Daniel E. Acuna

Almene De Meran Meguimtsop, Maria Leonor Pacheco, Daniel E. Acuna

Large language models (LLMs) are increasingly used to support scientific work, but it is unclear whether they uphold responsible conduct of research (RCR) norms or help undermine them. We introduce SciIntBench, an adversarial benchmark of 810 prompts across ten RCR categories and three scientific domains. Each scenario appears as an Overt Adversarial, Covert Adversarial, and Benign version, allowing us to jointly measure framing-sensitive refusal of misconduct and helpfulness on legitimate requests. We evaluate 16 commercial and open-weight LLMs from six providers (2024--2026), producing 12,960 responses. We find that scientific integrity alignment is strongly framing-sensitive: models refuse explicit misconduct far more reliably than covert violations, especially failing when misconduct is presented as a pressure-driven shortcut. Refusals vary by RCR category, with weaker boundaries around transparency, plagiarism, and fabrication.

Chao Zhou, Cheng Qiu, Lizhen Liang et al.

The rapid progress of Natural Language Processing (NLP) technologies has led to the widespread availability and effectiveness of text generation tools such as ChatGPT and Claude. While highly useful, these technologies also pose significant risks to the credibility of various media forms if they are employed for paraphrased plagiarism -- one of the most subtle forms of content misuse in scientific literature and general text media. Although automated methods for paraphrase identification have been developed, detecting this type of plagiarism remains challenging due to the inconsistent nature of the datasets used to train these methods. In this article, we examine traditional and contemporary approaches to paraphrase identification, investigating how the under-representation of certain paraphrase types in popular datasets, including those used to train Large Language Models (LLMs), affects the ability to detect plagiarism. We introduce and validate a new refined typology for paraphrases (ReParaphrased, REfined PARAPHRASE typology definitions) to better understand the disparities in paraphrase type representation. Lastly, we propose new directions for future research and dataset development to enhance AI-based paraphrase detection.

Daniel E. Acuna, Kartik Nagre, Priya Matnani

Finding relevant scientific articles is crucial for advancing knowledge. Recommendation systems are helpful for such purpose, although they have only been applied to science recently. This article describes EILEEN (Exploratory Innovator of LitEraturE Networks), a recommendation system for scientific publications and grants with open source code and datasets. We describe EILEEN's architecture for ingesting and processing documents and modeling the recommendation system and keyphrase estimator. Using a unique dataset of log-in user behavior, we validate our recommendation system against Latent Semantic Analysis (LSA) and the standard ranking from Elasticsearch (Lucene scoring). We find that a learning-to-rank with Random Forest achieves an AUC of 0.9, significantly outperforming both baselines. Our results suggest that we can substantially improve science recommendations and learn about scientists' behavior through their search behavior. We make our system available through eileen.io

Titipat Achakulvisut, Daniel E. Acuna, Tulakan Ruangrong et al.

Finding relevant publications is important for scientists who have to cope with exponentially increasing numbers of scholarly material. Algorithms can help with this task as they help for music, movie, and product recommendations. However, we know little about the performance of these algorithms with scholarly material. Here, we develop an algorithm, and an accompanying Python library, that implements a recommendation system based on the content of articles. Design principles are to adapt to new content, provide near-real time suggestions, and be open source. We tested the library on 15K posters from the Society of Neuroscience Conference 2015. Human curated topics are used to cross validate parameters in the algorithm and produce a similarity metric that maximally correlates with human judgments. We show that our algorithm significantly outperformed suggestions based on keywords. The work presented here promises to make the exploration of scholarly material faster and more accurate.

Tong Zeng, Daniel E. Acuna

Scientist learn early on how to cite scientific sources to support their claims. Sometimes, however, scientists have challenges determining where a citation should be situated -- or, even worse, fail to cite a source altogether. Automatically detecting sentences that need a citation (i.e., citation worthiness) could solve both of these issues, leading to more robust and well-constructed scientific arguments. Previous researchers have applied machine learning to this task but have used small datasets and models that do not take advantage of recent algorithmic developments such as attention mechanisms in deep learning. We hypothesize that we can develop significantly accurate deep learning architectures that learn from large supervised datasets constructed from open access publications. In this work, we propose a Bidirectional Long Short-Term Memory (BiLSTM) network with attention mechanism and contextual information to detect sentences that need citations. We also produce a new, large dataset (PMOA-CITE) based on PubMed Open Access Subset, which is orders of magnitude larger than previous datasets. Our experiments show that our architecture achieves state of the art performance on the standard ACL-ARC dataset ($F_{1}=0.507$) and exhibits high performance ($F_{1}=0.856$) on the new PMOA-CITE. Moreover, we show that it can transfer learning across these datasets. We further use interpretable models to illuminate how specific language is used to promote and inhibit citations. We discover that sections and surrounding sentences are crucial for our improved predictions. We further examined purported mispredictions of the model, and uncovered systematic human mistakes in citation behavior and source data. This opens the door for our model to check documents during pre-submission and pre-archival procedures. We make this new dataset, the code, and a web-based tool available to the community.

Tong Zeng, Daniel E. Acuna

Obtaining funding is an important part of becoming a successful scientist. Junior faculty spend a great deal of time finding the right agencies and programs that best match their research profile. But what are the factors that influence the best publication--grant matching? Some universities might employ pre-award personnel to understand these factors, but not all institutions can afford to hire them. Historical records of publications funded by grants can help us understand the matching process and also help us develop recommendation systems to automate it. In this work, we present \textsc{GotFunding} (Grant recOmmendaTion based on past FUNDING), a recommendation system trained on National Institutes of Health's (NIH) grant--publication records. Our system achieves a high performance (NDCG@1 = 0.945) by casting the problem as learning to rank. By analyzing the features that make predictions effective, our results show that the ranking considers most important 1) the year difference between publication and grant grant, 2) the amount of information provided in the publication, and 3) the relevance of the publication to the grant. We discuss future improvements of the system and an online tool for scientists to try.

Lizhen Liang, Han Zhuang, James Zou et al.

Artificial intelligence (AI) has seen fast paced development in industry and academia. However, striking recent advances by industry have stunned the field, inviting a fresh perspective on the role of academic research on this progress. Here, we characterize the impact and type of AI produced by both environments over the last 25 years and establish several patterns. We find that articles published by teams consisting exclusively of industry researchers tend to get greater attention, with a higher chance of being highly cited and citation-disruptive, and several times more likely to produce state-of-the-art models. In contrast, we find that exclusively academic teams publish the bulk of AI research and tend to produce higher novelty work, with single papers having several times higher likelihood of being unconventional and atypical. The respective impact-novelty advantages of industry and academia are robust to controls for subfield, team size, seniority, and prestige. We find that academic-industry collaborations produce the most impactful work overall but do not have the novelty level of academic teams. Together, our findings identify the unique and nearly irreplaceable contributions that both academia and industry make toward the progress of AI.

Pawin Taechoyotin, Daniel E. Acuna

Most automated peer review systems rely on textual manuscript content alone, leaving visual elements such as figures and external scholarly signals underutilized. We introduce REM-CTX, a reinforcement-learning system that incorporates auxiliary context into the review generation process via correspondence-aware reward functions. REM-CTX trains an 8B-parameter language model with Group Relative Policy Optimization (GRPO) and combines a multi-aspect quality reward with two correspondence rewards that explicitly encourage alignment with auxiliary context. Experiments on manuscripts across Computer, Biological, and Physical Sciences show that REM-CTX achieves the highest overall review quality among six baselines, outperforming other systems with substantially larger commercial models, and surpassing the next-best RL baseline across both quality and contextual grounding metrics. Ablation studies confirm that the two correspondence rewards are complementary: each selectively improves its targeted correspondence reward while preserving all quality dimensions, and the full model outperforms all partial variants. Analysis of training dynamics reveals that the criticism aspect is negatively correlated with other metrics during training, suggesting that future studies should group multi-dimension rewards for review generation.

Daniel E. Acuna, Ziyue Xiang

When there is a suspicious figure reuse case in science, research integrity investigators often find it difficult to rebut authors claiming that "it happened by chance". In other words, when there is a "collision" of image features, it is difficult to justify whether it appears rarely or not. In this article, we provide a method to predict the rarity of an image feature by statistically estimating the chance of it randomly occurring across all scientific imagery. Our method is based on high-dimensional density estimation of ORB features using 7+ million images in the PubMed Open Access Subset dataset. We show that this method can lead to meaningful feedback during research integrity investigations by providing a null hypothesis for scientific image reuse and thus a p-value during deliberations. We apply the model to a sample of increasingly complex imagery and confirm that it produces decreasingly smaller p-values as expected. We discuss applications to research integrity investigations as well as future work.

Ziyue Xiang, Daniel E. Acuna

Scientific image tampering is a problem that affects not only authors but also the general perception of the research community. Although previous researchers have developed methods to identify tampering in natural images, these methods may not thrive under the scientific setting as scientific images have different statistics, format, quality, and intentions. Therefore, we propose a scientific-image specific tampering detection method based on noise inconsistencies, which is capable of learning and generalizing to different fields of science. We train and test our method on a new dataset of manipulated western blot and microscopy imagery, which aims at emulating problematic images in science. The test results show that our method can detect various types of image manipulation in different scenarios robustly, and it outperforms existing general-purpose image tampering detection schemes. We discuss applications beyond these two types of images and suggest next steps for making detection of problematic images a systematic step in peer review and science in general.

Tong Zeng, Longfeng Wu, Sarah Bratt et al.

A citation is a well-established mechanism for connecting scientific artifacts. Citation networks are used by citation analysis for a variety of reasons, prominently to give credit to scientists' work. However, because of current citation practices, scientists tend to cite only publications, leaving out other types of artifacts such as datasets. Datasets then do not get appropriate credit even though they are increasingly reused and experimented with. We develop a network flow measure, called DataRank, aimed at solving this gap. DataRank assigns a relative value to each node in the network based on how citations flow through the graph, differentiating publication and dataset flow rates. We evaluate the quality of DataRank by estimating its accuracy at predicting the usage of real datasets: web visits to GenBank and downloads of Figshare datasets. We show that DataRank is better at predicting this usage compared to alternatives while offering additional interpretable outcomes. We discuss improvements to citation behavior and algorithms to properly track and assign credit to datasets.

Lizhen Liang, Daniel E. Acuna

Detecting biases in artificial intelligence has become difficult because of the impenetrable nature of deep learning. The central difficulty is in relating unobservable phenomena deep inside models with observable, outside quantities that we can measure from inputs and outputs. For example, can we detect gendered perceptions of occupations (e.g., female librarian, male electrician) using questions to and answers from a word embedding-based system? Current techniques for detecting biases are often customized for a task, dataset, or method, affecting their generalization. In this work, we draw from Psychophysics in Experimental Psychology---meant to relate quantities from the real world (i.e., "Physics") into subjective measures in the mind (i.e., "Psyche")---to propose an intellectually coherent and generalizable framework to detect biases in AI. Specifically, we adapt the two-alternative forced choice task (2AFC) to estimate potential biases and the strength of those biases in black-box models. We successfully reproduce previously-known biased perceptions in word embeddings and sentiment analysis predictions. We discuss how concepts in experimental psychology can be naturally applied to understanding artificial mental phenomena, and how psychophysics can form a useful methodological foundation to study fairness in AI.