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Vipin Kumar

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Published work

14 published item(s)

preprint2026arXiv

To Use AI as Dice of Possibilities with Timing Computation

The dominant noun-based modeling paradigm has fundamentally constrained AI development, precluding any adequate representation of the future as an open temporal dimension. This paper introduces a verb-based paradigm, together with precise definitions of \emph{timing computation} and \emph{possibility}, that enables AI to function as an effective instrument for realizing the grammar of our thought. Applied to longitudinal EHR data from 3,276 breast cancer patients, the framework empirically demonstrates: (1) automatic discovery of clinically significant patient trajectories, and (2) counterfactual timing deduction. Both results are purely data-driven, require no prior domain knowledge, and, to our knowledge, represent the first such demonstrations in the machine learning literature.

preprint2022arXiv

Integrating Scientific Knowledge with Machine Learning for Engineering and Environmental Systems

There is a growing consensus that solutions to complex science and engineering problems require novel methodologies that are able to integrate traditional physics-based modeling approaches with state-of-the-art machine learning (ML) techniques. This paper provides a structured overview of such techniques. Application-centric objective areas for which these approaches have been applied are summarized, and then classes of methodologies used to construct physics-guided ML models and hybrid physics-ML frameworks are described. We then provide a taxonomy of these existing techniques, which uncovers knowledge gaps and potential crossovers of methods between disciplines that can serve as ideas for future research.

preprint2022arXiv

Investigating star-formation activity towards the southern HII region RCW 42

The star-forming activity in the HII region RCW 42 is investigated using multiple wavebands, from near-infrared to radio wavelengths. Located at a distance of 5.8 kpc, this southern region has a bolometric luminosity of 1.8 $\times$ 10$^6$ L$_{\odot}$. The ionized gas emission has been imaged at low radio frequencies of 610 and 1280 MHz using the Giant Metrewave Radio Telescope, India and shows a large expanse of the HII region, spanning $20\times 15$ pc$^2$. The average electron number density in the region is estimated to be $\sim70$ cm$^{-3}$, which suggests an average ionization fraction of the cloud to be $11\%$. An extended green object EGO G274.0649-01.1460 and several young stellar objects have been identified in the region using data from the 2MASS and Spitzer surveys. The dust emission from the associated molecular cloud is probed using Herschel Space Telescope, which reveals the presence of 5 clumps, C1-C5, in this region. Two millimetre emission cores of masses 380 and 390 M$_{\odot}$ towards the radio emission peak have been identified towards C1 from the ALMA map at 1.4 mm. The clumps are investigated for their evolutionary stages based on association with various star-formation tracers, and we find that all the clumps are in active/evolved stage.

preprint2022arXiv

Robust Inverse Framework using Knowledge-guided Self-Supervised Learning: An application to Hydrology

Machine Learning is beginning to provide state-of-the-art performance in a range of environmental applications such as streamflow prediction in a hydrologic basin. However, building accurate broad-scale models for streamflow remains challenging in practice due to the variability in the dominant hydrologic processes, which are best captured by sets of process-related basin characteristics. Existing basin characteristics suffer from noise and uncertainty, among many other things, which adversely impact model performance. To tackle the above challenges, in this paper, we propose a novel Knowledge-guided Self-Supervised Learning (KGSSL) inverse framework to extract system characteristics from driver and response data. This first-of-its-kind framework achieves robust performance even when characteristics are corrupted. We show that KGSSL achieves state-of-the-art results for streamflow modeling for CAMELS (Catchment Attributes and MEteorology for Large-sample Studies) which is a widely used hydrology benchmark dataset. Specifically, KGSSL outperforms other methods by up to 16 \% in reconstructing characteristics. Furthermore, we show that KGSSL is relatively more robust to distortion than baseline methods, and outperforms the baseline model by 35\% when plugging in KGSSL inferred characteristics.

preprint2021arXiv

Optical and near-infrared spectroscopy of Nova V2891 Cygni: evidence for shock-induced dust formation

We present multi-epoch optical and near-infrared observations of the highly reddened, \pion{Fe}{ii} class slow nova V2891 Cygni. The observations span 15 months since its discovery. The initial rapid brightening from quiescence, and the presence of a $\sim$35 day long pre-maximum halt, is well documented. The evidence that the current outburst of V2891 Cyg has undergone several distinct episodes of mass ejection is seen through time-varying P Cygni profiles of the O\,{\sc i} 7773\,$Å$ line. A highlight is the occurrence of a dust formation event centred around $\sim$+273d, which coincides with a phase of coronal line emission. The dust mass is found to be $\sim0.83-1.25 \times 10^{-10} M_{\odot}$. There is strong evidence to suggest that the coronal lines are created by shock heating rather than by photoionization. The simultaneous occurrence of the dust and coronal lines (with varying velocity shifts) supports the possibility that dust formation is shock-induced. Such a route for dust formation has not previously been seen in a nova, although the mechanism has been proposed for dust formation in some core-collapse supernovae. Analysis of the coronal lines indicates a gas mass and temperature of 8.35--8.42$\times10^{-7}$ M$_\odot$ and $\sim(4.8-9.1)\times10^{5}$~K respectively, and an overabundance of aluminium and silicon. A Case B analysis of the hydrogen lines yields a mass of the ionized gas of ($8.60\pm1.73)\times10^{-5}$ M$_{\odot}$. The reddening and distance to the nova are estimated to be $E(B-V)$ = 2.21$\pm$0.15 and $d$ = 5.50 kpc respectively.

preprint2020arXiv

First Results from MFOSC-P : Low Resolution Optical Spectroscopy of a Sample of M dwarfs within 100 parsecs

Mt. Abu Faint Object Spectrograph and Camera (MFOSC-P) is an in-house developed instrument for Physical Research Laboratory (PRL) 1.2m telescope at Mt. Abu India, commissioned in February 2019. Here we present the first science results derived from the low resolution spectroscopy program of a sample of M Dwarfs carried out during the commissioning run of MFOSC-P between February-June 2019. M dwarfs carry great significance for exoplanets searches in habitable zone and are among the promising candidates for the observatory's several ongoing observational campaigns. Determination of their accurate atmospheric properties and fundamental parameters is essential to constrain both their atmospheric and evolutionary models. In this study, we provide a low resolution (R$\sim$500) spectroscopic catalogue of 80 bright M dwarfs (J$<$10) and classify them using their optical spectra. We have also performed the spectral synthesis and $χ^2$ minimisation techniques to determine their fundamental parameters viz. effective temperature and surface gravity by comparing the observed spectra with the most recent BT-Settl synthetic spectra. Spectral type of M dwarfs in our sample ranges from M0 to M5. The derived effective temperature and surface gravity are ranging from 4000 K to 3000 K and 4.5 to 5.5 dex, respectively. In most of the cases, the derived spectral types are in good agreement with previously assigned photometric classification.

preprint2020arXiv

Inverse Problems, Deep Learning, and Symmetry Breaking

In many physical systems, inputs related by intrinsic system symmetries are mapped to the same output. When inverting such systems, i.e., solving the associated inverse problems, there is no unique solution. This causes fundamental difficulties for deploying the emerging end-to-end deep learning approach. Using the generalized phase retrieval problem as an illustrative example, we show that careful symmetry breaking on the training data can help get rid of the difficulties and significantly improve the learning performance. We also extract and highlight the underlying mathematical principle of the proposed solution, which is directly applicable to other inverse problems.

preprint2020arXiv

Physics-Guided Machine Learning for Scientific Discovery: An Application in Simulating Lake Temperature Profiles

Physics-based models of dynamical systems are often used to study engineering and environmental systems. Despite their extensive use, these models have several well-known limitations due to simplified representations of the physical processes being modeled or challenges in selecting appropriate parameters. While-state-of-the-art machine learning models can sometimes outperform physics-based models given ample amount of training data, they can produce results that are physically inconsistent. This paper proposes a physics-guided recurrent neural network model (PGRNN) that combines RNNs and physics-based models to leverage their complementary strengths and improves the modeling of physical processes. Specifically, we show that a PGRNN can improve prediction accuracy over that of physics-based models, while generating outputs consistent with physical laws. An important aspect of our PGRNN approach lies in its ability to incorporate the knowledge encoded in physics-based models. This allows training the PGRNN model using very few true observed data while also ensuring high prediction accuracy. Although we present and evaluate this methodology in the context of modeling the dynamics of temperature in lakes, it is applicable more widely to a range of scientific and engineering disciplines where physics-based (also known as mechanistic) models are used, e.g., climate science, materials science, computational chemistry, and biomedicine.

preprint2020arXiv

Semi-supervised Classification using Attention-based Regularization on Coarse-resolution Data

Many real-world phenomena are observed at multiple resolutions. Predictive models designed to predict these phenomena typically consider different resolutions separately. This approach might be limiting in applications where predictions are desired at fine resolutions but available training data is scarce. In this paper, we propose classification algorithms that leverage supervision from coarser resolutions to help train models on finer resolutions. The different resolutions are modeled as different views of the data in a multi-view framework that exploits the complementarity of features across different views to improve models on both views. Unlike traditional multi-view learning problems, the key challenge in our case is that there is no one-to-one correspondence between instances across different views in our case, which requires explicit modeling of the correspondence of instances across resolutions. We propose to use the features of instances at different resolutions to learn the correspondence between instances across resolutions using an attention mechanism.Experiments on the real-world application of mapping urban areas using satellite observations and sentiment classification on text data show the effectiveness of the proposed methods.

preprint2016arXiv

Causal Inference in Observational Data

Our aging population increasingly suffers from multiple chronic diseases simultaneously, necessitating the comprehensive treatment of these conditions. Finding the optimal set of drugs for a combinatorial set of diseases is a combinatorial pattern exploration problem. Association rule mining is a popular tool for such problems, but the requirement of health care for finding causal, rather than associative, patterns renders association rule mining unsuitable. To address this issue, we propose a novel framework based on the Rubin-Neyman causal model for extracting causal rules from observational data, correcting for a number of common biases. Specifically, given a set of interventions and a set of items that define subpopulations (e.g., diseases), we wish to find all subpopulations in which effective intervention combinations exist and in each such subpopulation, we wish to find all intervention combinations such that dropping any intervention from this combination will reduce the efficacy of the treatment. A key aspect of our framework is the concept of closed intervention sets which extend the concept of quantifying the effect of a single intervention to a set of concurrent interventions. We also evaluated our causal rule mining framework on the Electronic Health Records (EHR) data of a large cohort of patients from Mayo Clinic and showed that the patterns we extracted are sufficiently rich to explain the controversial findings in the medical literature regarding the effect of a class of cholesterol drugs on Type-II Diabetes Mellitus (T2DM).

preprint2012arXiv

Enhancing the functional content of protein interaction networks

Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, they face important data quality challenges of noise and incompleteness that adversely affect the results obtained from their analysis. Here, we explore the use of the concept of common neighborhood similarity (CNS), which is a form of local structure in networks, to address these issues. Although several CNS measures have been proposed in the literature, an understanding of their relative efficacies for the analysis of interaction networks has been lacking. We follow the framework of graph transformation to convert the given interaction network into a transformed network corresponding to a variety of CNS measures evaluated. The effectiveness of each measure is then estimated by comparing the quality of protein function predictions obtained from its corresponding transformed network with those from the original network. Using a large set of S. cerevisiae interactions, and a set of 136 GO terms, we find that several of the transformed networks produce more accurate predictions than those obtained from the original network. In particular, the $HC.cont$ measure proposed here performs particularly well for this task. Further investigation reveals that the two major factors contributing to this improvement are the abilities of CNS measures, especially $HC.cont$, to prune out noisy edges and introduce new links between functionally related proteins.

preprint2011arXiv

Characterizing Discriminative Patterns

Discriminative patterns are association patterns that occur with disproportionate frequency in some classes versus others, and have been studied under names such as emerging patterns and contrast sets. Such patterns have demonstrated considerable value for classification and subgroup discovery, but a detailed understanding of the types of interactions among items in a discriminative pattern is lacking. To address this issue, we propose to categorize discriminative patterns according to four types of item interaction: (i) driver-passenger, (ii) coherent, (iii) independent additive and (iv) synergistic beyond independent additive. Either of the last three is of practical importance, with the latter two representing a gain in the discriminative power of a pattern over its subsets. Synergistic patterns are most restrictive, but perhaps the most interesting since they capture a cooperative effect. For domains such as genetic research, differentiating among these types of patterns is critical since each yields very different biological interpretations. For general domains, the characterization provides a novel view of the nature of the discriminative patterns in a dataset, which yields insights beyond those provided by current approaches that focus mostly on pattern-based classification and subgroup discovery. This paper presents a comprehensive discussion that defines these four pattern types and investigates their properties and their relationship to one another. In addition, these ideas are explored for a variety of datasets (ten UCI datasets, one gene expression dataset and two genetic-variation datasets). The results demonstrate the existence, characteristics and statistical significance of the different types of patterns. They also illustrate how pattern characterization can provide novel insights into discriminative pattern mining and the discriminative structure of different datasets.

preprint2011arXiv

Construction and Functional Analysis of Human Genetic Interaction Networks with Genome-wide Association Data

Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic interactions has revealed genetic interaction networks that provide novel insights either when analyzed by themselves or when integrated with other functional genomic datasets. For higher eukaryotes such as human, the above reverse-genetics approaches are not straightforward since the phenotypes of interest for higher eukaryotes are difficult to study in a cell based assay. We propose a general framework for constructing and analyzing human genetic interaction networks from genome-wide single nucleotide polymorphism (SNP) data used for case-control studies on complex diseases. Specifically, the approach contains three major steps: (1) estimating SNP-SNP genetic interactions, (2) identifying linkage disequilibrium (LD) blocks and mapping SNP-SNP interactions to block-block interactions, and (3) functional mapping for LD blocks. We performed two sets of functional analyses for each of the six datasets used in the paper, and demonstrated that (i) the constructed genetic interaction networks are supported by functional evidence from independent biological databases, and (ii) the network can be used to discover pairs of compensatory gene modules (between-pathway models) in their joint association with a disease phenotype. The proposed framework should provide novel insights beyond existing approaches that either ignore interactions between SNPs or model different SNP-SNP pairs with genetic interactions separately. Furthermore, our study provides evidence that some of the core properties of genetic interaction networks based on reverse genetics in model organisms like yeast are also present in genetic interactions revealed by natural variation in human populations.

preprint2011arXiv

Integration of Differential Gene-combination Search and Gene Set Enrichment Analysis: A General Approach

Gene Set Enrichment Analysis (GSEA) and its variations aim to discover collections of genes that show moderate but coordinated differences in expression. However, such techniques may be ineffective if many individual genes in a phenotype-related gene set have weak discriminative power. A potential solution is to search for combinations of genes that are highly differentiating even when individual genes are not. Although such techniques have been developed, these approaches have not been used with GSEA to any significant degree because of the large number of potential gene combinations and the heterogeneity of measures that assess the differentiation provided by gene groups of different sizes. To integrate the search for differentiating gene combinations and GSEA, we propose a general framework with two key components: (A) a procedure that reduces the number of scores to be handled by GSEA to the number of genes by summarizing the scores of the gene combinations involving a particular gene in a single score, and (B) a procedure to integrate the heterogeneous scores from combinations of different sizes and from different gene combination measures by mapping the scores to p-values. Experiments on four gene expression data sets demonstrate that the integration of GSEA and gene combination search can enhance the power of traditional GSEA by discovering gene sets that include genes with weak individual differentiation but strong joint discriminative power. Also, gene sets discovered by the integrative framework share several common biological processes and improve the consistency of the results among three lung cancer data sets.