Manuel Serna-Aguilera

Manuel Serna-Aguilera, Khoa Luu, Nathaniel Harris et al.

The biomedical imaging world is notorious for working with small amounts of data, frustrating state-of-the-art efforts in the computer vision and deep learning worlds. With large datasets, it is easier to make progress we have seen from the natural image distribution. It is the same with microscopy videos of neuron cells moving in a culture. This problem presents several challenges as it can be difficult to grow and maintain the culture for days, and it is expensive to acquire the materials and equipment. In this work, we explore how to alleviate this data scarcity problem by synthesizing the videos. We, therefore, take the recent work of the video diffusion model to synthesize videos of cells from our training dataset. We then analyze the model's strengths and consistent shortcomings to guide us on improving video generation to be as high-quality as possible. To improve on such a task, we propose modifying the denoising function and adding motion information (dense optical flow) so that the model has more context regarding how video frames transition over time and how each pixel changes over time.

Manuel Serna-Aguilera, Raegan Anderes, Page Dobbs et al.

The nicotine addiction public health crisis continues to be pervasive. In this century alone, the tobacco industry has released and marketed new products in an aggressive effort to lure new and young customers for life. Such innovations and product development, namely flavored nicotine or tobacco such as nicotine pouches, have undone years of anti-tobacco campaign work. Past work is limited both in scope and in its ability to connect large-scale data points. Thus, we introduce the Nicotine Innovation Counter-Offensive (NICO) Dataset to provide public health researchers with over 200,000 multimodal samples, including images and text descriptions, on 55 tobacco and nicotine product brands. In addition, to provide public health researchers with factual connections across a large-scale dataset, we propose NICO-RAG, a retrieval-augmented generation (RAG) framework that can retrieve image features without incurring the high-cost of language models, as well as the added cost of processing image tokens with large-scale datasets such as NICO. At construction time, NICO-RAG organizes image- and text-extracted entities and relations into hypergraphs to produce as factual responses as possible. This joint multimodal knowledge representation enables NICO-RAG to retrieve images for query answering not only by visual similarity but also by the semantic similarity of image descriptions. Experimentals show that without needing to process additional tokens from images for over 100 questions, NICO-RAG performs comparably to the state-of-the-art RAG method adapted for images.

Manuel Serna-Aguilera, Xuan Bac Nguyen, Han-Seok Seo et al.

Facial expressions and actions differ among different individuals at varying degrees of intensity given responses to external stimuli, particularly among those that are neurodivergent. Such behaviors affect people in terms of overall health, communication, and sensory processing. Deep learning can be responsibly leveraged to improve productivity in addressing this task, and help medical professionals to accurately understand such behaviors. In this work, we introduce the Video ASD dataset-a dataset that contains video frame convolutional and attention map feature data-to foster further progress in the task of ASD classification. Unlike many recent studies in ASD classification with MRI data, which require expensive specialized equipment, our method utilizes a powerful but relatively affordable GPU, a standard computer setup, and a video camera for inference. Results show that our model effectively generalizes and understands key differences in the distinct movements of the children. Additionally, we test foundation models on this data to showcase how movement noise affects performance and the need for more data and more complex labels.

Xuan-Bac Nguyen, Manuel Serna-Aguilera, Arabinda Kumar Choudhary et al.

Vision-Brain Understanding (VBU) aims to extract visual information perceived by humans from brain activity recorded through functional Magnetic Resonance Imaging (fMRI). Despite notable advancements in recent years, existing studies in VBU continue to face the challenge of catastrophic forgetting, where models lose knowledge from prior subjects as they adapt to new ones. Addressing continual learning in this field is, therefore, essential. This paper introduces a novel framework called Continual Learning for Vision-Brain (COBRA) to address continual learning in VBU. Our approach includes three novel modules: a Subject Commonality (SC) module, a Prompt-based Subject Specific (PSS) module, and a transformer-based module for fMRI, denoted as MRIFormer module. The SC module captures shared vision-brain patterns across subjects, preserving this knowledge as the model encounters new subjects, thereby reducing the impact of catastrophic forgetting. On the other hand, the PSS module learns unique vision-brain patterns specific to each subject. Finally, the MRIFormer module contains a transformer encoder and decoder that learns the fMRI features for VBU from common and specific patterns. In a continual learning setup, COBRA is trained in new PSS and MRIFormer modules for new subjects, leaving the modules of previous subjects unaffected. As a result, COBRA effectively addresses catastrophic forgetting and achieves state-of-the-art performance in both continual learning and vision-brain reconstruction tasks, surpassing previous methods.

Manuel Serna-Aguilera, Fiona L. Goggin, Aranyak Goswami et al.

Understanding which genes control which traits in an organism remains one of the central challenges in biology. Despite significant advances in data collection technology, our ability to map genes to traits is still limited. This genome-to-phenome (G2P) challenge spans several problem domains, including plant breeding, and requires models capable of reasoning over high-dimensional, heterogeneous, and biologically structured data. Currently, however, many datasets solely capture genetic information or solely capture phenotype information. Additionally, phenotype data is very heterogeneous, which many datasets do not fully capture. The critical drawback is that these datasets are not integrated, that is, they do not link with each other to describe the same biological specimens. This limits machine learning models' ability to be informed on the various aspects of these specimens, impacting the breadth of correlations learned, and therefore their ability to make more accurate predictions. To address this gap, we present the Arabidopsis Genomics-Phenomics (AGP) Dataset, a curated multi-modal dataset linking gene expression profiles with phenotypic trait measurements in Arabidopsis thaliana, a model organism in plant biology. AGP supports tasks such as phenotype prediction and interpretable graph learning. In addition, we benchmark conventional regression and explanatory baselines, including a biologically-informed hypergraph baseline, to validate gene-trait associations. To the best of our knowledge, this is the first dataset that provides multi-modal gene information and heterogeneous trait or phenotype data for the same Arabidopsis thaliana specimens. With AGP, we aim to foster the research community towards accurately understanding the connection between genotypes and phenotypes using gene information, higher-order gene pairings, and trait data from several sources.