Devam Mondal

Devam Mondal, Atharva Inamdar

RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like Illumina's next-generation sequencing (NGS) are used to produce the raw data for this experimental procedure. This raw FASTQ data must then be prepared via a complex series of data manipulations by bioinformaticians. This process currently takes place on an unwieldy textual user interface like a terminal/command line that requires the user to install and import multiple program packages, preventing the untrained biologist from initiating data analysis. Open-source platforms like Galaxy have produced a more user-friendly pipeline, yet the visual interface remains cluttered and highly technical, remaining uninviting for the natural scientist. To address this, SeqMate is a user-friendly tool that allows for one-click analytics by utilizing the power of a large language model (LLM) to automate both data preparation and analysis (differential expression, trajectory analysis, etc). Furthermore, by utilizing the power of generative AI, SeqMate is also capable of analyzing such findings and producing written reports of upregulated/downregulated/user-prompted genes with sources cited from known repositories like PubMed, PDB, and Uniprot.

Devam Mondal, Carlo Lipizzi

In light of recent legal allegations brought by publishers, newspapers, and other creators of copyrighted corpora against large language model developers who use their copyrighted materials for training or fine-tuning purposes, we propose a novel system, a variant of a plagiarism detection system, that assesses whether a knowledge source has been used in the training or fine-tuning of a large language model. Unlike current methods, we utilize an approach that uses Resource Description Framework (RDF) triples to create knowledge graphs from both a source document and an LLM continuation of that document. These graphs are then analyzed with respect to content using cosine similarity and with respect to structure using a normalized version of graph edit distance that shows the degree of isomorphism. Unlike traditional plagiarism systems that focus on content matching and keyword identification between a source and a target corpus, our approach enables a broader and more accurate evaluation of similarity between a source document and LLM continuation by focusing on relationships between ideas and their organization with regards to others. Additionally, our approach does not require access to LLM metrics like perplexity that may be unavailable in closed large language model "black-box" systems, as well as the training corpus. We thus assess whether an LLM has "plagiarized" a corpus in its continuation through similarity measures. A prototype of our system will be found on a hyperlinked GitHub repository.

Devam Mondal, Carlo Lipizzi

Despite the growing capabilities of large language models, there exists concerns about the biases they develop. In this paper, we propose a novel, automated mechanism for debiasing through specified dataset augmentation in the lens of bias producers and in the context of 'restricted industries' with limited data. We additionally create two new additional metrics, the mb-index and db-index, to quantify bias, considering the idea that bias occurs due to both intrinsic model architecture and dataset.