Dimitrios Papadopoulos

Petros Stylianos Giouroukis, Dimitris Dimitriadis, Dimitrios Papadopoulos et al.

Slide decks, serving as digital reports that bridge the gap between presentation slides and written documents, are a prevalent medium for conveying information in both academic and corporate settings. Their multimodal nature, combining text, images, and charts, presents challenges for retrieval-augmented generation systems, where the quality of retrieval directly impacts downstream performance. Traditional approaches to slide retrieval often involve separate indexing of modalities, which can increase complexity and lose contextual information. This paper investigates various methodologies for effective slide retrieval, including visual late-interaction embedding models like ColPali, the use of visual rerankers, and hybrid retrieval techniques that combine dense retrieval with BM25, further enhanced by textual rerankers and fusion methods like Reciprocal Rank Fusion. A novel Vision-Language Models-based captioning pipeline is also evaluated, demonstrating significantly reduced embedding storage requirements compared to visual late-interaction techniques, alongside comparable retrieval performance. Our analysis extends to the practical aspects of these methods, evaluating their runtime performance and storage demands alongside retrieval efficacy, thus offering practical guidance for the selection and development of efficient and robust slide retrieval systems for real-world applications.

Bin Liu, Dimitrios Papadopoulos, Fragkiskos D. Malliaros et al.

The discovery of drug-target interactions (DTIs) is a very promising area of research with great potential. The accurate identification of reliable interactions among drugs and proteins via computational methods, which typically leverage heterogeneous information retrieved from diverse data sources, can boost the development of effective pharmaceuticals. Although random walk and matrix factorization techniques are widely used in DTI prediction, they have several limitations. Random walk-based embedding generation is usually conducted in an unsupervised manner, while the linear similarity combination in matrix factorization distorts individual insights offered by different views. To tackle these issues, we take a multi-layered network approach to handle diverse drug and target similarities, and propose a novel optimization framework, called Multiple similarity DeepWalk-based Matrix Factorization (MDMF), for DTI prediction. The framework unifies embedding generation and interaction prediction, learning vector representations of drugs and targets that not only retain higher-order proximity across all hyper-layers and layer-specific local invariance, but also approximate the interactions with their inner product. Furthermore, we develop an ensemble method (MDMF2A) that integrates two instantiations of the MDMF model, optimizing the area under the precision-recall curve (AUPR) and the area under the receiver operating characteristic curve (AUC) respectively. The empirical study on real-world DTI datasets shows that our method achieves statistically significant improvement over current state-of-the-art approaches in four different settings. Moreover, the validation of highly ranked non-interacting pairs also demonstrates the potential of MDMF2A to discover novel DTIs.