Shubham Agarwal

Shubham Agarwal, Thomas Searle, Mart Ratas et al.

Electronic Health Records are large repositories of valuable clinical data, with a significant portion stored in unstructured text format. This textual data includes clinical events (e.g., disorders, symptoms, findings, medications and procedures) in context that if extracted accurately at scale can unlock valuable downstream applications such as disease prediction. Using an existing Named Entity Recognition and Linking methodology, MedCAT, these identified concepts need to be further classified (contextualised) for their relevance to the patient, and their temporal and negated status for example, to be useful downstream. This study performs a comparative analysis of various natural language models for medical text classification. Extensive experimentation reveals the effectiveness of transformer-based language models, particularly BERT. When combined with class imbalance mitigation techniques, BERT outperforms Bi-LSTM models by up to 28% and the baseline BERT model by up to 16% for recall of the minority classes. The method has been implemented as part of CogStack/MedCAT framework and made available to the community for further research.

Audrey Cheng, Shu Liu, Melissa Pan et al.

Artificial Intelligence (AI) is beginning to transform the research process by automating the discovery of new solutions. This shift depends on the availability of reliable verifiers, which AI-driven approaches require to validate candidate solutions. Research focused on improving systems performance is especially well-suited to this paradigm because system performance problems naturally admit such verifiers: candidates can be implemented in real systems or simulators and evaluated against predefined workloads. We term this iterative cycle of generation, evaluation, and refinement AI-Driven Research for Systems (ADRS). Using several open-source ADRS instances (i.e., OpenEvolve, GEPA, and ShinkaEvolve), we demonstrate across ten case studies (e.g., multi-region cloud scheduling, mixture-of-experts load balancing, LLM-based SQL, transaction scheduling) that ADRS-generated solutions can match or even outperform human state-of-the-art designs. Based on these findings, we outline best practices (e.g., level of prompt specification, amount of feedback, robust evaluation) for effectively using ADRS, and we discuss future research directions and their implications. Although we do not yet have a universal recipe for applying ADRS across all of systems research, we hope our preliminary findings, together with the challenges we identify, offer meaningful guidance for future work as researcher effort shifts increasingly toward problem formulation and strategic oversight. Note: This paper is an extension of our prior work [14]. It adds extensive evaluation across multiple ADRS frameworks and provides deeper analysis and insights into best practices.

Shubham Agarwal, Gaurav Sahu, Abhay Puri et al.

Conducting literature reviews for scientific papers is essential for understanding research, its limitations, and building on existing work. It is a tedious task which makes an automatic literature review generator appealing. Unfortunately, many existing works that generate such reviews using Large Language Models (LLMs) have significant limitations. They tend to hallucinate-generate non-factual information-and ignore the latest research they have not been trained on. To address these limitations, we propose a toolkit that operates on Retrieval Augmented Generation (RAG) principles, specialized prompting and instructing techniques with the help of LLMs. Our system first initiates a web search to retrieve relevant papers by summarizing user-provided abstracts into keywords using an off-the-shelf LLM. Authors can enhance the search by supplementing it with relevant papers or keywords, contributing to a tailored retrieval process. Second, the system re-ranks the retrieved papers based on the user-provided abstract. Finally, the related work section is generated based on the re-ranked results and the abstract. There is a substantial reduction in time and effort for literature review compared to traditional methods, establishing our toolkit as an efficient alternative. Our project page including the demo and toolkit can be accessed here: https://litllm.github.io

Shubham Agarwal, Gaurav Sahu, Abhay Puri et al.

Literature reviews are an essential component of scientific research, but they remain time-intensive and challenging to write, especially due to the recent influx of research papers. This paper explores the zero-shot abilities of recent Large Language Models (LLMs) in assisting with the writing of literature reviews based on an abstract. We decompose the task into two components: 1. Retrieving related works given a query abstract, and 2. Writing a literature review based on the retrieved results. We analyze how effective LLMs are for both components. For retrieval, we introduce a novel two-step search strategy that first uses an LLM to extract meaningful keywords from the abstract of a paper and then retrieves potentially relevant papers by querying an external knowledge base. Additionally, we study a prompting-based re-ranking mechanism with attribution and show that re-ranking doubles the normalized recall compared to naive search methods, while providing insights into the LLM's decision-making process. In the generation phase, we propose a two-step approach that first outlines a plan for the review and then executes steps in the plan to generate the actual review. To evaluate different LLM-based literature review methods, we create test sets from arXiv papers using a protocol designed for rolling use with newly released LLMs to avoid test set contamination in zero-shot evaluations. We release this evaluation protocol to promote additional research and development in this regard. Our empirical results suggest that LLMs show promising potential for writing literature reviews when the task is decomposed into smaller components of retrieval and planning. Our project page including a demonstration system and toolkit can be accessed here: https://litllm.github.io.

Shubham Agarwal, Vlad Dinu, Thomas Searle et al.

This study introduces RelCAT (Relation Concept Annotation Toolkit), an interactive tool, library, and workflow designed to classify relations between entities extracted from clinical narratives. Building upon the CogStack MedCAT framework, RelCAT addresses the challenge of capturing complete clinical relations dispersed within text. The toolkit implements state-of-the-art machine learning models such as BERT and Llama along with proven evaluation and training methods. We demonstrate a dataset annotation tool (built within MedCATTrainer), model training, and evaluate our methodology on both openly available gold-standard and real-world UK National Health Service (NHS) hospital clinical datasets. We perform extensive experimentation and a comparative analysis of the various publicly available models with varied approaches selected for model fine-tuning. Finally, we achieve macro F1-scores of 0.977 on the gold-standard n2c2, surpassing the previous state-of-the-art performance, and achieve performance of >=0.93 F1 on our NHS gathered datasets.

Ishita Kumar, Snigdha Viswanathan, Sushrita Yerra et al.

Long-text generation is seemingly ubiquitous in real-world applications of large language models such as generating an email or writing a review. Despite the fundamental importance and prevalence of long-text generation in many practical applications, existing work on personalized generation has focused on the generation of very short text. To overcome these limitations, we study the problem of personalized long-text generation, that is, generating long-text that is personalized for a specific user while being practically useful for the vast majority of real-world applications that naturally require the generation of longer text. In this work, we demonstrate the importance of user-specific personalization for long-text generation tasks and develop the Long-text Language Model Personalization (LongLaMP) Benchmark. LongLaMP provides a comprehensive and diverse evaluation framework for personalized long-text generation. Extensive experiments on LongLaMP for zero-shot and fine-tuned language tasks demonstrate the effectiveness of the proposed benchmark and its utility for developing and evaluating techniques for personalized long-text generation across a wide variety of long-text generation tasks. The results highlight the importance of personalization across a wide variety of long-text generation tasks. Finally, we release the benchmark for others to use for this important problem.