD is designed to simultaneously analyze multiple types of healthcare data streams, such as medications and diagnoses, by attending to segments within and across these data streams. Our model tested on the data from 392,492 patients with long-term back pain problems showed significantly better performance than the traditional models and recently developed deep learning models.

cs.LG↗

arXiv2020

Literature Retrieval for Precision Medicine with Neural Matching and Faceted Summarization

Information retrieval (IR) for precision medicine (PM) often involves looking for multiple pieces of evidence that characterize a patient case. This typically includes at least the name of a condition and a genetic variation that applies to the patient. Other factors such as demographic attributes, comorbidities, and social determinants may also be pertinent. As such, the retrieval problem is often formulated as ad hoc search but with multiple facets (e.g., disease, mutation) that may need to be incorporated. In this paper, we present a document reranking approach that combines neural query-document matching and text summarization toward such retrieval scenarios. Our architecture builds on the basic BERT model with three specific components for reranking: (a). document-query matching (b). keyword extraction and (c). facet-conditioned abstractive summarization. The outcomes of (b) and (c) are used to essentially transform a candidate document into a concise summary that can be compared with the query at hand to compute a relevance score. Component (a) directly generates a matching score of a candidate document for a query. The full architecture benefits from the complementary potential of document-query matching and the novel document transformation approach based on summarization along PM facets. Evaluations using NIST's TREC-PM track datasets (2017--2019) show that our model achieves state-of-the-art performance. To foster reproducibility, our code is made available here: https://github.com/bionlproc/text-summ-for-doc-retrieval.

cs.CL↗