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Paul Denny

Paul Denny contributes to research discovery and scholarly infrastructure.

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Published work

4 published item(s)

preprint2026arXiv

RLearner-LLM: Balancing Logical Grounding and Fluency in Large Language Models via Hybrid Direct Preference Optimization

Direct Preference Optimization (DPO), the efficient alternative to PPO-based RLHF, falls short on knowledge-intensive generation: standard preference signals from human annotators or LLM judges exhibit a systematic verbosity bias that rewards fluency over logical correctness. This blindspot leaves a logical alignment gap -- SFT models reach NLI entailment of only 0.05-0.22 despite producing fluent text. We propose RLearner-LLM with Hybrid-DPO: an automated preference pipeline that fuses a DeBERTa-v3 NLI signal with a verifier LLM score, removing human annotation while overcoming the "alignment tax" of single-signal optimization. Evaluated across five academic domains (Biology, Medicine, Law) with three base architectures (LLaMA-2-13B, Qwen3-8B, Gemma 4 E4B-it), RLearner-LLM yields up to 6x NLI improvement over SFT, with NLI gains in 11 of 15 cells and consistent answer-coverage gains. On Gemma 4 E4B-it (4.5B effective params), Hybrid-DPO lifts NLI in four of five domains (+11.9% to +2.4x) with faster inference across all five, scaling down to compact base models without losing the alignment-tax mitigation. Our Qwen3-8B RLearner-LLM wins 95% of pairwise comparisons against its own SFT baseline; GPT-4o-mini in turn wins 95% against our concise output -- alongside the 69% win the same judge gives a verbose SFT over our DPO model, this replicates verbosity bias on a frontier comparator and motivates logic-aware metrics (NLI, ACR) over LLM-as-a-judge for knowledge-intensive generation.

preprint2023arXiv

Many bioinformatics programming tasks can be automated with ChatGPT

Computer programming is a fundamental tool for life scientists, allowing them to carry out many essential research tasks. However, despite a variety of educational efforts, learning to write code can be a challenging endeavor for both researchers and students in life science disciplines. Recent advances in artificial intelligence have made it possible to translate human-language prompts to functional code, raising questions about whether these technologies can aid (or replace) life scientists' efforts to write code. Using 184 programming exercises from an introductory-bioinformatics course, we evaluated the extent to which one such model -- OpenAI's ChatGPT -- can successfully complete basic- to moderate-level programming tasks. On its first attempt, ChatGPT solved 139 (75.5%) of the exercises. For the remaining exercises, we provided natural-language feedback to the model, prompting it to try different approaches. Within 7 or fewer attempts, ChatGPT solved 179 (97.3%) of the exercises. These findings have important implications for life-sciences research and education. For many programming tasks, researchers no longer need to write code from scratch. Instead, machine-learning models may produce usable solutions. Instructors may need to adapt their pedagogical approaches and assessment techniques to account for these new capabilities that are available to the general public.

preprint2023arXiv

Patterns of Student Help-Seeking When Using a Large Language Model-Powered Programming Assistant

Providing personalized assistance at scale is a long-standing challenge for computing educators, but a new generation of tools powered by large language models (LLMs) offers immense promise. Such tools can, in theory, provide on-demand help in large class settings and be configured with appropriate guardrails to prevent misuse and mitigate common concerns around learner over-reliance. However, the deployment of LLM-powered tools in authentic classroom settings is still rare, and very little is currently known about how students will use them in practice and what type of help they will seek. To address this, we examine students' use of an innovative LLM-powered tool that provides on-demand programming assistance without revealing solutions directly. We deployed the tool for 12 weeks in an introductory computer and data science course ($n = 52$), collecting more than 2,500 queries submitted by students throughout the term. We manually categorized all student queries based on the type of assistance sought, and we automatically analyzed several additional query characteristics. We found that most queries requested immediate help with programming assignments, whereas fewer requests asked for help on related concepts or for deepening conceptual understanding. Furthermore, students often provided minimal information to the tool, suggesting this is an area in which targeted instruction would be beneficial. We also found that students who achieved more success in the course tended to have used the tool more frequently overall. Lessons from this research can be leveraged by programming educators and institutions who plan to augment their teaching with emerging LLM-powered tools.

preprint2022arXiv

Automatic Generation of Programming Exercises and Code Explanations using Large Language Models

This article explores the natural language generation capabilities of large language models with application to the production of two types of learning resources common in programming courses. Using OpenAI Codex as the large language model, we create programming exercises (including sample solutions and test cases) and code explanations, assessing these qualitatively and quantitatively. Our results suggest that the majority of the automatically generated content is both novel and sensible, and in some cases ready to use as is. When creating exercises we find that it is remarkably easy to influence both the programming concepts and the contextual themes they contain, simply by supplying keywords as input to the model. Our analysis suggests that there is significant value in massive generative machine learning models as a tool for instructors, although there remains a need for some oversight to ensure the quality of the generated content before it is delivered to students. We further discuss the implications of OpenAI Codex and similar tools for introductory programming education and highlight future research streams that have the potential to improve the quality of the educational experience for both teachers and students alike.