arXiv subjects

Cemre Zor

Publications and source records attributed to Cemre Zor.

6 recordsLinked to original sources

arXiv2025

Pub-Guard-LLM: Detecting Retracted Biomedical Articles with Reliable Explanations

A significant and growing number of published scientific articles is found to involve fraudulent practices, posing a serious threat to the credibility and safety of research in fields such as medicine. We propose Pub-Guard-LLM, the first large language model-based system tailored to fraud detection of biomedical scientific articles. We provide three application modes for deploying Pub-Guard-LLM: vanilla reasoning, retrieval-augmented generation, and multi-agent debate. Each mode allows for textual explanations of predictions. To assess the performance of our system, we introduce an open-source benchmark, PubMed Retraction, comprising over 11K real-world biomedical articles, including metadata and retraction labels. We show that, across all modes, Pub-Guard-LLM consistently surpasses the performance of various baselines and provides more reliable explanations, namely explanations which are deemed more relevant and coherent than those generated by the baselines when evaluated by multiple assessment methods. By enhancing both detection performance and explainability in scientific fraud detection, Pub-Guard-LLM contributes to safeguarding research integrity with a novel, effective, open-source tool.

cs.CL↗

arXiv2021

Deep Convolutional Neural Network Ensembles using ECOC

Deep neural networks have enhanced the performance of decision making systems in many applications including image understanding, and further gains can be achieved by constructing ensembles. However, designing an ensemble of deep networks is often not very beneficial since the time needed to train the networks is very high or the performance gain obtained is not very significant. In this paper, we analyse error correcting output coding (ECOC) framework to be used as an ensemble technique for deep networks and propose different design strategies to address the accuracy-complexity trade-off. We carry out an extensive comparative study between the introduced ECOC designs and the state-of-the-art ensemble techniques such as ensemble averaging and gradient boosting decision trees. Furthermore, we propose a combinatory technique which is shown to achieve the highest classification performance amongst all.

cs.LG↗

arXiv2021

A unifying approach on bias and variance analysis for classification

Standard bias and variance (B&V) terminologies were originally defined for the regression setting and their extensions to classification have led to several different models / definitions in the literature. In this paper, we aim to provide the link between the commonly used frameworks of Tumer & Ghosh (T&G) and James. By unifying the two approaches, we relate the B&V defined for the 0/1 loss to the standard B&V of the boundary distributions given for the squared error loss. The closed form relationships provide a deeper understanding of classification performance, and their use is demonstrated in two case studies.

cs.LG↗

arXiv2019

ABCD Neurocognitive Prediction Challenge 2019: Predicting individual fluid intelligence scores from structural MRI using probabilistic segmentation and kernel ridge regression

We applied several regression and deep learning methods to predict fluid intelligence scores from T1-weighted MRI scans as part of the ABCD Neurocognitive Prediction Challenge (ABCD-NP-Challenge) 2019. We used voxel intensities and probabilistic tissue-type labels derived from these as features to train the models. The best predictive performance (lowest mean-squared error) came from Kernel Ridge Regression (KRR; $λ=10$), which produced a mean-squared error of 69.7204 on the validation set and 92.1298 on the test set. This placed our group in the fifth position on the validation leader board and first place on the final (test) leader board.

q-bio.NC↗

arXiv2019

ABCD Neurocognitive Prediction Challenge 2019: Predicting individual residual fluid intelligence scores from cortical grey matter morphology

We predicted residual fluid intelligence scores from T1-weighted MRI data available as part of the ABCD NP Challenge 2019, using morphological similarity of grey-matter regions across the cortex. Individual structural covariance networks (SCN) were abstracted into graph-theory metrics averaged over nodes across the brain and in data-driven communities/modules. Metrics included degree, path length, clustering coefficient, centrality, rich club coefficient, and small-worldness. These features derived from the training set were used to build various regression models for predicting residual fluid intelligence scores, with performance evaluated both using cross-validation within the training set and using the held-out validation set. Our predictions on the test set were generated with a support vector regression model trained on the training set. We found minimal improvement over predicting a zero residual fluid intelligence score across the sample population, implying that structural covariance networks calculated from T1-weighted MR imaging data provide little information about residual fluid intelligence.

q-bio.NC↗

arXiv2016

Delta divergence: A novel decision cognizant measure of classifier incongruence

Disagreement between two classifiers regarding the class membership of an observation in pattern recognition can be indicative of an anomaly and its nuance. As in general classifiers base their decision on class aposteriori probabilities, the most natural approach to detecting classifier incongruence is to use divergence. However, existing divergences are not particularly suitable to gauge classifier incongruence. In this paper, we postulate the properties that a divergence measure should satisfy and propose a novel divergence measure, referred to as Delta divergence. In contrast to existing measures, it is decision cognizant. The focus in Delta divergence on the dominant hypotheses has a clutter reducing property, the significance of which grows with increasing number of classes. The proposed measure satisfies other important properties such as symmetry, and independence of classifier confidence. The relationship of the proposed divergence to some baseline measures is demonstrated experimentally, showing its superiority.

cs.LG↗