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Carrie Wright

Publications and source records attributed to Carrie Wright.

5 recordsLinked to original sources

PanCanBench: A Comprehensive Benchmark for Evaluating Large Language Models in Pancreatic Oncology

Large language models (LLMs) have achieved expert-level performance on standardized examinations, yet multiple-choice accuracy poorly reflects real-world clinical utility and safety. As patients and clinicians increasingly use LLMs for guidance on complex conditions such as pancreatic cancer, evaluation must extend beyond general medical knowledge. Existing frameworks, such as HealthBench, rely on simulated queries and lack disease-specific depth. Moreover, high rubric-based scores do not ensure factual correctness, underscoring the need to assess hallucinations. We developed a human-in-the-loop pipeline to create expert rubrics for de-identified patient questions from the Pancreatic Cancer Action Network (PanCAN). The resulting benchmark, PanCanBench, includes 3,130 question-specific criteria across 282 authentic patient questions. We evaluated 22 proprietary and open-source LLMs using an LLM-as-a-judge framework, measuring clinical completeness, factual accuracy, and web-search integration. Models showed substantial variation in rubric-based completeness, with scores ranging from 46.5% to 82.3%. Factual errors were common, with hallucination rates (the percentages of responses containing at least one factual error) ranging from 6.0% for Gemini-2.5 Pro and GPT-4o to 53.8% for Llama-3.1-8B. Importantly, newer reasoning-optimized models did not consistently improve factuality: although o3 achieved the highest rubric score, it produced inaccuracies more frequently than other GPT-family models. Web-search integration did not inherently guarantee better responses. The average score changed from 66.8% to 63.9% for Gemini-2.5 Pro and from 73.8% to 72.8% for GPT-5 when web search was enabled. Synthetic AI-generated rubrics inflated absolute scores by 17.9 points on average while generally maintaining similar relative ranking.

cs.CL

Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?

Software is vital for the advancement of biology and medicine. Analysis of usage and impact metrics can help developers determine user and community engagement, justify additional funding, encourage additional use, identify unanticipated use cases, and help define improvement areas. However, there are challenges associated with these analyses including distorted or misleading metrics, as well as ethical and security concerns. More attention to the nuances involved in capturing impact across the spectrum of biological software is needed. Furthermore, some tools may be especially beneficial to a small audience, yet may not have compelling typical usage metrics. We propose more general guidelines, as well as strategies for more specific types of software. We highlight outstanding issues regarding how communities measure or evaluate software impact. To get a deeper understanding of current practices for software evaluations, we performed a survey of participants in the Informatics Technology for Cancer Research (ITCR) program funded by the National Cancer Institute (NCI). We also investigated software among this community and others to assess how often infrastructure that supports such evaluations is implemented and how this impacts rates of papers describing usage of the software. We find that developers recognize the utility of analyzing software usage, but struggle to find the time or funding for such analyses. We also find that infrastructure such as social media presence, more in-depth documentation, the presence of software health metrics, and clear information on how to contact developers seem to be associated with increased usage rates. Our findings can help scientific software developers make the most out of evaluations of their software.

cs.SE

Motivation, inclusivity, and realism should drive data science education

Data science education provides tremendous opportunities but remains inaccessible to many communities. Increasing the accessibility of data science to these communities not only benefits the individuals entering data science, but also increases the field's innovation and potential impact as a whole. Education is the most scalable solution to meet these needs, but many data science educators lack formal training in education. Our group has led education efforts for a variety of audiences: from professional scientists to high school students to lay audiences. These experiences have helped form our teaching philosophy which we have summarized into three main ideals: 1) motivation, 2) inclusivity, and 3) realism. To put these ideals better into practice, we also aim to iteratively update our teaching approaches and curriculum as we find ways to better reach these ideals. In this manuscript we discuss these ideals as well practical ideas for how to implement these philosophies in the classroom.

cs.CY

Open Case Studies: Statistics and Data Science Education through Real-World Applications

With unprecedented and growing interest in data science education, there are limited educator materials that provide meaningful opportunities for learners to practice statistical thinking, as defined by Wild and Pfannkuch (1999), with messy data addressing real-world challenges. As a solution, Nolan and Speed (1999) advocated for bringing applications to the forefront in undergraduate statistics curriculum with the use of in-depth case studies to encourage and develop statistical thinking in the classroom. Limitations to this approach include the significant time investment required to develop a case study -- namely, to select a motivating question and to create an illustrative data analysis -- and the domain expertise needed. As a result, case studies based on realistic challenges, not toy examples, are scarce. To address this, we developed the Open Case Studies (https://www.opencasestudies.org) project, which offers a new statistical and data science education case study model. This educational resource provides self-contained, multimodal, peer-reviewed, and open-source guides (or case studies) from real-world examples for active experiences of complete data analyses. We developed an educator's guide describing how to most effectively use the case studies, how to modify and adapt components of the case studies in the classroom, and how to contribute new case studies. (https://www.opencasestudies.org/OCS_Guide).

stat.AP

Open-source Tools for Training Resources -- OTTR

Data science and informatics tools are developing at a blistering rate, but their users often lack the educational background or resources to efficiently apply the methods to their research. Training resources often deprecate because their maintenance is not prioritized by funding, giving teams little time to devote to such endeavors. Our group has developed Open-source Tools for Training Resources (OTTR) to offer greater efficiency and flexibility for creating and maintaining online course content. OTTR empowers creators to customize their work and allows for a simple workflow to publish using multiple platforms. OTTR allows content creators to publish material to multiple massive online learner communities using familiar rendering mechanics. OTTR allows the incorporation of pedagogical practices like formative and summative assessments in the form of multiple choice questions and fill in the blank problems that are automatically graded. No local installation of any software is required to begin creating content with OTTR. Thus far, 15 courses have been created with OTTR repository template. By using the OTTR system, the maintenance workload for updating these courses across platforms has been drastically reduced.

cs.CY