Aditya Lahiri
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View article: Targeting colorectal cancer liver metastasis through repurposing metabolic and immune inhibitors: A theoretical study
Targeting colorectal cancer liver metastasis through repurposing metabolic and immune inhibitors: A theoretical study Open
Liver metastasis from colorectal cancer is a major cause of death in patients with advanced colorectal cancer (CRC) and remains a difficult challenge in oncology. In spite of commendable developments in medical inventions, the complexity a…
View article: Benchmarking transformer embedding models for biomedical terminology standardization
Benchmarking transformer embedding models for biomedical terminology standardization Open
View article: Targeting Colorectal Cancer Liver Metastasis Through Repurposing Metabolic and Immune Inhibitors : A Theoretical Study
Targeting Colorectal Cancer Liver Metastasis Through Repurposing Metabolic and Immune Inhibitors : A Theoretical Study Open
Liver metastasis from colorectal cancer is a major cause of death in patients with advanced colorectal cancer (CRC) and remains a difficult challenge in oncology. Inspite of commnedable developments in medical inventions, the complexity an…
View article: The Open Pediatric Cancer Project
The Open Pediatric Cancer Project Open
Background In 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we present…
View article: Integrating Immunotherapy With Targeted Therapy: Evaluating Efficacy in NSCLC Treatment Through Computational Analysis of Gene Regulatory Networks
Integrating Immunotherapy With Targeted Therapy: Evaluating Efficacy in NSCLC Treatment Through Computational Analysis of Gene Regulatory Networks Open
Non-Small Cell Lung Cancer (NSCLC) remains a leading cause of cancer-related deaths, often characterized by complex mutational landscapes and resistance to monotherapies. To address this, we developed a novel Boolean network (BN) model tha…
View article: Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data
Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data Open
Over the past decade, there has been substantial growth in both the quantity and complexity of available biomedical data. In order to more efficiently harness this extensive data and alleviate challenges associated with integration of mult…
View article: Characterization of aberrant splicing in pediatric central nervous system tumors reveals <i>CLK1</i> as a candidate oncogenic dependency
Characterization of aberrant splicing in pediatric central nervous system tumors reveals <i>CLK1</i> as a candidate oncogenic dependency Open
Background Pediatric brain cancer is the leading cause of disease-related mortality in children, yet many aggressive tumors lack effective therapies. Aberrant RNA splicing is a hallmark of cancer, but its role in pediatric central nervous …
View article: The Open Pediatric Cancer Project
The Open Pediatric Cancer Project Open
Background In 2019, the Open Pediatric Brain Tumor Atlas (OpenPBTA) was created as a global, collaborative open-science initiative to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Here, we present…
View article: Enforcing Conditional Independence for Fair Representation Learning and Causal Image Generation
Enforcing Conditional Independence for Fair Representation Learning and Causal Image Generation Open
Conditional independence (CI) constraints are critical for defining and evaluating fairness in machine learning, as well as for learning unconfounded or causal representations. Traditional methods for ensuring fairness either blindly learn…
View article: A Computational Study of Efficient Combinations of FDA-approved drugs and dietary supplements in Endometrial Cancer
A Computational Study of Efficient Combinations of FDA-approved drugs and dietary supplements in Endometrial Cancer Open
Endometrial cancer (EC) develops in the uterine lining, and in 2024, there will be approximately 67,880 reported cases of uterine cancer in the USA, with 90% of them being EC. Many unfit or elderly cancer patients are unable to undergo sta…
View article: HGG-21. ABERRANT SPLICING OF CLK1 IN PEDIATRIC HIGH-GRADE GLIOMAS DISRUPTS KEY ONCOGENIC TRANSCRIPTIONAL PROGRAMS
HGG-21. ABERRANT SPLICING OF CLK1 IN PEDIATRIC HIGH-GRADE GLIOMAS DISRUPTS KEY ONCOGENIC TRANSCRIPTIONAL PROGRAMS Open
While the majority of somatic DNA coding alterations in pediatric brain tumors have been profiled, studies exploring transcriptional mechanisms remain underexplored. We systematically characterized aberrant splicing in primary tumors of se…
View article: Deterministic Algorithmic Approaches to Solve Generalised Wordle
Deterministic Algorithmic Approaches to Solve Generalised Wordle Open
Wordle is a single-player word-based game where the objective is to guess the 5-letter word in a maximum of 6 tries. The game was released to the public in October 2021 and has since gained popularity with people competing against each oth…
View article: Drug Target Identification in Triple Negative Breast Cancer Stem Cell Pathways: a computational study of gene regulatory pathways using Boolean networks
Drug Target Identification in Triple Negative Breast Cancer Stem Cell Pathways: a computational study of gene regulatory pathways using Boolean networks Open
Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer associated with an early age of onset, greater propensity towards metastasis, and poorer clinical outcomes. It accounts for 10% to 20% of newly diagnosed breast ca…
View article: Drug Target Identification in Triple Negative Breast Cancer Stem Cell Pathways: A Computational Study of Gene Regulatory Pathways Using Boolean Networks
Drug Target Identification in Triple Negative Breast Cancer Stem Cell Pathways: A Computational Study of Gene Regulatory Pathways Using Boolean Networks Open
Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer associated with an early age of onset, greater propensity towards metastasis, and poorer clinical outcomes. It accounts for 10% to 20% of newly diagnosed breast ca…
View article: Combining Counterfactuals With Shapley Values To Explain Image Models
Combining Counterfactuals With Shapley Values To Explain Image Models Open
With the widespread use of sophisticated machine learning models in sensitive applications, understanding their decision-making has become an essential task. Models trained on tabular data have witnessed significant progress in explanation…
View article: Explaining Image Classifiers Using Contrastive Counterfactuals in Generative Latent Spaces
Explaining Image Classifiers Using Contrastive Counterfactuals in Generative Latent Spaces Open
Despite their high accuracies, modern complex image classifiers cannot be trusted for sensitive tasks due to their unknown decision-making process and potential biases. Counterfactual explanations are very effective in providing transparen…
View article: Predicting Airbnb Rental Prices Using Multiple Feature Modalities
Predicting Airbnb Rental Prices Using Multiple Feature Modalities Open
Figuring out the price of a listed Airbnb rental is an important and difficult task for both the host and the customer. For the former, it can enable them to set a reasonable price without compromising on their profits. For the customer, i…
View article: GiulioRossetti/ndlib:
GiulioRossetti/ndlib: Open
Minor bugfixes
View article: Detecting drought regulators using stochastic inference in Bayesian networks
Detecting drought regulators using stochastic inference in Bayesian networks Open
Drought is a natural hazard that affects crops by inducing water stress. Water stress, induced by drought accounts for more loss in crop yield than all the other causes combined. With the increasing frequency and intensity of droughts worl…
View article: Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice
Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice Open
Lysine is the first limiting essential amino acid in rice because it is present in the lowest quantity compared to all the other amino acids. Amino acids are the building block of proteins and play an essential role in maintaining the huma…
View article: Detecting Drought Regulators using Stochastic Inference in Bayesian Networks
Detecting Drought Regulators using Stochastic Inference in Bayesian Networks Open
Drought is a natural hazard that affects crops by inducing water stress. Water stress, induced by drought, accounts for more loss in crop yield than all the other causes combined. With the increasing frequency and intensity of droughts wor…
View article: Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice
Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice Open
Lysine is the first limiting essential amino acid in rice because it is present in the lowest quantity compared to all the other amino acids. Amino acids are the building block of proteins and play an essential role in maintaining the huma…
View article: Detecting Drought Regulators using Stochastic Inference in Bayesian Networks
Detecting Drought Regulators using Stochastic Inference in Bayesian Networks Open
Background: Drought is a natural hazard that affects crops by inducing water stress. Water stress, induced by drought, accounts for more loss in crop yield than all the other causes combined. With the increasing frequency and intensity of …
View article: Bayesian modeling of plant drought resistance pathway
Bayesian modeling of plant drought resistance pathway Open
Our analysis revealed that activating the transcription factor WRKY18 had the highest likelihood of inducing drought response among all the other elements of the WRKY transcription factor network. Our observation was also supported by biol…
View article: Additional file 4 of Bayesian modeling of plant drought resistance pathway
Additional file 4 of Bayesian modeling of plant drought resistance pathway Open
R code to normalize the data. (R 1 kb)
View article: Additional file 7 of Bayesian modeling of plant drought resistance pathway
Additional file 7 of Bayesian modeling of plant drought resistance pathway Open
R code to generate synthetic data. (R 1 kb)
View article: Additional file 9 of Bayesian modeling of plant drought resistance pathway
Additional file 9 of Bayesian modeling of plant drought resistance pathway Open
Excel file containing the data used from dataset GSE65046 to support the conclusion of this article.The complete dataset can be publicly accessed online from NCBI GEO database with the accession number of GSE65046. (XLSX 10.1 kb)
View article: Additional file 3 of Bayesian modeling of plant drought resistance pathway
Additional file 3 of Bayesian modeling of plant drought resistance pathway Open
R code for finding MLE. (R 1.06 kb)
View article: Additional file 8 of Bayesian modeling of plant drought resistance pathway
Additional file 8 of Bayesian modeling of plant drought resistance pathway Open
Excel file containing the data used from dataset GSE46365 to support the conclusion of this article.The complete dataset can be publicly accessed online from NCBI GEO database with the accession number of GSE46365. (XLSX 9.89 kb)
View article: Additional file 5 of Bayesian modeling of plant drought resistance pathway
Additional file 5 of Bayesian modeling of plant drought resistance pathway Open
R code to calculate shape parameters of Beta distribution. (R 4.20 kb)