Vaibhav Rajan

Hansheng Xue, Vaibhav Rajan, Yu Lin

Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which yields the variation across multiple copies of chromosomes. Variations among fast evolving viruses that lead to different strains (called quasispecies) are also deciphered with similar approaches. In both these cases, high-throughput sequencing technologies that provide oversampled mixtures of large noisy fragments (reads) of genomes, are used to infer constituent components (haplotypes or quasispecies). The problem is harder for polyploid species where there are more than two copies of chromosomes. State-of-the-art neural approaches to solve this NP-hard problem do not adequately model relations among the reads that are important for deconvolving the input signal. We address this problem by developing a new method, called NeurHap, that combines graph representation learning with combinatorial optimization. Our experiments demonstrate substantially better performance of NeurHap in real and synthetic datasets compared to competing approaches.

Piyush Tiwary, Utkarsh Ahuja, Depanshu Sani et al.

Agricultural landscape segmentation in the Global South is challenging as it is characterized by fragmented plots, high intra-class variance, and a scarcity of labeled training data. Recent advances in segmentation have been made by Multimodal Large Language Models (MLLMs). However, current approaches encounter critical context length bottlenecks and a domain alignment gap in understanding satellite features. We address these limitations through MAgSeg, a novel, decoder-free MLLM segmentation approach. MAgSeg is an architecturally efficient approach that enables standard MLLMs to perform segmentation of complex smallholder agricultural landscapes from high-resolution satellite imagery, without requiring auxiliary vision decoders. We introduce a novel instruction tuning data format designed to enable scalable fine-tuning and post-training on high resolution satellite imagery, which enables MAgSeg to learn from the global context of the image while generating text tokens for only a patch within the image. Extensive evaluations on datasets spanning three countries in the Global South demonstrate that MAgSeg significantly outperforms state-of-the-art MLLM baselines, offering a scalable solution to map smallholder agricultural environments.

Siva Rajesh Kasa, Hu Yijie, Santhosh Kumar Kasa et al.

\texttt{Mixture-Models} is an open-source Python library for fitting Gaussian Mixture Models (GMM) and their variants, such as Parsimonious GMMs, Mixture of Factor Analyzers, MClust models, Mixture of Student's t distributions, etc. It streamlines the implementation and analysis of these models using various first/second order optimization routines such as Gradient Descent and Newton-CG through automatic differentiation (AD) tools. This helps in extending these models to high-dimensional data, which is first of its kind among Python libraries. The library provides user-friendly model evaluation tools, such as BIC, AIC, and log-likelihood estimation. The source-code is licensed under MIT license and can be accessed at \url{https://github.com/kasakh/Mixture-Models}. The package is highly extensible, allowing users to incorporate new distributions and optimization techniques with ease. We conduct a large scale simulation to compare the performance of various gradient based approaches against Expectation Maximization on a wide range of settings and identify the corresponding best suited approach.

Kumar Shubham, Aishwarya Jayagopal, Syed Mohammed Danish et al.

Cancer, a leading cause of death globally, occurs due to genomic changes and manifests heterogeneously across patients. To advance research on personalized treatment strategies, the effectiveness of various drugs on cells derived from cancers (`cell lines') is experimentally determined in laboratory settings. Nevertheless, variations in the distribution of genomic data and drug responses between cell lines and humans arise due to biological and environmental differences. Moreover, while genomic profiles of many cancer patients are readily available, the scarcity of corresponding drug response data limits the ability to train machine learning models that can predict drug response in patients effectively. Recent cancer drug response prediction methods have largely followed the paradigm of unsupervised domain-invariant representation learning followed by a downstream drug response classification step. Introducing supervision in both stages is challenging due to heterogeneous patient response to drugs and limited drug response data. This paper addresses these challenges through a novel representation learning method in the first phase and weak supervision in the second. Experimental results on real patient data demonstrate the efficacy of our method (WISER) over state-of-the-art alternatives on predicting personalized drug response.

Aishwarya Jayagopal, Hansheng Xue, Ziyang He et al.

Cancer remains a global challenge due to its growing clinical and economic burden. Its uniquely personal manifestation, which makes treatment difficult, has fuelled the quest for personalized treatment strategies. Thus, genomic profiling is increasingly becoming part of clinical diagnostic panels. Effective use of such panels requires accurate drug response prediction (DRP) models, which are challenging to build due to limited labelled patient data. Previous methods to address this problem have used various forms of transfer learning. However, they do not explicitly model the variable length sequential structure of the list of mutations in such diagnostic panels. Further, they do not utilize auxiliary information (like patient survival) for model training. We address these limitations through a novel transformer based method, which surpasses the performance of state-of-the-art DRP models on benchmark data. We also present the design of a treatment recommendation system (TRS), which is currently deployed at the National University Hospital, Singapore and is being evaluated in a clinical trial.

Aditi Agarwal, Anjali Jain, Nikita Saxena et al.

Delineating farm boundaries through segmentation of satellite images is a fundamental step in many agricultural applications. The task is particularly challenging for smallholder farms, where accurate delineation requires the use of high resolution (HR) imagery which are available only at low revisit frequencies (e.g., annually). To support more frequent (sub-) seasonal monitoring, HR images could be combined as references (ref) with low resolution (LR) images -- having higher revisit frequency (e.g., weekly) -- using reference-based super-resolution (Ref-SR) methods. However, current Ref-SR methods optimize perceptual quality and smooth over crucial features needed for downstream tasks, and are unable to meet the large scale-factor requirements for this task. Further, previous two-step approaches of SR followed by segmentation do not effectively utilize diverse satellite sources as inputs. We address these problems through a new approach, $\textbf{SEED-SR}$, which uses a combination of conditional latent diffusion models and large-scale multi-spectral, multi-source geo-spatial foundation models. Our key innovation is to bypass the explicit SR task in the pixel space and instead perform SR in a segmentation-aware latent space. This unique approach enables us to generate segmentation maps at an unprecedented 20$\times$ scale factor, and rigorous experiments on two large, real datasets demonstrate up to $\textbf{25.5}$ and $\textbf{12.9}$ relative improvement in instance and semantic segmentation metrics respectively over approaches based on state-of-the-art Ref-SR methods.

Ishan Deshpande, Amandeep Kaur Reehal, Chandan Nath et al.

Accurate, timely, and farm-level crop type information is paramount for national food security, agricultural policy formulation, and economic planning, particularly in agriculturally significant nations like India. While remote sensing and machine learning have become vital tools for crop monitoring, existing approaches often grapple with challenges such as limited geographical scalability, restricted crop type coverage, the complexities of mixed-pixel and heterogeneous landscapes, and crucially, the robust in-season identification essential for proactive decision-making. We present a framework designed to address the critical data gaps for targeted data driven decision making which generates farm-level, in-season, multi-crop identification at national scale (India) using deep learning. Our methodology leverages the strengths of Sentinel-1 and Sentinel-2 satellite imagery, integrated with national-scale farm boundary data. The model successfully identifies 12 major crops (which collectively account for nearly 90% of India's total cultivated area showing an agreement with national crop census 2023-24 of 94% in winter, and 75% in monsoon season). Our approach incorporates an automated season detection algorithm, which estimates crop sowing and harvest periods. This allows for reliable crop identification as early as two months into the growing season and facilitates rigorous in-season performance evaluation. Furthermore, we have engineered a highly scalable inference pipeline, culminating in what is, to our knowledge, the first pan-India, in-season, farm-level crop type data product. The system's effectiveness and scalability are demonstrated through robust validation against national agricultural statistics, showcasing its potential to deliver actionable, data-driven insights for transformative agricultural monitoring and management across India.

Prakash Chandra Sukhwal, Vaibhav Rajan, Atreyi Kankanhalli

Medical question answer (QA) assistants respond to lay users' health-related queries by synthesizing information from multiple sources using natural language processing and related techniques. They can serve as vital tools to alleviate issues of misinformation, information overload, and complexity of medical language, thus addressing lay users' information needs while reducing the burden on healthcare professionals. QA systems, the engines of such assistants, have typically used either language models (LMs) or knowledge graphs (KG), though the approaches could be complementary. LM-based QA systems excel at understanding complex questions and providing well-formed answers, but are prone to factual mistakes. KG-based QA systems, which represent facts well, are mostly limited to answering short-answer questions with pre-created templates. While a few studies have jointly used LM and KG approaches for text-based QA, this was done to answer multiple-choice questions. Extant QA systems also have limitations in terms of automation and performance. We address these challenges by designing a novel, automated disease QA system which effectively utilizes both LM and KG techniques through a joint-reasoning approach to answer disease-related questions appropriate for lay users. Our evaluation of the system using a range of quality metrics demonstrates its efficacy over benchmark systems, including the popular ChatGPT.

Shivin Srivastava, Kenji Kawaguchi, Vaibhav Rajan

A widely used paradigm to improve the generalization performance of high-capacity neural models is through the addition of auxiliary unsupervised tasks during supervised training. Tasks such as similarity matching and input reconstruction have been shown to provide a beneficial regularizing effect by guiding representation learning. Real data often has complex underlying structures and may be composed of heterogeneous subpopulations that are not learned well with current approaches. In this work, we design ExpertNet, which uses novel training strategies to learn clustered latent representations and leverage them by effectively combining cluster-specific classifiers. We theoretically analyze the effect of clustering on its generalization gap, and empirically show that clustered latent representations from ExpertNet lead to disentangling the intrinsic structure and improvement in classification performance. ExpertNet also meets an important real-world need where classifiers need to be tailored for distinct subpopulations, such as in clinical risk models. We demonstrate the superiority of ExpertNet over state-of-the-art methods on 6 large clinical datasets, where our approach leads to valuable insights on group-specific risks.

Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang et al.

Mixed communities of organisms are found in many environments (from the human gut to marine ecosystems) and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through high-throughput sequencing that yields DNA subsequences for subsequent analysis. A fundamental problem in the standard workflow, called binning, is to discover clusters, of genomic subsequences, associated with the unknown constituent organisms. Inherent noise in the subsequences, various biological constraints that need to be imposed on them and the skewed cluster size distribution exacerbate the difficulty of this unsupervised learning problem. In this paper, we present a new formulation using a graph where the nodes are subsequences and edges represent homophily information. In addition, we model biological constraints providing heterophilous signal about nodes that cannot be clustered together. We solve the binning problem by developing new algorithms for (i) graph representation learning that preserves both homophily relations and heterophily constraints (ii) constraint-based graph clustering method that addresses the problems of skewed cluster size distribution. Extensive experiments, on real and synthetic datasets, demonstrate that our approach, called RepBin, outperforms a wide variety of competing methods. Our constraint-based graph representation learning and clustering methods, that may be useful in other domains as well, advance the state-of-the-art in both metagenomics binning and graph representation learning.

Ragunathan Mariappan, Vaibhav Rajan

Heterogeneous multi-typed, multimodal relational data is increasingly available in many domains and their exploratory analysis poses several challenges. We advance the state-of-the-art in neural unsupervised learning to analyze such data. We design the first neural method for collective matrix tri-factorization of arbitrary collections of matrices to perform spectral clustering of all constituent entities and learn cluster associations. Experiments on benchmark datasets demonstrate its efficacy over previous non-neural approaches. Leveraging signals from multi-way clustering and collective matrix completion we design a unique technique, called Discordance Analysis, to reveal information discrepancies across subsets of matrices in a collection with respect to two entities. We illustrate its utility in quality assessment of knowledge bases and in improving representation learning.

Debabrata Mahapatra, Vaibhav Rajan

Given multiple non-convex objective functions and objective-specific weights, Chebyshev scalarization (CS) is a well-known approach to obtain an Exact Pareto Optimal (EPO), i.e., a solution on the Pareto front (PF) that intersects the ray defined by the inverse of the weights. First-order optimizers that use the CS formulation to find EPO solutions encounter practical problems of oscillations and stagnation that affect convergence. Moreover, when initialized with a PO solution, they do not guarantee a controlled trajectory that lies completely on the PF. These shortcomings lead to modeling limitations and computational inefficiency in multi-task learning (MTL) and multi-criteria decision-making (MCDM) methods that utilize CS for their underlying non-convex multi-objective optimization (MOO). To address these shortcomings, we design a new MOO method, EPO Search. We prove that EPO Search converges to an EPO solution and empirically illustrate its computational efficiency and robustness to initialization. When initialized on the PF, EPO Search can trace the PF and converge to the required EPO solution at a linear rate of convergence. Using EPO Search we develop new algorithms: PESA-EPO for approximating the PF in a posteriori MCDM, and GP-EPO for preference elicitation in interactive MCDM; experiments on benchmark datasets confirm their advantages over competing alternatives. EPO Search scales linearly with the number of decision variables which enables its use for training deep networks. Empirical results on real data from personalized medicine, e-commerce and hydrometeorology demonstrate the efficacy of EPO Search for deep MTL.

Shivin Srivastava, Siddharth Bhatia, Lingxiao Huang et al.

In data containing heterogeneous subpopulations, classification performance benefits from incorporating the knowledge of cluster structure in the classifier. Previous methods for such combined clustering and classification either 1) are classifier-specific and not generic, or 2) independently perform clustering and classifier training, which may not form clusters that can potentially benefit classifier performance. The question of how to perform clustering to improve the performance of classifiers trained on the clusters has received scant attention in previous literature, despite its importance in several real-world applications. In this paper, first, we theoretically analyze the generalization performance of classifiers trained on clustered data and find conditions under which clustering can potentially aid classification. This motivates the design of a simple k-means-based classification algorithm called Clustering Aware Classification (CAC) and its neural variant {DeepCAC}. DeepCAC effectively leverages deep representation learning to learn latent embeddings and finds clusters in a manner that make the clustered data suitable for training classifiers for each underlying subpopulation. Our experiments on synthetic and real benchmark datasets demonstrate the efficacy of DeepCAC over previous methods for combined clustering and classification.

Hansheng Xue, Luwei Yang, Vaibhav Rajan et al.

A bipartite network is a graph structure where nodes are from two distinct domains and only inter-domain interactions exist as edges. A large number of network embedding methods exist to learn vectorial node representations from general graphs with both homogeneous and heterogeneous node and edge types, including some that can specifically model the distinct properties of bipartite networks. However, these methods are inadequate to model multiplex bipartite networks (e.g., in e-commerce), that have multiple types of interactions (e.g., click, inquiry, and buy) and node attributes. Most real-world multiplex bipartite networks are also sparse and have imbalanced node distributions that are challenging to model. In this paper, we develop an unsupervised Dual HyperGraph Convolutional Network (DualHGCN) model that scalably transforms the multiplex bipartite network into two sets of homogeneous hypergraphs and uses spectral hypergraph convolutional operators, along with intra- and inter-message passing strategies to promote information exchange within and across domains, to learn effective node embedding. We benchmark DualHGCN using four real-world datasets on link prediction and node classification tasks. Our extensive experiments demonstrate that DualHGCN significantly outperforms state-of-the-art methods, and is robust to varying sparsity levels and imbalanced node distributions.

Ragunathan Mariappan, Siva Rajesh Kasa, Vaibhav Rajan

We present the first deep learning based architecture for collective matrix tri-factorization (DCMTF) of arbitrary collections of matrices, also known as augmented multi-view data. DCMTF can be used for multi-way spectral clustering of heterogeneous collections of relational data matrices to discover latent clusters in each input matrix, across both dimensions, as well as the strengths of association across clusters. The source code for DCMTF is available on our public repository: https://bitbucket.org/cdal/dcmtf_generic

Siva Rajesh Kasa, Vaibhav Rajan

We study two practically important cases of model based clustering using Gaussian Mixture Models: (1) when there is misspecification and (2) on high dimensional data, in the light of recent advances in Gradient Descent (GD) based optimization using Automatic Differentiation (AD). Our simulation studies show that EM has better clustering performance, measured by Adjusted Rand Index, compared to GD in cases of misspecification, whereas on high dimensional data GD outperforms EM. We observe that both with EM and GD there are many solutions with high likelihood but poor cluster interpretation. To address this problem we design a new penalty term for the likelihood based on the Kullback Leibler divergence between pairs of fitted components. Closed form expressions for the gradients of this penalized likelihood are difficult to derive but AD can be done effortlessly, illustrating the advantage of AD-based optimization. Extensions of this penalty for high dimensional data and for model selection are discussed. Numerical experiments on synthetic and real datasets demonstrate the efficacy of clustering using the proposed penalized likelihood approach.

Sudeshna Roy, Meghana Madhyastha, Sheril Lawrence et al.

The Internet has rich and rapidly increasing sources of high quality educational content. Inferring prerequisite relations between educational concepts is required for modern large-scale online educational technology applications such as personalized recommendations and automatic curriculum creation. We present PREREQ, a new supervised learning method for inferring concept prerequisite relations. PREREQ is designed using latent representations of concepts obtained from the Pairwise Latent Dirichlet Allocation model, and a neural network based on the Siamese network architecture. PREREQ can learn unknown concept prerequisites from course prerequisites and labeled concept prerequisite data. It outperforms state-of-the-art approaches on benchmark datasets and can effectively learn from very less training data. PREREQ can also use unlabeled video playlists, a steadily growing source of training data, to learn concept prerequisites, thus obviating the need for manual annotation of course prerequisites.

Ragunathan Mariappan, Vaibhav Rajan

Learning by integrating multiple heterogeneous data sources is a common requirement in many tasks. Collective Matrix Factorization (CMF) is a technique to learn shared latent representations from arbitrary collections of matrices. It can be used to simultaneously complete one or more matrices, for predicting the unknown entries. Classical CMF methods assume linearity in the interaction of latent factors which can be restrictive and fails to capture complex non-linear interactions. In this paper, we develop the first deep-learning based method, called dCMF, for unsupervised learning of multiple shared representations, that can model such non-linear interactions, from an arbitrary collection of matrices. We address optimization challenges that arise due to dependencies between shared representations through Multi-Task Bayesian Optimization and design an acquisition function adapted for collective learning of hyperparameters. Our experiments show that dCMF significantly outperforms previous CMF algorithms in integrating heterogeneous data for predictive modeling. Further, on two tasks - recommendation and prediction of gene-disease association - dCMF outperforms state-of-the-art matrix completion algorithms that can utilize auxiliary sources of information.

Abhishek Sengupta, Vaibhav Rajan, Sakyajit Bhattacharya et al.

Stroke is a major cause of mortality and long--term disability in the world. Predictive outcome models in stroke are valuable for personalized treatment, rehabilitation planning and in controlled clinical trials. In this paper we design a new model to predict outcome in the short-term, the putative therapeutic window for several treatments. Our regression-based model has a parametric form that is designed to address many challenges common in medical datasets like highly correlated variables and class imbalance. Empirically our model outperforms the best--known previous models in predicting short--term outcomes and in inferring the most effective treatments that improve outcome.