Daniel E. Acuña

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, 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.

Tong Zeng, Daniel Acuna

Datasets are critical for scientific research, playing an important role in replication, reproducibility, and efficiency. Researchers have recently shown that datasets are becoming more important for science to function properly, even serving as artifacts of study themselves. However, citing datasets is not a common or standard practice in spite of recent efforts by data repositories and funding agencies. This greatly affects our ability to track their usage and importance. A potential solution to this problem is to automatically extract dataset mentions from scientific articles. In this work, we propose to achieve such extraction by using a neural network based on a Bi-LSTM-CRF architecture. Our method achieves F1 = 0.885 in social science articles released as part of the Rich Context Dataset. We discuss the limitations of the current datasets and propose modifications to the model to be done in the future.

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.

Titipat Achakulvisut, Chandra Bhagavatula, Daniel Acuna et al.

Claims are a fundamental unit of scientific discourse. The exponential growth in the number of scientific publications makes automatic claim extraction an important problem for researchers who are overwhelmed by this information overload. Such an automated claim extraction system is useful for both manual and programmatic exploration of scientific knowledge. In this paper, we introduce a new dataset of 1,500 scientific abstracts from the biomedical domain with expert annotations for each sentence indicating whether the sentence presents a scientific claim. We introduce a new model for claim extraction and compare it to several baseline models including rule-based and deep learning techniques. Moreover, we show that using a transfer learning approach with a fine-tuning step allows us to improve performance from a large discourse-annotated dataset. Our final model increases F1-score by over 14 percent points compared to a baseline model without transfer learning. We release a publicly accessible tool for discourse and claims prediction along with an annotation tool. We discuss further applications beyond biomedical literature.

Andrea Lancichinetti, M. Irmak Sirer, Jane X. Wang et al.

Much of human knowledge sits in large databases of unstructured text. Leveraging this knowledge requires algorithms that extract and record metadata on unstructured text documents. Assigning topics to documents will enable intelligent search, statistical characterization, and meaningful classification. Latent Dirichlet allocation (LDA) is the state-of-the-art in topic classification. Here, we perform a systematic theoretical and numerical analysis that demonstrates that current optimization techniques for LDA often yield results which are not accurate in inferring the most suitable model parameters. Adapting approaches for community detection in networks, we propose a new algorithm which displays high-reproducibility and high-accuracy, and also has high computational efficiency. We apply it to a large set of documents in the English Wikipedia and reveal its hierarchical structure. Our algorithm promises to make "big data" text analysis systems more reliable.