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  • AI models are using material from retracted scientific papers Ananya
    Some AI chatbots rely on flawed research from retracted scientific papers to answer questions, according to recent studies. The findings, confirmed by MIT Technology Review, raise questions about how reliable AI tools are at evaluating scientific research and could complicate efforts by countries and industries seeking to invest in AI tools for scientists. AI search tools and chatbots are already known to fabricate links and references. But answers based on the material from actual papers can
     

AI models are using material from retracted scientific papers

By: Ananya
23 September 2025 at 17:00

Some AI chatbots rely on flawed research from retracted scientific papers to answer questions, according to recent studies. The findings, confirmed by MIT Technology Review, raise questions about how reliable AI tools are at evaluating scientific research and could complicate efforts by countries and industries seeking to invest in AI tools for scientists.

AI search tools and chatbots are already known to fabricate links and references. But answers based on the material from actual papers can mislead as well if those papers have been retracted. The chatbot is “using a real paper, real material, to tell you something,” says Weikuan Gu, a medical researcher at the University of Tennessee in Memphis and an author of one of the recent studies. But, he says, if people only look at the content of the answer and do not click through to the paper and see that it’s been retracted, that’s really a problem. 

Gu and his team asked OpenAI’s ChatGPT, running on the GPT-4o model, questions based on information from 21 retracted papers about medical imaging. The chatbot’s answers referenced retracted papers in five cases but advised caution in only three. While it cited non-retracted papers for other questions, the authors note that it may not have recognized the retraction status of the articles. In a study from August, a different group of researchers used ChatGPT-4o mini to evaluate the quality of 217 retracted and low-quality papers from different scientific fields; they found that none of the chatbot’s responses mentioned retractions or other concerns. (No similar studies have been released on GPT-5, which came out in August.)

The public uses AI chatbots to ask for medical advice and diagnose health conditions. Students and scientists increasingly use science-focused AI tools to review existing scientific literature and summarize papers. That kind of usage is likely to increase. The US National Science Foundation, for instance, invested $75 million in building AI models for science research this August.

“If [a tool is] facing the general public, then using retraction as a kind of quality indicator is very important,” says Yuanxi Fu, an information science researcher at the University of Illinois Urbana-Champaign. There’s “kind of an agreement that retracted papers have been struck off the record of science,” she says, “and the people who are outside of science—they should be warned that these are retracted papers.” OpenAI did not provide a response to a request for comment about the paper results.

The problem is not limited to ChatGPT. In June, MIT Technology Review tested AI tools specifically advertised for research work, such as Elicit, Ai2 ScholarQA (now part of the Allen Institute for Artificial Intelligence’s Asta tool), Perplexity, and Consensus, using questions based on the 21 retracted papers in Gu’s study. Elicit referenced five of the retracted papers in its answers, while Ai2 ScholarQA referenced 17, Perplexity 11, and Consensus 18—all without noting the retractions.

Some companies have since made moves to correct the issue. “Until recently, we didn’t have great retraction data in our search engine,” says Christian Salem, cofounder of Consensus. His company has now started using retraction data from a combination of sources, including publishers and data aggregators, independent web crawling, and Retraction Watch, which manually curates and maintains a database of retractions. In a test of the same papers in August, Consensus cited only five retracted papers. 

Elicit told MIT Technology Review that it removes retracted papers flagged by the scholarly research catalogue OpenAlex from its database and is “still working on aggregating sources of retractions.” Ai2 told us that its tool does not automatically detect or remove retracted papers currently. Perplexity said that it “[does] not ever claim to be 100% accurate.” 

However, relying on retraction databases may not be enough. Ivan Oransky, the cofounder of Retraction Watch, is careful not to describe it as a comprehensive database, saying that creating one would require more resources than anyone has: “The reason it’s resource intensive is because someone has to do it all by hand if you want it to be accurate.”

Further complicating the matter is that publishers don’t share a uniform approach to retraction notices. “Where things are retracted, they can be marked as such in very different ways,” says Caitlin Bakker from University of Regina, Canada, an expert in research and discovery tools. “Correction,” “expression of concern,” “erratum,” and “retracted” are among some labels publishers may add to research papers—and these labels can be added for many reasons, including concerns about the content, methodology, and data or the presence of conflicts of interest. 

Some researchers distribute their papers on preprint servers, paper repositories, and other websites, causing copies to be scattered around the web. Moreover, the data used to train AI models may not be up to date. If a paper is retracted after the model’s training cutoff date, its responses might not instantaneously reflect what’s going on, says Fu. Most academic search engines don’t do a real-time check against retraction data, so you are at the mercy of how accurate their corpus is, says Aaron Tay, a librarian at Singapore Management University.

Oransky and other experts advocate making more context available for models to use when creating a response. This could mean publishing information that already exists, like peer reviews commissioned by journals and critiques from the review site PubPeer, alongside the published paper.  

Many publishers, such as Nature and the BMJ, publish retraction notices as separate articles linked to the paper, outside paywalls. Fu says companies need to effectively make use of such information, as well as any news articles in a model’s training data that mention a paper’s retraction. 

The users and creators of AI tools need to do their due diligence. “We are at the very, very early stages, and essentially you have to be skeptical,” says Tay.

Ananya is a freelance science and technology journalist based in Bengaluru, India.

Deciphering the Heterogeneity of Pancreatic Cancer: DNA Methylation-Based Cell Type Deconvolution Unveils Distinct Subgroups and Immune Landscapes

Epigenomes. 2025 Sep 5;9(3):34. doi: 10.3390/epigenomes9030034.

ABSTRACT

Background: Pancreatic ductal adenocarcinoma (PDAC) is a highly heterogeneous malignancy, characterized by low tumor cellularity, a dense stromal response, and intricate cellular and molecular interactions within the tumor microenvironment (TME). Although bulk omics technologies have enhanced our understanding of the molecular landscape of PDAC, the specific contributions of non-malignant immune and stromal components to tumor progression and therapeutic response remain poorly understood. Methods: We explored genome-wide DNA methylation and transcriptomic data from the Cancer Genome Atlas Pancreatic Adenocarcinoma cohort (TCGA-PAAD) to profile the immune composition of the TME and uncover gene co-expression networks. Bioinformatic analyses included DNA methylation profiling followed by hierarchical deconvolution, epigenetic age estimation, and a weighted gene co-expression network analysis (WGCNA). Results: The unsupervised clustering of methylation profiles identified two major tumor groups, with Group 2 (n = 98) exhibiting higher tumor purity and a greater frequency of KRAS mutations compared to Group 1 (n = 87) (p < 0.0001). The hierarchical deconvolution of DNA methylation data revealed three distinct TME subtypes, termed hypo-inflamed (immune-deserted), myeloid-enriched, and lymphoid-enriched (notably T-cell predominant). These immune clusters were further supported by co-expression modules identified via WGCNA, which were enriched in immune regulatory and signaling pathways. Conclusions: This integrative epigenomic-transcriptomic analysis offers a robust framework for stratifying PDAC patients based on the tumor immune microenvironment (TIME), providing valuable insights for biomarker discovery and the development of precision immunotherapies.

PMID:40981070 | PMC:PMC12452622 | DOI:10.3390/epigenomes9030034

Cancer in a drop: Liquid biopsy highlights from the American Society of Clinical Oncology (ASCO) 2025 annual congress

J Liq Biopsy. 2025 Aug 6;9:100320. doi: 10.1016/j.jlb.2025.100320. eCollection 2025 Sep.

ABSTRACT

Over the past decade, liquid biopsy has progressively expanded its role in oncology, supported by mounting evidence demonstrating an increasing number of clinical applications. At the 2025 American Society of Clinical Oncology (ASCO) Annual Meeting, liquid biopsy emerged as a central theme across multiple sessions, with more than 700 abstracts, investigating the clinical utility of liquid biopsy across a wide range of tumor types and disease stages. Applications presented included cancer screening, minimal residual disease (MRD) detection, management of metastatic disease, and potential use for matching patients to clinical trials. This editorial, authored on the behalf of the Young Committee of the International Society of Liquid Biopsy (ISLB) highlights the result of selected studies, grouped by tumor type.

PMID:40980343 | PMC:PMC12447415 | DOI:10.1016/j.jlb.2025.100320

Cell-free DNA fragmentomics: a universal framework for early cancer detection and monitoring

22 September 2025 at 18:00

Am J Clin Exp Immunol. 2025 Aug 15;14(4):237-240. doi: 10.62347/EBRY4326. eCollection 2025.

ABSTRACT

Cell-free DNA (cfDNA) fragmentomics has emerged as a powerful and noninvasive approach for cancer detection, characterization, and monitoring. By analyzing genome-wide fragmentation patterns - including fragment length distributions, end motifs, nucleosome footprints, and copy number variations - cfDNA fragmentomics provides high-resolution insights into tumor-specific biological signals even at low tumor burden. This technology offers advantages over conventional mutation-based assays by capturing aggregate structural and epigenomic alterations without requiring prior knowledge of driver mutations. In non-small cell lung cancer (NSCLC), cfDNA fragmentomics enables early detection, discrimination of malignant pulmonary nodules, and post-surgical monitoring of minimal residual disease. Recent studies have demonstrated that fragmentomic risk scores can accurately stratify recurrence risk and improve prognostic sensitivity beyond traditional genomic assays. In hepatocellular carcinoma (HCC), integration of fragment size selection, CNV profiling, and end-motif analysis has led to high-performing models for early diagnosis, particularly in high-risk populations. Moreover, cfDNA fragmentomics has proven effective in detecting malignant transformation in patients with neurofibromatosis-associated peripheral nerve sheath tumors, distinguishing benign from premalignant or malignant lesions with high precision. Expanding beyond these major cancers, fragmentomic approaches have demonstrated diagnostic potential in gastric, urological, hematologic, and pediatric malignancies. Notably, the DELFI-TF (DNA Evaluation of Fragments for early Interception-Tumor Fraction) framework has shown prognostic relevance by correlating pre-treatment cfDNA features with survival outcomes in colorectal and lung cancer patients, outperforming conventional imaging. All of these results highlight the translational importance of cfDNA fragmentomics as a cutting-edge precision oncology tool. Its continued integration into clinical workflows may redefine early cancer detection, facilitate subtype-specific interventions, and enable real-time, individualized treatment monitoring.

PMID:40977920 | PMC:PMC12444407 | DOI:10.62347/EBRY4326

Circulating tumor DNA in patients with cancer: insights from clinical laboratory

Adv Lab Med. 2025 Jun 16;6(3):259-276. doi: 10.1515/almed-2025-0010. eCollection 2025 Sep.

ABSTRACT

Blood-based circulating tumor DNA (ctDNA) analysis has emerged as a highly relevant non-invasive method for molecular profiling of solid tumors, offering valuable information about the genetic landscape of cancer. Somatic mutation analysis of ctDNA is now used clinically to guide targeted therapies for advanced cancers. Recent advancements have also revealed its potential in early detection, prognosis, minimal residual disease assessment, and prediction/monitoring of therapeutic response. In recent years, significant progress has been made with the development of various PCR and NGS-based methods designed for assessing gene variants in ctDNA of patients with cancer. However, despite the transformative possibilities that ctDNA analysis presents, challenges persist. Standardization of preanalytical and analytical protocols, assay sensitivity, and the interpretation of results remain critical hurdles that need to be addressed for the widespread clinical implementation of ctDNA testing. In addition to somatic mutations, emerging studies on DNA methylation (epigenomics) and fragment size patterns (fragmentomics) in several types of biological fluids are yielding promising results as non-invasive biomarkers for effective cancer management. This review addresses the clinical applications of somatic gene variants in ctDNA, emphasizes their potential as cancer biomarkers, and highlights essential factors for successful implementation in clinical laboratories and cancer management.

PMID:40977813 | PMC:PMC12446922 | DOI:10.1515/almed-2025-0010

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