arXiv subjects

Areejit Samal

Publications and source records attributed to Areejit Samal.

At least 19 recordsLinked to original sources

arXiv2026

Computational investigation of single herbal drugs in Ayurveda for diabetes and obesity using knowledge graph and network pharmacology

Metabolic diseases such as type 2 diabetes and obesity represent a rapidly escalating global health burden, yet current therapeutic strategies largely target isolated symptoms or single molecular pathways. To this end, we developed an integrated computational pipeline leveraging knowledge graph, pathway analysis and network pharmacology to elucidate the multi-target mechanisms of Ayurvedic Single Herbal Drugs (SHDs). SHDs associated with diabetes and obesity were curated from the Ayurvedic Pharmacopoeia of India, followed by phytochemical identification using IMPPAT database, yielding a shortlist of 11 SHDs and their 188 phytochemicals after drug-likeness and bioavailability filtering. Subsequently, molecular targets of the phytochemicals in SHDs, disease-associated genes and therapeutic targets of FDA-approved drugs, were curated via integration of data from several databases. Pathway enrichment analysis revealed significant functional overlap between SHD-associated and disease-associated pathways. All curated data were embedded into a Neo4j-based knowledge graph, enabling SHD-disease intersection analysis that prioritized key disease-relevant targets, including PTPN1, GLP1R, and DPP4. Also, the SHD-Target-FDA-approved drug profile elucidated the molecular and mechanistic aspects of the SHDs as a phytochemical cocktail, and is in alignment with the clinically studied synergistic FDA-approved drug combinations. Network pharmacology based protein-protein interaction analysis identified PPARG as another central regulator. Using a quantitative framework, we identified phytochemical pairs within SHDs, which were structurally dissimilar and target-wise distinct, yet acted on shared or different disease-associated pathways, indicating complementary and potentially synergistic interactions. Molecular docking analysis of two selected druggable targets identified putative lead phytochemicals.

q-bio.MN↗

arXiv2025

Application of discrete Ricci curvature in pruning randomly wired neural networks: A case study with chest x-ray classification of COVID-19

Randomly Wired Neural Networks (RWNNs) serve as a valuable testbed for investigating the impact of network topology in deep learning by capturing how different connectivity patterns impact both learning efficiency and model performance. At the same time, they provide a natural framework for exploring edge-centric network measures as tools for pruning and optimization. In this study, we investigate three edge-centric network measures: Forman-Ricci curvature (FRC), Ollivier-Ricci curvature (ORC), and edge betweenness centrality (EBC), to compress RWNNs by selectively retaining important synapses (or edges) while pruning the rest. As a baseline, RWNNs are trained for COVID-19 chest x-ray image classification, aiming to reduce network complexity while preserving performance in terms of accuracy, specificity, and sensitivity. We extend prior work on pruning RWNN using ORC by incorporating two additional edge-centric measures, FRC and EBC, across three network generators: Erd\"{o}s-R\'{e}nyi (ER) model, Watts-Strogatz (WS) model, and Barab\'{a}si-Albert (BA) model. We provide a comparative analysis of the pruning performance of the three measures in terms of compression ratio and theoretical speedup. A central focus of our study is to evaluate whether FRC, which is computationally more efficient than ORC, can achieve comparable pruning effectiveness. Along with performance evaluation, we further investigate the structural properties of the pruned networks through modularity and global efficiency, offering insights into the trade-off between modular segregation and network efficiency in compressed RWNNs. Our results provide initial evidence that FRC-based pruning can effectively simplify RWNNs, offering significant computational advantages while maintaining performance comparable to ORC.

cs.CV↗

arXiv2024

Bakry-\'Emery-Ricci curvature: An alternative network geometry measure in the expanding toolbox of graph Ricci curvatures

The characterization of complex networks with tools originating in geometry, for instance through the statistics of so-called Ricci curvatures, is a well established tool of network science. There exist various types of such Ricci curvatures, capturing different aspects of network geometry. In the present work, we investigate Bakry-\'Emery-Ricci curvature, a notion of discrete Ricci curvature that has been studied much in geometry, but so far has not been applied to networks. We explore on standard classes of artificial networks as well as on selected empirical ones to what the statistics of that curvature are similar to or different from that of other curvatures, how it is correlated to other important network measures, and what it tells us about the underlying network. We observe that most vertices typically have negative curvature. Random and small-world networks exhibit a narrow curvature distribution whereas other classes and most of the real-world networks possess a wide curvature distribution. When we compare Bakry-\'Emery-Ricci curvature with two other discrete notions of Ricci-curvature, Forman-Ricci and Ollivier-Ricci curvature for both model and real-world networks, we observe a high positive correlation between Bakry-\'Emery-Ricci and both Forman-Ricci and Ollivier-Ricci curvature, and in particular with the augmented version of Forman-Ricci curvature. Bakry-\'Emery-Ricci curvature also exhibits a high negative correlation with the vertex centrality measure and degree for most of the model and real-world networks. However, it does not correlate with the clustering coefficient. Also, we investigate the importance of vertices with highly negative curvature values to maintain communication in the network. The computational time for Bakry-\'Emery-Ricci curvature is shorter than that required for Ollivier-Ricci curvature but higher than for Augmented Forman-Ricci curvature.

physics.comp-ph↗

arXiv2023

Investigation of Indian stock markets using topological data analysis and geometry-inspired network measures

Geometry-inspired measures (such as discrete Ricci curvatures) and topological data analysis (TDA) based methods (such as persistent homology) have become attractive tools for characterizing the higher-order structure of networks representing the financial systems. In this study, our goal is to perform a comparative analysis of both these approaches, especially by assessing the fragility and systemic risk in the Indian stock markets, which is known for its high volatility and risk. To achieve this goal, we analyze the time series of daily log-returns of stocks comprising the National Stock Exchange (NSE) and the Bombay Stock Exchange (BSE). Specifically, our aim is to monitor the changes in standard network measures, edge-centric discrete Ricci curvatures, and persistent homology based topological measures computed from cross-correlation matrices of stocks. In this study, the edge-centric discrete Ricci curvatures have been employed for the first time in the analysis of the Indian stock markets. The Indian stock markets are known to be less diverse in comparison to the US market, and hence provides us an interesting example. Our results point that, among the persistent homology based topological measures, persistent entropy is simple and more robust than $L^1$-norm and $L^2$-norm of persistence landscape. In a broader comparison between network analysis and TDA, we highlight that the network analysis is sensitive to the way of constructing the networks (threshold or minimum spanning tree), as well as the threshold values used to construct the correlation-based threshold networks. On the other hand, the persistent homology is a more robust approach and is able to capture the higher-order interactions and eliminate noisy data in financial systems, since it does not take into account a single value of threshold but rather a range of values.

physics.soc-ph↗

arXiv2021

Network-centric indicators for fragility in global financial indices

Over the last two decades, financial systems have been studied and analysed from the perspective of complex networks, where the nodes and edges in the network represent the various financial components and the strengths of correlations between them. Here, we adopt a similar network-based approach to analyse the daily closing prices of 69 global financial market indices across 65 countries over a period of 2000-2014. We study the correlations among the indices by constructing threshold networks superimposed over minimum spanning trees at different time frames. We investigate the effect of critical events in financial markets (crashes and bubbles) on the interactions among the indices by performing both static and dynamic analyses of the correlations. We compare and contrast the structures of these networks during periods of crashes and bubbles, with respect to the normal periods in the market. In addition, we study the temporal evolution of traditional market indicators, various global network measures and the recently developed edge-based curvature measures. We show that network-centric measures can be extremely useful in monitoring the fragility in the global financial market indices.

q-fin.ST↗

arXiv2020

Edge-based analysis of networks: Curvatures of graphs and hypergraphs

The relations, rather than the elements, constitute the structure of networks. We therefore develop a systematic approach to the analysis of networks, modelled as graphs or hypergraphs, that is based on structural properties of (hyper)edges, instead of vertices. For that purpose, we utilize so-called network curvatures. These curvatures quantify the local structural properties of (hyper)edges, that is, how, and how well, they are connected to others. In the case of directed networks, they assess the input they receive and the output they produce, and relations between them. With those tools, we can investigate biological networks. As examples, we apply our methods here to protein-protein interaction, transcriptional regulatory and metabolic networks.

cs.DM↗

arXiv2020

Network geometry and market instability

The complexity of financial markets arise from the strategic interactions among agents trading stocks, which manifest in the form of vibrant correlation patterns among stock prices. Over the past few decades, complex financial markets have often been represented as networks whose interacting pairs of nodes are stocks, connected by edges that signify the correlation strengths. However, we often have interactions that occur in groups of three or more nodes, and these cannot be described simply by pairwise interactions but we also need to take the relations between these interactions into account. Only recently, researchers have started devoting attention to the higher-order architecture of complex financial systems, that can significantly enhance our ability to estimate systemic risk as well as measure the robustness of financial systems in terms of market efficiency. Geometry-inspired network measures, such as the Ollivier-Ricci curvature and Forman-Ricci curvature, can be used to capture the network fragility and continuously monitor financial dynamics. Here, we explore the utility of such discrete Ricci curvatures in characterizing the structure of financial systems, and further, evaluate them as generic indicators of the market instability. For this purpose, we examine the daily returns from a set of stocks comprising the USA S&P-500 and the Japanese Nikkei-225 over a 32-year period, and monitor the changes in the edge-centric network curvatures. We find that the different geometric measures capture well the system-level features of the market and hence we can distinguish between the normal or `business-as-usual' periods and all the major market crashes. This can be very useful in strategic designing of financial systems and regulating the markets in order to tackle financial instabilities.

q-fin.ST↗

arXiv2020

Degree difference: A simple measure to characterize structural heterogeneity in complex networks

Despite the growing interest in characterizing the local geometry leading to the global topology of networks, our understanding of the local structure of complex networks, especially real-world networks, is still incomplete. Here, we analyze a simple, elegant yet underexplored measure, `degree difference' (DD) between vertices of an edge, to understand the local network geometry. We describe the connection between DD and global assortativity of the network from both formal and conceptual perspective, and show that DD can reveal structural properties that are not obtained from other such measures in network science. Typically, edges with different DD play different structural roles and the DD distribution is an important network signature. Notably, DD is the basic unit of assortativity. We provide an explanation as to why DD can characterize structural heterogeneity in mixing patterns unlike global assortativity and local node assortativity. By analyzing synthetic and real networks, we show that DD distribution can be used to distinguish between different types of networks including those networks that cannot be easily distinguished using degree sequence and global assortativity. Moreover, we show DD to be an indicator for topological robustness of scale-free networks. Overall, DD is a local measure that is simple to define, easy to evaluate, and that reveals structural properties of networks not readily seen from other measures.

cs.SI↗

arXiv2020

In silico identification of potential natural product inhibitors of human proteases key to SARS-CoV-2 infection

Presently, there are no approved drugs or vaccines to treat COVID-19 which has spread to over 200 countries and is responsible for over 3,65,000 deaths worldwide. Recent studies have shown that two human proteases, TMPRSS2 and cathepsin L, play a key role in host cell entry of SARS-CoV-2. Importantly, inhibitors of these proteases were shown to block SARS-CoV-2 infection. Here, we perform virtual screening of 14010 phytochemicals produced by Indian medicinal plants to identify natural product inhibitors of TMPRSS2 and cathepsin L. We built a homology model of TMPRSS2 as an experimentally determined structure is not available. AutoDock Vina was used to perform molecular docking of phytochemicals against TMPRSS2 model structure and cathepsin L crystal structure. Potential phytochemical inhibitors were filtered by comparing their docked binding energies with those of known inhibitors of TMPRSS2 and cathepsin L. Further, the ligand binding site residues and non-covalent protein-ligand interactions were used as an additional filter to identify phytochemical inhibitors that either bind to or form interactions with residues important for the specificity of the target proteases. We have identified 96 inhibitors of TMPRSS2 and 9 inhibitors of cathepsin L among phytochemicals of Indian medicinal plants. The top inhibitors of TMPRSS2 are Edgeworoside C, Adlumidine and Qingdainone, and of cathepsin L is Ararobinol. Interestingly, several herbal sources of identified phytochemical inhibitors have antiviral or anti-inflammatory use in traditional medicine. Further in vitro and in vivo testing is needed before clinical trials of the promising phytochemical inhibitors identified here.

q-bio.BM↗

arXiv2020

A Simple Differential Geometry for Complex Networks

We introduce new definitions of sectional, Ricci and scalar curvature for networks and their higher dimensional counterparts, derived from two classical notions of curvature for curves in general metric spaces, namely, the Menger curvature and the Haantjes curvature. These curvatures are applicable to unweighted or weighted and undirected or directed networks, and are more intuitive and easier to compute than other network curvatures. In particular, the proposed curvatures based on the interpretation of Haantjes definition as geodesic curvature allow us to give a network analogue of the classical local Gauss-Bonnet theorem. Furthermore, we propose even simpler and more intuitive proxies for the Haantjes curvature that allow for even faster and easier computations in large-scale networks. In addition, we also investigate the embedding properties of the proposed Ricci curvatures. Lastly, we also investigate the behaviour, both on model and real-world networks, of the curvatures introduced herein with more established notions of Ricci curvature and other widely-used network measures.

math.MG↗

arXiv2019

Forman-Ricci curvature and Persistent homology of unweighted complex networks

We present the application of topological data analysis (TDA) to study unweighted complex networks via their persistent homology. By endowing appropriate weights that capture the inherent topological characteristics of such a network, we convert an unweighted network into a weighted one. Standard TDA tools are then used to compute their persistent homology. To this end, we use two main quantifiers: a local measure based on Forman's discretized version of Ricci curvature, and a global measure based on edge betweenness centrality. We have employed these methods to study various model and real-world networks. Our results show that persistent homology can be used to distinguish between model and real networks with different topological properties.

cs.DM↗

arXiv2019

A Simple Differential Geometry for Networks and its Generalizations

Based on two classical notions of curvature for curves in general metric spaces, namely the Menger and Haantjes curvatures, we introduce new definitions of sectional, Ricci and scalar curvature for networks and their higher dimensional counterparts. These new types of curvature, that apply to weighted and unweighted, directed or undirected networks, are far more intuitive and easier to compute, than other network curvatures. In particular, the proposed curvatures based on the interpretation of Haantjes definition as geodesic curvature, and derived via a fitting discrete Gauss-Bonnet Theorem, are quite flexible. We also propose even simpler and more intuitive substitutes of the Haantjes curvature, that allow for even faster and easier computations in large-scale networks.

math.MG↗

arXiv2019

Persistent homology of unweighted complex networks via discrete Morse theory

Topological data analysis can reveal higher-order structure beyond pairwise connections between vertices in complex networks. We present a new method based on discrete Morse theory to study topological properties of unweighted and undirected networks using persistent homology. Leveraging on the features of discrete Morse theory, our method not only captures the topology of the clique complex of such graphs via the concept of critical simplices, but also achieves close to the theoretical minimum number of critical simplices in several analyzed model and real networks. This leads to a reduced filtration scheme based on the subsequence of the corresponding critical weights, thereby leading to a significant increase in computational efficiency. We have employed our filtration scheme to explore the persistent homology of several model and real-world networks. In particular, we show that our method can detect differences in the higher-order structure of networks, and the corresponding persistence diagrams can be used to distinguish between different model networks. In summary, our method based on discrete Morse theory further increases the applicability of persistent homology to investigate the global topology of complex networks.

cs.DM↗

arXiv2018

Discrete Ricci curvatures for directed networks

A goal in network science is the geometrical characterization of complex networks. In this direction, we have recently introduced Forman's discretization of Ricci curvature to the realm of undirected networks. Investigation of this edge-centric network measure, Forman-Ricci curvature, in diverse model and real-world undirected networks revealed that the curvature measure captures several aspects of the organization of undirected complex networks. However, many important real-world networks are inherently directed in nature, and the definition of the Forman-Ricci curvature for undirected networks is unsuitable for the analysis of such directed networks. Hence, we here extend the Forman-Ricci curvature for undirected networks to the case of directed networks. The simple mathematical formula for the Forman-Ricci curvature of a directed edge elegantly incorporates vertex weights, edge weights and edge direction. Furthermore we have compared the Forman-Ricci curvature with the adaptation to directed networks of another discrete notion of Ricci curvature, namely, the well established Ollivier-Ricci curvature. However, the two above-mentioned curvature measures do not account for higher-order correlations between vertices. To this end, we adjusted Forman's original definition of Ricci curvature to account for directed simplicial complexes and also explored the potential of this new, augmented type of Forman-Ricci curvature, in directed complex networks.

math.MG↗

arXiv2018

Comparative analysis of two discretizations of Ricci curvature for complex networks

We have performed an empirical comparison of two distinct notions of discrete Ricci curvature for graphs or networks, namely, the Forman-Ricci curvature and Ollivier-Ricci curvature. Importantly, these two discretizations of the Ricci curvature were developed based on different properties of the classical smooth notion, and thus, the two notions shed light on different aspects of network structure and behavior. Nevertheless, our extensive computational analysis in a wide range of both model and real-world networks shows that the two discretizations of Ricci curvature are highly correlated in many networks. Moreover, we show that if one considers the augmented Forman-Ricci curvature which also accounts for the two-dimensional simplicial complexes arising in graphs, the observed correlation between the two discretizations is even higher, especially, in real networks. Besides the potential theoretical implications of these observations, the close relationship between the two discretizations has practical implications whereby Forman-Ricci curvature can be employed in place of Ollivier-Ricci curvature for faster computation in larger real-world networks whenever coarse analysis suffices.

math.DG↗

arXiv2017

Network approach towards understanding the crazing in glassy amorphous polymers

We have used molecular dynamics to simulate an amorphous glassy polymer with long chains to study deformation mechanism of crazing and associated void statistics. The Van der Waals interactions and the entanglements between chains constituting the polymer play a crucial role in crazing. Thus, we have reconstructed two underlying weighted networks, namely, the Van der Waals network and the Entanglement network from polymer configurations extracted from the molecular dynamics simulation. Subsequently, we have performed graph-theoretic analysis of the two reconstructed networks to reveal the role played by them in crazing of polymers. Our analysis captured various stages of crazing through specific trends in the network measures for Van der Waals networks and entanglement networks. To further corroborate the effectiveness of network analysis in unraveling the underlying physics of crazing in polymers, we have contrasted the trends in network measures for Van der Waals networks and entanglement networks in the light of stress-strain behaviour and voids statistics during deformation. We find that Van der Waals network plays a crucial role in craze initiation and growth. Although, the entanglement network was found to maintain its structure during craze initiation stage, it was found to progressively weaken and undergo dynamic changes during the hardening and failure stages of crazing phenomena. Our work demonstrates the utility of network theory in quantifying the underlying physics of polymer crazing and widens the scope of applications of network science to characterization of deformation mechanisms in diverse polymers.

cond-mat.soft↗

arXiv2017

Systematic evaluation of a new combinatorial curvature for complex networks

We have recently introduced Forman's discretization of Ricci curvature to the realm of complex networks. Forman curvature is an edge-based measure whose mathematical definition elegantly encapsulates the weights of nodes and edges in a complex network. In this contribution, we perform a comparative analysis of Forman curvature with other edge-based measures such as edge betweenness, embeddedness and dispersion in diverse model and real networks. We find that Forman curvature in comparison to embeddedness or dispersion is a better indicator of the importance of an edge for the large-scale connectivity of complex networks. Based on the definition of the Forman curvature of edges, there are two natural ways to define the Forman curvature of nodes in a network. In this contribution, we also examine these two possible definitions of Forman curvature of nodes in diverse model and real networks. Based on our empirical analysis, we find that in practice the unnormalized definition of the Forman curvature of nodes with the choice of combinatorial node weights is a better indicator of the importance of nodes in complex networks.

q-bio.MN↗

arXiv2017

Forman curvature for directed networks

A goal in network science is the geometrical characterization of complex networks. In this direction, we (arXiv:1603.00386; J. Stat. Mech. (2016) P063206) have recently introduced the Forman's discretization of Ricci curvature to the realm of undirected networks. Investigation of Forman curvature in diverse model and real-world undirected networks revealed that this measure captures several aspects of the organization of complex undirected networks. However, many important real-world networks are inherently directed in nature, and the Forman curvature for undirected networks is unsuitable for analysis of such directed networks. Hence, we here extend the Forman curvature for undirected networks to the case of directed networks. The simple mathematical formula for the Forman curvature in directed networks elegantly incorporates node weights, edge weights and edge direction. By applying the Forman curvature for directed networks to a variety of model and real-world directed networks, we show that the measure can be used to characterize the structure of complex directed networks. Furthermore, our results also hold in real directed networks which are weighted or spatial in nature. These results in combination with our previous results suggest that the Forman curvature can be readily employed to study the organization of both directed and undirected complex networks.

q-bio.MN↗