Arunkumar Bagavathi

Farhan Tanvir, Khaled Mohammed Saifuddin, Tanvir Hossain et al.

Modeling the interactions between drugs, targets, and diseases is paramount in drug discovery and has significant implications for precision medicine and personalized treatments. Current approaches frequently consider drug-target or drug-disease interactions individually, ignoring the interdependencies among all three entities. Within human metabolic systems, drugs interact with protein targets in cells, influencing target activities and subsequently impacting biological pathways to promote healthy functions and treat diseases. Moving beyond binary relationships and exploring tighter triple relationships is essential to understanding drugs' mechanism of action (MoAs). Moreover, identifying the heterogeneity of drugs, targets, and diseases, along with their distinct characteristics, is critical to model these complex interactions appropriately. To address these challenges, we effectively model the interconnectedness of all entities in a heterogeneous graph and develop a novel Heterogeneous Graph Triplet Attention Network (\texttt{HeTriNet}). \texttt{HeTriNet} introduces a novel triplet attention mechanism within this heterogeneous graph structure. Beyond pairwise attention as the importance of an entity for the other one, we define triplet attention to model the importance of pairs for entities in the drug-target-disease triplet prediction problem. Experimental results on real-world datasets show that \texttt{HeTriNet} outperforms several baselines, demonstrating its remarkable proficiency in uncovering novel drug-target-disease relationships.

Sai Narayanan, Sathyanarayanan N. Aakur, Priyadharsini Ramamurthy et al.

Next-generation sequencing technologies have enhanced the scope of Internet-of-Things (IoT) to include genomics for personalized medicine through the increased availability of an abundance of genome data collected from heterogeneous sources at a reduced cost. Given the sheer magnitude of the collected data and the significant challenges offered by the presence of highly similar genomic structure across species, there is a need for robust, scalable analysis platforms to extract actionable knowledge such as the presence of potentially zoonotic pathogens. The emergence of zoonotic diseases from novel pathogens, such as the influenza virus in 1918 and SARS-CoV-2 in 2019 that can jump species barriers and lead to pandemic underscores the need for scalable metagenome analysis. In this work, we propose MG2Vec, a deep learning-based solution that uses the transformer network as its backbone, to learn robust features from raw metagenome sequences for downstream biomedical tasks such as targeted and generalized pathogen detection. Extensive experiments on four increasingly challenging, yet realistic diagnostic settings, show that the proposed approach can help detect pathogens from uncurated, real-world clinical samples with minimal human supervision in the form of labels. Further, we demonstrate that the learned representations can generalize to completely unrelated pathogens across diseases and species for large-scale metagenome analysis. We provide a comprehensive evaluation of a novel representation learning framework for metagenome-based disease diagnostics with deep learning and provide a way forward for extracting and using robust vector representations from low-cost next generation sequencing to develop generalizable diagnostic tools.

Sadia Kamal, Brenner Little, Jade Gullic et al.

Developing machine learning models to characterize political polarization on online social media presents significant challenges. These challenges mainly stem from various factors such as the lack of annotated data, presence of noise in social media datasets, and the sheer volume of data. The common research practice typically examines the biased structure of online user communities for a given topic or qualitatively measuring the impacts of polarized topics on social media. However, there is limited work focusing on analyzing polarization at the ground-level, specifically in the social media posts themselves. Such existing analysis heavily relies on annotated data, which often requires laborious human labeling, offers labels only to specific problems, and lacks the ability to determine the near-future bias state of a social media conversations. Understanding the degree of political orientation conveyed in social media posts is crucial for quantifying the bias of online user communities and investigating the spread of polarized content. In this work, we first introduce two heuristic methods that leverage on news media bias and post content to label social media posts. Next, we compare the efficacy and quality of heuristically labeled dataset with a randomly sampled human-annotated dataset. Additionally, we demonstrate that current machine learning models can exhibit improved performance in predicting political orientation of social media posts, employing both traditional supervised learning and few-shot learning setups. We conduct experiments using the proposed heuristic methods and machine learning approaches to predict the political orientation of posts collected from two social media forums with diverse political ideologies: Gab and Twitter.

Sadia Kamal, Jimmy Hartford, Jeremy Willis et al.

Quantification of the political leaning of online news articles can aid in understanding the dynamics of political ideology in social groups and measures to mitigating them. However, predicting the accurate political leaning of a news article with machine learning models is a challenging task. This is due to (i) the political ideology of a news article is defined by several factors, and (ii) the innate nature of existing learning models to be biased with the political bias of the news publisher during the model training. There is only a limited number of methods to study the political leaning of news articles which also do not consider the algorithmic political bias which lowers the generalization of machine learning models to predict the political leaning of news articles published by any new news publishers. In this work, we propose a knowledge-infused deep learning model that utilizes relatively reliable external data resources to learn unbiased representations of news articles using their global and local contexts. We evaluate the proposed model by setting the data in such a way that news domains or news publishers in the test set are completely unseen during the training phase. With this setup we show that the proposed model mitigates algorithmic political bias and outperforms baseline methods to predict the political leaning of news articles with up to 73% accuracy.

Srinath Sai Tripuraneni, Sadia Kamal, Arunkumar Bagavathi

Understanding and mitigating political bias in online social media platforms are crucial tasks to combat misinformation and echo chamber effects. However, characterizing political bias temporally using computational methods presents challenges due to the high frequency of noise in social media datasets. While existing research has explored various approaches to political bias characterization, the ability to forecast political bias and anticipate how political conversations might evolve in the near future has not been extensively studied. In this paper, we propose a heuristic approach to classify social media posts into five distinct political leaning categories. Since there is a lack of prior work on forecasting political bias, we conduct an in-depth analysis of existing baseline models to identify which model best fits to forecast political leaning time series. Our approach involves utilizing existing time series forecasting models on two social media datasets with different political ideologies, specifically Twitter and Gab. Through our experiments and analyses, we seek to shed light on the challenges and opportunities in forecasting political bias in social media platforms. Ultimately, our work aims to pave the way for developing more effective strategies to mitigate the negative impact of political bias in the digital realm.

Mohammed Rakib, Arunkumar Bagavathi

Multimodal learning aims to leverage information from diverse data modalities to achieve more comprehensive performance. However, conventional multimodal models often suffer from modality imbalance, where one or a few modalities dominate model optimization, leading to suboptimal feature representation and underutilization of weak modalities. To address this challenge, we introduce Gradient-Guided Distillation (G$^{2}$D), a knowledge distillation framework that optimizes the multimodal model with a custom-built loss function that fuses both unimodal and multimodal objectives. G$^{2}$D further incorporates a dynamic sequential modality prioritization (SMP) technique in the learning process to ensure each modality leads the learning process, avoiding the pitfall of stronger modalities overshadowing weaker ones. We validate G$^{2}$D on multiple real-world datasets and show that G$^{2}$D amplifies the significance of weak modalities while training and outperforms state-of-the-art methods in classification and regression tasks. Our code is available at https://github.com/rAIson-Lab/G2D.

S M Rafiuddin, Mohammed Rakib, Sadia Kamal et al.

Aspect-Based Sentiment Analysis (ABSA) is a fine-grained linguistics problem that entails the extraction of multifaceted aspects, opinions, and sentiments from the given text. Both standalone and compound ABSA tasks have been extensively used in the literature to examine the nuanced information present in online reviews and social media posts. Current ABSA methods often rely on static hyperparameters for attention-masking mechanisms, which can struggle with context adaptation and may overlook the unique relevance of words in varied situations. This leads to challenges in accurately analyzing complex sentences containing multiple aspects with differing sentiments. In this work, we present adaptive masking methods that remove irrelevant tokens based on context to assist in Aspect Term Extraction and Aspect Sentiment Classification subtasks of ABSA. We show with our experiments that the proposed methods outperform the baseline methods in terms of accuracy and F1 scores on four benchmark online review datasets. Further, we show that the proposed methods can be extended with multiple adaptations and demonstrate a qualitative analysis of the proposed approach using sample text for aspect term extraction.

S M Rafiuddin, Sadia Kamal, Mohammed Rakib et al.

We introduce AdaptiSent, a new framework for Multimodal Aspect-Based Sentiment Analysis (MABSA) that uses adaptive cross-modal attention mechanisms to improve sentiment classification and aspect term extraction from both text and images. Our model integrates dynamic modality weighting and context-adaptive attention, enhancing the extraction of sentiment and aspect-related information by focusing on how textual cues and visual context interact. We tested our approach against several baselines, including traditional text-based models and other multimodal methods. Results from standard Twitter datasets show that AdaptiSent surpasses existing models in precision, recall, and F1 score, and is particularly effective in identifying nuanced inter-modal relationships that are crucial for accurate sentiment and aspect term extraction. This effectiveness comes from the model's ability to adjust its focus dynamically based on the context's relevance, improving the depth and accuracy of sentiment analysis across various multimodal data sets. AdaptiSent sets a new standard for MABSA, significantly outperforming current methods, especially in understanding complex multimodal information.

Sathyanarayanan N. Aakur, Vineela Indla, Vennela Indla et al.

Advances in next-generation metagenome sequencing have the potential to revolutionize the point-of-care diagnosis of novel pathogen infections, which could help prevent potential widespread transmission of diseases. Given the high volume of metagenome sequences, there is a need for scalable frameworks to analyze and segment metagenome sequences from clinical samples, which can be highly imbalanced. There is an increased need for learning robust representations from metagenome reads since pathogens within a family can have highly similar genome structures (some more than 90%) and hence enable the segmentation and identification of novel pathogen sequences with limited labeled data. In this work, we propose Metagenome2Vec - a contextualized representation that captures the global structural properties inherent in metagenome data and local contextualized properties through self-supervised representation learning. We show that the learned representations can help detect six (6) related pathogens from clinical samples with less than 100 labeled sequences. Extensive experiments on simulated and clinical metagenome data show that the proposed representation encodes compositional properties that can generalize beyond annotations to segment novel pathogens in an unsupervised setting.

Prasad hajare, Sadia Kamal, Siddharth Krishnan et al.

Computational methods to model political bias in social media involve several challenges due to heterogeneity, high-dimensional, multiple modalities, and the scale of the data. Political bias in social media has been studied in multiple viewpoints like media bias, political ideology, echo chambers, and controversies using machine learning pipelines. Most of the current methods rely heavily on the manually-labeled ground-truth data for the underlying political bias prediction tasks. Limitations of such methods include human-intensive labeling, labels related to only a specific problem, and the inability to determine the near future bias state of a social media conversation. In this work, we address such problems and give machine learning approaches to study political bias in two ideologically diverse social media forums: Gab and Twitter without the availability of human-annotated data. Our proposed methods exploit the use of transcripts collected from political speeches in US congress to label the data and achieve the highest accuracy of 70.5% and 65.1% in Twitter and Gab data respectively to predict political bias. We also present a machine learning approach that combines features from cascades and text to forecast cascade's political bias with an accuracy of about 85%.

Sathyanarayanan N. Aakur, Sai Narayanan, Vineela Indla et al.

The emergence of novel pathogens and zoonotic diseases like the SARS-CoV-2 have underlined the need for developing novel diagnosis and intervention pipelines that can learn rapidly from small amounts of labeled data. Combined with technological advances in next-generation sequencing, metagenome-based diagnostic tools hold much promise to revolutionize rapid point-of-care diagnosis. However, there are significant challenges in developing such an approach, the chief among which is to learn self-supervised representations that can help detect novel pathogen signatures with very low amounts of labeled data. This is particularly a difficult task given that closely related pathogens can share more than 90% of their genome structure. In this work, we address these challenges by proposing MG-Net, a self-supervised representation learning framework that leverages multi-modal context using pseudo-imaging data derived from clinical metagenome sequences. We show that the proposed framework can learn robust representations from unlabeled data that can be used for downstream tasks such as metagenome sequence classification with limited access to labeled data. Extensive experiments show that the learned features outperform current baseline metagenome representations, given only 1000 samples per class.

Joshua Melton, Arunkumar Bagavathi, Siddharth Krishnan

Online hate speech on social media has become a fast-growing problem in recent times. Nefarious groups have developed large content delivery networks across several main-stream (Twitter and Facebook) and fringe (Gab, 4chan, 8chan, etc.) outlets to deliver cascades of hate messages directed both at individuals and communities. Thus addressing these issues has become a top priority for large-scale social media outlets. Three key challenges in automated detection and classification of hateful content are the lack of clearly labeled data, evolving vocabulary and lexicon - hashtags, emojis, etc. - and the lack of baseline models for fringe outlets such as Gab. In this work, we propose a novel framework with three major contributions. (a) We engineer an ensemble of deep learning models that combines the strengths of state-of-the-art approaches, (b) we incorporate a tuning factor into this framework that leverages transfer learning to conduct automated hate speech classification on unlabeled datasets, like Gab, and (c) we develop a weak supervised learning methodology that allows our framework to train on unlabeled data. Our ensemble models achieve an 83% hate recall on the HON dataset, surpassing the performance of the state-of-the-art deep models. We demonstrate that weak supervised training in combination with classifier tuning significantly increases model performance on unlabeled data from Gab, achieving a hate recall of 67%.

Sai Narayanan, Akhilesh Ramachandran, Sathyanarayanan N. Aakur et al.

Bovine Respiratory Disease Complex (BRDC) is a complex respiratory disease in cattle with multiple etiologies, including bacterial and viral. It is estimated that mortality, morbidity, therapy, and quarantine resulting from BRDC account for significant losses in the cattle industry. Early detection and management of BRDC are crucial in mitigating economic losses. Current animal disease diagnostics is based on traditional tests such as bacterial culture, serolog, and Polymerase Chain Reaction (PCR) tests. Even though these tests are validated for several diseases, their main challenge is their limited ability to detect the presence of multiple pathogens simultaneously. Advancements of data analytics and machine learning and applications over metagenome sequencing are setting trends on several applications. In this work, we demonstrate a machine learning approach to identify pathogen signatures present in bovine metagenome sequences using k-mer-based network embedding followed by a deep learning-based classification task. With experiments conducted on two different simulated datasets, we show that networks-based machine learning approaches can detect pathogen signature with up to 89.7% accuracy. We will make the data available publicly upon request to tackle this important problem in a difficult domain.

Michael Ridenhour, Arunkumar Bagavathi, Elaheh Raisi et al.

The ubiquity of social media has transformed online interactions among individuals. Despite positive effects, it has also allowed anti-social elements to unite in alternative social media environments (eg. Gab.com) like never before. Detecting such hateful speech using automated techniques can allow social media platforms to moderate their content and prevent nefarious activities like hate speech propagation. In this work, we propose a weak supervision deep learning model that - (i) quantitatively uncover hateful users and (ii) present a novel qualitative analysis to uncover indirect hateful conversations. This model scores content on the interaction level, rather than the post or user level, and allows for characterization of users who most frequently participate in hateful conversations. We evaluate our model on 19.2M posts and show that our weak supervision model outperforms the baseline models in identifying indirect hateful interactions. We also analyze a multilayer network, constructed from two types of user interactions in Gab(quote and reply) and interaction scores from the weak supervision model as edge weights, to predict hateful users. We utilize the multilayer network embedding methods to generate features for the prediction task and we show that considering user context from multiple networks help achieving better predictions of hateful users in Gab. We receive up to 7% performance gain compared to single layer or homogeneous network embedding models.

Sathyanarayanan N. Aakur, Arunkumar Bagavathi

Egocentric perception has grown rapidly with the advent of immersive computing devices. Human gaze prediction is an important problem in analyzing egocentric videos and has primarily been tackled through either saliency-based modeling or highly supervised learning. We quantitatively analyze the generalization capabilities of supervised, deep learning models on the egocentric gaze prediction task on unseen, out-of-domain data. We find that their performance is highly dependent on the training data and is restricted to the domains specified in the training annotations. In this work, we tackle the problem of jointly predicting human gaze points and temporal segmentation of egocentric videos without using any training data. We introduce an unsupervised computational model that draws inspiration from cognitive psychology models of event perception. We use Grenander's pattern theory formalism to represent spatial-temporal features and model surprise as a mechanism to predict gaze fixation points. Extensive evaluation on two publicly available datasets - GTEA and GTEA+ datasets-shows that the proposed model can significantly outperform all unsupervised baselines and some supervised gaze prediction baselines. Finally, we show that the model can also temporally segment egocentric videos with a performance comparable to more complex, fully supervised deep learning baselines.

Arunkumar Bagavathi, Siddharth Krishnan, Sanjay Subrahmanyan et al.

South Indian classical music (Carnatic music) is best consumed through live concerts. A carnatic recital requires meticulous planning accounting for several parameters like the performers' repertoire, composition variety, musical versatility, thematic structure, the recital's arrangement, etc. to ensure that the audience have a comprehensive listening experience. In this work, we present ragamAI a novel machine learning framework that utilizes the tonic nuances and musical structures in the carnatic music to generate a concert recital that melodically captures the entire range in an octave. Utilizing the underlying idea of playlist and session-based recommender models, the proposed model studies the mathematical structure present in past concerts and recommends relevant items for the playlist/concert. ragamAI ensembles recommendations given by multiple models to learn user idea and past preference of sequences in concerts to extract recommendations. Our experiments on a vast collection of concert show that our model performs 25%-50% better than baseline models. ragamAI's applications are two-fold. 1) it will assist musicians to customize their performance with the necessary variety required to sustain the interest of the audience for the entirety of the concert 2) it will generate carefully curated lists of south Indian classical music so that the listener can discover the wide range of melody that the musical system can offer.

Arunkumar Bagavathi, Pedram Bashiri, Shannon Reid et al.

Online social media, periodically serves as a platform for cascading polarizing topics of conversation. The inherent community structure present in online social networks (homophily) and the advent of fringe outlets like Gab have created online "echo chambers" that amplify the effects of polarization, which fuels detrimental behavior. Recently, in October 2018, Gab made headlines when it was revealed that Robert Bowers, the individual behind the Pittsburgh Synagogue massacre, was an active member of this social media site and used it to express his anti-Semitic views and discuss conspiracy theories. Thus to address the need of automated data-driven analyses of such fringe outlets, this research proposes novel methods to discover topics that are prevalent in Gab and how they cascade within the network. Specifically, using approximately 34 million posts, and 3.7 million cascading conversation threads with close to 300k users; we demonstrate that there are essentially five cascading patterns that manifest in Gab and the most "viral" ones begin with an echo-chamber pattern and grow out to the entire network. Also, we empirically show, through two models viz. Susceptible-Infected and Bass, how the cascades structurally evolve from one of the five patterns to the other based on the topic of the conversation with upto 84% accuracy.