Nitesh V Chawla

University of Notre Dame | ND · Department of Computer Science and Engineering

Inspired by the success of foundation models in applications such as ChatGPT, as graph data has been ubiquitous, one can envision the far-reaching impacts that can be brought by Graph Foundation Models (GFMs) with broader applications in the areas such as scientific research, social network analysis, drug discovery, and e-commerce. Despite the sign...

The unique characteristics of text data make classification tasks a complex problem. Advances in unsupervised and semi-supervised learning and autoencoder architectures addressed several challenges. However, they still struggle with imbalanced text classification tasks, a common scenario in real-world applications, demonstrating a tendency to produ...

Laboratory accidents pose significant risks to human life and property, underscoring the importance of robust safety protocols. Despite advancements in safety training, laboratory personnel may still unknowingly engage in unsafe practices. With the increasing reliance on large language models (LLMs) for guidance in various fields, including laborat...

Molecule optimization is a critical task in drug discovery to optimize desired properties of a given molecule through chemical modification. Despite Large Language Models (LLMs) holding the potential to efficiently simulate this task by using natural language to direct the optimization, straightforwardly utilizing shows limited performance. In this...

Large language models (LLMs) offer powerful capabilities but also introduce significant risks. One way to mitigate these risks is through comprehensive pre-deployment evaluations using benchmarks designed to test for specific vulnerabilities. However, the rapidly expanding body of LLM benchmark literature lacks a standardized method for documenting...

LLM-as-a-Judge has been widely utilized as an evaluation method in various benchmarks and served as supervised rewards in model training. However, despite their excellence in many domains, potential issues are under-explored, undermining their reliability and the scope of their utility. Therefore, we identify 12 key potential biases and propose a n...

Significant work has been conducted in the domain of food computing, yet these studies typically focus on single tasks such as t2t (instruction generation from food titles and ingredients), i2t (recipe generation from food images), or t2i (food image generation from recipes). None of these approaches integrate all modalities simultaneously. To addr...

Large Language Models (LLMs) have achieved remarkable success across a wide array of tasks. Due to their notable capabilities in planning and reasoning, LLMs have been utilized as autonomous agents for the automatic execution of various tasks. Recently, LLM-based agent systems have rapidly evolved from single-agent planning or decision-making to op...

We developed SaludConectaMX as a comprehensive system to track and understand the determinants of complications throughout chemotherapy treatment for children with cancer in Mexico. SaludConectaMX is unique in that it integrates patient clinical indicators with social determinants and caregiver mental health, forming a social-clinical perspective o...

The rapid progress in machine learning (ML) has brought forth many large language models (LLMs) that excel in various tasks and areas. These LLMs come with different abilities and costs in terms of computation or pricing. Since the demand for each query can vary, e.g., because of the queried domain or its complexity, defaulting to one LLM in an app...

Machine learning (ML) models have difficulty generalizing when the number of training class instances are numerically imbalanced. The problem of generalization in the face of data imbalance has largely been attributed to the lack of training data for under-represented classes and to feature overlap. The typical remedy is to implement data augmentat...

With the rise of artificial intelligence in our everyday lives, the need for human interpretation of machine learning models’ predictions emerges as a critical issue. Generally, interpretability is viewed as a binary notion with a performance trade-off. Either a model is fully-interpretable but lacks the ability to capture more complex patterns in...

Oversampling and imputation for imbalanced missing data Imbalanced data is a widespread issue that is naturally occurring. For instance, fraudulent banking transactions are less frequent than normal transactions, and the number of cancer cases is lower than that of patients. Furthermore, it is common for data to contain missing values. Dealing with...

Recently, Large Language Models (LLMs) with their strong task-handling capabilities have shown remarkable advancements across a spectrum of fields, moving beyond natural language understanding. However, their proficiency within the chemistry domain remains restricted, especially in solving professional molecule-related tasks. This challenge is attr...

Unmanned aerial vehicles (UAVs) have become popular, and accordingly, diagnosing failure is essential but not easy due to its difficulty and complexity. Online UAV forums can help users diagnose the failures since they contain abundant information from diverse users. However, matching responses to user needs is not easy because forum comments are o...

A long-standing dilemma prevents the broader application of explanation methods: general applicability and inference speed. On the one hand, existing model-agnostic explanation methods usually make minimal pre-assumptions about the prediction models to be explained. Still, they require additional queries to the model through propagation or back-pro...

Many evaluation metrics can be used to assess the performance of models in binary classification tasks. However, most of them are derived from a confusion matrix in a non-differentiable form, making it very difficult to generate a differentiable loss function that could directly optimize them. The lack of solutions to bridge this challenge not only...

Graph Machine Learning (Graph ML) has witnessed substantial advancements in recent years. With their remarkable ability to process graph-structured data, Graph ML techniques have been extensively utilized across diverse applications, including critical domains like finance, healthcare, and transportation. Despite their societal benefits, recent res...

Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data, pre-training with massive unlabeled data has emerged as a promising solution. However, this process faces a serie...

Machine learning (ML) is playing an increasingly important role in rendering decisions that affect a broad range of groups in society. This posits the requirement of algorithmic fairness , which holds that automated decisions should be equitable with respect to protected features (e.g., gender, race). Training datasets can contain both class imbala...

Large language models (LLMs) have shown remarkable generalization capability with exceptional performance in various language modeling tasks. However, they still exhibit inherent limitations in precisely capturing and returning grounded knowledge. While existing work has explored utilizing knowledge graphs (KGs) to enhance language modeling via joi...

The human race is facing one of the most meaningful public health emergencies in the modern era caused by the COVID-19 pandemic. This pandemic introduced various challenges, from lock-downs with significant economic costs to fundamentally altering the way of life for many people around the world. The battle to understand and control the virus is st...

Large Language Models (LLMs) have achieved remarkable success across a wide array of tasks. Due to the impressive planning and reasoning abilities of LLMs, they have been used as autonomous agents to do many tasks automatically. Recently, based on the development of using one LLM as a single planning or decision-making agent, LLM-based multi-agent...

There is a gap between current methods that explain deep learning models that work on imbalanced image data and the needs of the imbalanced learning community. Existing methods that explain imbalanced data are geared toward binary classification, single layer machine learning models and low dimensional data. Current eXplainable Artificial Intellige...

Introduction Maintaining an affordable and nutritious diet can be challenging, especially for those living under the conditions of poverty. To fulfill a healthy diet, consumers must make difficult decisions within a complicated food landscape. Decisions must factor information on health and budget constraints, the food supply and pricing options at...

As artificial intelligence becomes more pervasive, explainability and the need to interpret machine learning models’ behavior emerge as critical issues. Discussions are usually bounded by those who defend that interpretable models must be the rule or that non-interpretable models’ ability to capture more complex patterns warrants their use. In this...

Large Language Models (LLMs) have shown remarkable generalization capability with exceptional performance in various language modeling tasks. However, they still exhibit inherent limitations in precisely capturing and returning grounded knowledge. While existing work has explored utilizing knowledge graphs to enhance language modeling via joint tra...

Message Passing Neural Networks (MPNNs) have emerged as the {\em de facto} standard in graph representation learning. However, when it comes to link prediction, they often struggle, surpassed by simple heuristics such as Common Neighbor (CN). This discrepancy stems from a fundamental limitation: while MPNNs excel in node-level representation, they...

BACKGROUND Older adults often face technological exclusion as their needs and contexts are not considered in the design of digital tools. The user-centered design (UCD) approach, centered on the specific needs and contexts of the user, can potentially address this exclusion. OBJECTIVE This study aimed to use the UCD approach to develop a connected...

Graph neural networks (GNNs) have shown remarkable performance on diverse graph mining tasks. While sharing the same message passing framework, our study shows that different GNNs learn distinct knowledge from the same graph. This implies potential performance improvement by distilling the complementary knowledge from multiple models. However, know...

Generative self-supervised learning (SSL), especially masked autoencoders, has become one of the most exciting learning paradigms and has shown great potential in handling graph data. However, real-world graphs are always heterogeneous, which poses three critical challenges that existing methods ignore: 1) how to capture complex graph structure? 2)...

Cross-domain graph few-shot learning attempts to address the prevalent data scarcity issue in graph mining problems. However, the utilization of cross-domain data induces another intractable domain shift issue which severely degrades the generalization ability of cross-domain graph few-shot learning models. The combat with the domain shift issue is...

This tutorial paper provides a general overview of symbolic regression (SR) with specific focus on standards of interpretability. We posit that interpretable modeling, although its definition is still disputed in the literature, is a practical way to support the evaluation of successful information fusion. In order to convey the benefits of SR as a...

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark contai...

Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top of which the downstream tasks (e.g., property prediction) can be performed. Recently, MRL has achieved consider...

Data augmentation forms the cornerstone of many modern machine learning training pipelines; yet, the mechanisms by which it works are not clearly understood. Much of the research on data augmentation (DA) has focused on improving existing techniques, examining its regularization effects in the context of neural network over-fitting, or investigatin...

Convolutional neural networks (CNNs) have achieved impressive results on imbalanced image data, but they still have difficulty generalizing to minority classes and their decisions are difficult to interpret. These problems are related because the method by which CNNs generalize to minority classes, which requires improvement, is wrapped in a black-...

The rapid advancement in data-driven research has increased the demand for effective graph data analysis. However, real-world data often exhibits class imbalance, leading to poor performance of machine learning models. To overcome this challenge, class-imbalanced learning on graphs (CILG) has emerged as a promising solution that combines the streng...

Graph neural networks (GNNs) have shown remarkable performance on diverse graph mining tasks. While sharing the same message passing framework, our study shows that different GNNs learn distinct knowledge from the same graph. This implies potential performance improvement by distilling the complementary knowledge from multiple models. However, know...

The lack of publicly available, large, and unbiased datasets is a key bottleneck for the application of machine learning (ML) methods in synthetic chemistry. Data from electronic laboratory notebooks (ELNs) could provide less biased, large datasets, but no such datasets have been made publicly available. The first real-world dataset from the ELNs o...

italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">With the increasing deployment of small Unmanned Aerial Systems (sUAS) on various tasks, it becomes crucial to analyze and detect anomalies from their flight logs. To support research in this area, we curate DLA, the first real-world time series anomaly...

The human race is facing one of the most meaningful public health emergencies in the modern era caused by the COVID-19 pandemic. This pandemic introduced various challenges, from lock-downs with significant economic costs to fundamentally altering the way of life for many people around the world. The battle to understand and control the virus is st...

Spread of nonindigenous species by shipping is a large and growing global problem that harms coastal ecosystems and economies and may blur coastal biogeographic patterns. This study coupled eukaryotic environmental DNA (eDNA) metabarcoding with dissimilarity regression to test the hypothesis that ship-borne species spread homogenizes port communiti...

Graph Neural Networks (GNNs) have attracted tremendous attention by demonstrating their capability to handle graph data. However, they are difficult to be deployed in resource-limited devices due to model sizes and scalability constraints imposed by the multi-hop data dependency. In addition, real-world graphs usually possess complex structural inf...

This tutorial paper provides a general overview of symbolic regression (SR) with specific focus on standards of interpretability. We posit that interpretable modeling, although its definition is still disputed in the literature, is a practical way to support the evaluation of successful information fusion. In order to convey the benefits of SR as a...

Link prediction is a crucial problem in graph-structured data. Due to the recent success of graph neural networks (GNNs), a variety of GNN-based models were proposed to tackle the link prediction task. Specifically, GNNs leverage the message passing paradigm to obtain node representation, which relies on link connectivity. However, in a link predic...

Convolutional neural networks (CNNs) have achieved impressive results on imbalanced image data, but they still have difficulty generalizing to minority classes and their decisions are difficult to interpret. These problems are related because the method by which CNNs generalize to minority classes, which requires improvement, is wrapped in a blackb...

Mobile health (mHealth) technologies offer an opportunity to enable the care and support of community-dwelling older adults, however, research examining the use of mHealth in delivering quality of life (QoL) improvements in the older population is limited. We developed a tablet application (eSeniorCare) based on the Successful Aging framework and i...

Graph neural networks (GNNs) have shown remarkable performance on diverse graph mining tasks. Although different GNNs can be unified as the same message passing framework, they learn complementary knowledge from the same graph. Knowledge distillation (KD) is developed to combine the diverse knowledge from multiple models. It transfers knowledge fro...

Graph Neural Networks (GNNs) have been widely used on graph data and have shown exceptional performance in the task of link prediction. Despite their effectiveness, GNNs often suffer from high latency due to non-trivial neighborhood data dependency in practical deployments. To address this issue, researchers have proposed methods based on knowledge...

Tools that can help older adults self-manage multiple health goals in collaboration with their care managers are rare to find. Informed by the Self-Determination Theory, Goal-Oriented Care paradigm and our prior findings, we used an iterative, user-centered process to design a tablet application to facilitate Goal-Oriented care in community-dwellin...

While Graph Neural Networks (GNNs) have demonstrated their efficacy in dealing with non-Euclidean structural data, they are difficult to be deployed in real applications due to the scalability constraint imposed by multi-hop data dependency. Existing methods attempt to address this scalability issue by training multi-layer perceptrons (MLPs) exclus...

Generative self-supervised learning (SSL), especially masked autoencoders, has become one of the most exciting learning paradigms and has shown great potential in handling graph data. However, real-world graphs are always heterogeneous, which poses three critical challenges that existing methods ignore: 1) how to capture complex graph structure? 2)...

Background Febrile neutropenia (FN) is an early indicator of infection in oncology patients post-chemotherapy. We aimed to determine clinical predictors of septic shock and/or bacteremia in pediatric cancer patients experiencing FN and to create a model that classifies patients as low-risk for these outcomes. Methods This is a retrospective analys...

The self-supervised learning (SSL) paradigm is an essential exploration area, which tries to eliminate the need for expensive data labeling. Despite the great success of SSL methods in computer vision and natural language processing, most of them employ contrastive learning objectives that require negative samples, which are hard to define. This be...