Aleksandra Karolak

Dr. Aleksandra Karolak

orcid

Research Focus & Metrics

Academic Career Length

25Years (2002-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

View All Publications
8 September 2023 in Oncogene
Verified
Journal Article
Closed access
PDF file
Issam El NaqaIssam El Naqa
Issam El Naqa
AKAleksandra Karolak
Aleksandra Karolak
YLYi Luo
Yi Luo
LFLes Folio
Les Folio
ATAhmad A. Tarhini
Ahmad A. Tarhini
KPKatia Parodi
Katia Parodi

17 June 2024 in Cancers
Verified
Journal Article
Open access
PDF file
AMAshwin Mukund
Ashwin Mukund
MAMuhammad Ali Afridi
Muhammad Ali Afridi
AKAleksandra Karolak
Aleksandra Karolak
MPMargaret A. Park
Margaret A. Park
JPJennifer Permuth
Jennifer Permuth
Ghulam RasoolGhulam Rasool
Ghulam Rasool
Pancreatic Ductal Adenocarcinoma (PDAC) remains one of the most formidable challenges in oncology, characterized by its late detection and poor prognosis. Artificial intelligence (AI) and machine learning (ML) are emerging as pivotal tools in revolutionizing PDAC care across various dimensions. Consequently, many studies have focused on using AI to improve the standard of PDAC care. This review article attempts to consolidate the literature from the past five years to identify high-impact, novel, and meaningful studies focusing on their transformative potential in PDAC management. Our analysis spans a broad spectrum of applications, including but not limited to patient risk stratification, early detection, and prediction of treatment outcomes, thereby highlighting AI’s potential role in enhancing the quality and precision of PDAC care. By categorizing the literature into discrete sections reflective of a patient’s journey from screening and diagnosis through treatment and survivorship, this review offers a comprehensive examination of AI-driven methodologies in addressing the multifaceted challenges of PDAC. Each study is summarized by explaining the dataset, ML model, evaluation metrics, and impact the study has on improving PDAC-related outcomes. We also discuss prevailing obstacles and limitations inherent in the application of AI within the PDAC context, offering insightful perspectives on potential future directions and innovations.

20 February 2021 in Trends in Cancer
Verified
Journal Article
Open access
AKAleksandra Karolak
Aleksandra Karolak
SBSergio Branciamore
Sergio Branciamore
JMJeannine S. McCune
Jeannine S. McCune
PLPeter P. Lee
Peter P. Lee
ARAndrei Rodin
Andrei Rodin
RRRussell Rockne
Russell Rockne
Recent successes of immune-modulating therapies for cancer have stimulated research on information flow within the immune system and, in turn, clinical applications of concepts from information theory. Through information theory, one can describe and formalize, in a mathematically rigorous fashion, the function of interconnected components of the immune system in health and disease. Specifically, using concepts including entropy, mutual information, and channel capacity, one can quantify the storage, transmission, encoding, and flow of information within and between cellular components of the immune system on multiple temporal and spatial scales. To understand, at the quantitative level, immune signaling function and dysfunction in cancer, we present a methodology-oriented review of information-theoretic treatment of biochemical signal transduction and transmission coupled with mathematical modeling.

14 October 2016
Verified
Book Chapter
Closed access
PDF file
Judith Pérez-VelázquezJudith Pérez-Velázquez
Judith Pérez-Velázquez
JGJana Gevertz
Jana Gevertz
AKAleksandra Karolak
Aleksandra Karolak
Katarzyna RejniakKatarzyna Rejniak
Katarzyna Rejniak

30 January 2025 in Biophysical Journal
Verified
Journal Article
Open access
TNTrieu Nguyen
Trieu Nguyen
AKAleksandra Karolak
Aleksandra Karolak
In the field of drug discovery, the generation of new molecules with desirable properties remains a critical challenge. Traditional methods often rely on SMILES (Simplified Molecular Input Line Entry System) representations for molecular input data, which can limit the diversity and novelty of generated molecules. To address this, we present the Transformer Graph Variational Autoencoder (TGVAE), an innovative AI model that employs molecular graphs as input data, thus captures the complex structural relationships within molecules more effectively than string models. To enhance molecular generation capabilities, TGVAE combines a Transformer, Graph Neural Network (GNN), and Variational Autoencoder (VAE). Additionally, we address common issues like over-smoothing in training GNNs and posterior collapse in VAE to ensure robust training and improve the generation of chemically valid and diverse molecular structures. Our results demonstrate that TGVAE outperforms existing approaches, generating a larger collection of diverse molecules and discovering structures that were previously unexplored. This advancement not only brings more possibilities for drug discovery but also sets a new level for the use of AI in molecular generation.

8 February 2018 in Bulletin of Mathematical Biology
Verified
Journal Article
Closed access
PDF file
AKAleksandra Karolak
Aleksandra Karolak
Katarzyna RejniakKatarzyna Rejniak
Katarzyna Rejniak