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George Panagopoulos

Publications and source records attributed to George Panagopoulos.

At least 19 recordsLinked to original sources

Real vs. Semi-Simulated: Rethinking Evaluation for Treatment Effect Estimation

Estimating heterogeneous treatment effects with machine learning has attracted substantial attention in both academic research and industrial practice. However, the two communities often evaluate models under markedly different conditions. Methodological work typically relies on semi-simulated benchmarks and metrics that require counterfactual outcomes, whereas real-world applications rely on observable metrics based on ranking or test outcomes. Despite the well-known gap between methodological progress and practical deployment, the relationship between these evaluation regimes has not been examined systematically. We conduct a large-scale empirical study of treatment effect evaluation across standard semi-simulated benchmark families and real-world datasets. Our benchmark covers meta-learners paired with multiple base learners, as well as specialized causal machine learning models. We evaluate these methods using observable metrics common in application-oriented literature, alongside counterfactual metrics commonly used in methods papers. Our results reveal two complementary gaps. First, counterfactual metrics do not reliably recover the estimators preferred by observable metrics, even on the same semi-simulated benchmarks. Second, rankings obtained on semi-simulated benchmarks do not transfer to real datasets. We further find that simple meta-learners with strong base models are consistently competitive, in contrast to specialized causal models. Overall, our findings suggest that progress in treatment effect estimation research should not be assessed solely through counterfactual metrics and semi-simulated benchmarks, but it would benefit from incorporating observable metrics and real-data validation.

cs.LG

The most general four-derivative Unitary String Effective Action with Torsion and Stringy-Running-Vacuum-Model Inflation: Old ideas from a modern perspective

The string-inspired running vacuum model (StRVM) of inflation is based on a Chern-Simons (CS) gravity effective action, in which the only four-spacetime-derivative-order term is a gravitational anomalous CS Pontryagin density coupled to an axion. In this work, we revisit curvature-squared string-inspired effective actions, from the point of view of appropriate local field redefinitions, leaving the perturbative string scattering matrices invariant. We require simultaneously unitarity and torsion interpretation of the field strength of the Kalb-Ramond antisymmetric tensor, features characterising the (3+1)-dimensional StRVM Cosmology. Unlike the higher dimensional case, the above feature is possible in the context of (3+1)-dimensional spacetimes, obtained after string compactification. We demonstrate that the unitarity and torsion-interpretation requirements lead to a single-type of extra four-derivative terms in the effective gravitational action, not discussed in the previous literature of StRVM, which however is shown to be subleading by many orders of magnitude, compared to the terms of the StRVM framework. Hence, its presence has no practical implications for the relevant inflationary (and, hence, postinflationary) physics of the StRVM. This demonstrates the phenomenological completeness of the StRVM cosmological scenario, which is thus fully embeddable in the UV complete (quantum-gravity compatible) string theory framework.

gr-qc

Kolmogorov-Arnold Network for Gene Regulatory Network Inference

Gene regulation is central to understanding cellular processes and development, potentially leading to the discovery of new treatments for diseases and personalized medicine. Inferring gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data presents significant challenges due to its high dimensionality and complexity. Existing tree-based models, such as GENIE3 and GRNBOOST2, demonstrated scalability and explainability in GRN inference, but they cannot distinguish regulation types nor effectively capture continuous cellular dynamics. In this paper, we introduce scKAN, a novel model that employs a Kolmogorov-Arnold network (KAN) with explainable AI to infer GRNs from scRNA-seq data. By modeling gene expression as differentiable functions matching the smooth nature of cellular dynamics, scKAN can accurately and precisely detect activation and inhibition regulations through explainable AI and geometric tools. We conducted extensive experiments on the BEELINE benchmark, and scKAN surpasses and improves the leading signed GRN inference models ranging from 5.40\% to 28.37\% in AUROC and from 1.97\% to 40.45\% in AUPRC. These results highlight the potential of scKAN in capturing the underlying biological processes in gene regulation without prior knowledge of the graph structure.

cs.CE

Efficient Data Selection for Training Genomic Perturbation Models

Genomic studies face a vast hypothesis space, while interventions such as gene perturbations remain costly and time-consuming. To accelerate such experiments, gene perturbation models predict the transcriptional outcome of interventions. Since constructing the training set is challenging, active learning is often employed in a "lab-in-the-loop" process. While this strategy makes training more targeted, it is substantially slower, as it fails to exploit the inherent parallelizability of Perturb-seq experiments. Here, we focus on graph neural network-based gene perturbation models and propose a subset selection method that, unlike active learning, selects the training perturbations in one shot. Our method chooses the interventions that maximize the propagation of the supervision signal to the model. The selection criterion is defined over the input knowledge graph and is optimized with submodular maximization, ensuring a near-optimal guarantee. Experimental results across multiple datasets show that, in addition to providing months of acceleration compared to active learning, the method improves the stability of perturbation choices while maintaining competitive predictive accuracy.

q-bio.QM

Integrating Optimal Transport and Structural Inference Models for GRN Inference from Single-cell Data

We introduce a novel gene regulatory network (GRN) inference method that integrates optimal transport (OT) with a deep-learning structural inference model. Advances in next-generation sequencing enable detailed yet destructive gene expression assays at the single-cell level, resulting in the loss of cell evolutionary trajectories. Due to technological and cost constraints, single-cell experiments often feature cells sampled at irregular and sparse time points with a small sample size. Although trajectory-based structural inference models can accurately reveal the underlying interaction graph from observed data, their efficacy depends on the inputs of thousands of regularly sampled trajectories. The irregularly-sampled nature of single-cell data precludes the direct use of these powerful models for reconstructing GRNs. Optimal transport, a classical mathematical framework that minimize transportation costs between distributions, has shown promise in multi-omics data integration and cell fate prediction. Utilizing OT, our method constructs mappings between consecutively sampled cells to form cell-level trajectories, which are given as input to a structural inference model that recovers the GRN from single-cell data. Through case studies in two synthetic datasets, we demonstrate the feasibility of our proposed method and its promising performance over eight state-of-the-art GRN inference methods.

cs.CE

Metrics to Detect Small-Scale and Large-Scale Citation Orchestration

Citation counts and related metrics have pervasive uses and misuses in academia and research appraisal, serving as scholarly influence and recognition measures. Hence, comprehending the citation patterns exhibited by authors is essential for assessing their research impact and contributions within their respective fields. Although the h-index, introduced by Hirsch in 2005, has emerged as a popular bibliometric indicator, it fails to account for the intricate relationships between authors and their citation patterns. This limitation becomes particularly relevant in cases where citations are strategically employed to boost the perceived influence of certain individuals or groups, a phenomenon that we term "orchestration". Orchestrated citations can introduce biases in citation rankings and therefore necessitate the identification of such patterns. Here, we use Scopus data to investigate orchestration of citations across all scientific disciplines. Orchestration could be small-scale, when the author him/herself and/or a small number of other authors use citations strategically to boost citation metrics like h-index; or large-scale, where extensive collaborations among many co-authors lead to high h-index for many/all of them. We propose three orchestration indicators: extremely low values in the ratio of citations over the square of the h-index (indicative of small-scale orchestration); extremely small number of authors who can explain at least 50% of an author's total citations (indicative of either small-scale or large-scale orchestration); and extremely large number of co-authors with more than 50 co-authored papers (indicative of large-scale orchestration). The distributions, potential thresholds based on 1% (and 5%) percentiles, and insights from these indicators are explored and put into perspective across science.

cs.DL

KAGNNs: Kolmogorov-Arnold Networks meet Graph Learning

In recent years, Graph Neural Networks (GNNs) have become the de facto tool for learning node and graph representations. Most GNNs typically consist of a sequence of neighborhood aggregation (a.k.a., message-passing) layers, within which the representation of each node is updated based on those of its neighbors. The most expressive message-passing GNNs can be obtained through the use of the sum aggregator and of MLPs for feature transformation, thanks to their universal approximation capabilities. However, the limitations of MLPs recently motivated the introduction of another family of universal approximators, called Kolmogorov-Arnold Networks (KANs) which rely on a different representation theorem. In this work, we compare the performance of KANs against that of MLPs on graph learning tasks. We implement three new KAN-based GNN layers, inspired respectively by the GCN, GAT and GIN layers. We evaluate two different implementations of KANs using two distinct base families of functions, namely B-splines and radial basis functions. We perform extensive experiments on node classification, link prediction, graph classification and graph regression datasets. Our results indicate that KANs are on-par with or better than MLPs on all tasks studied in this paper. We also show that the size and training speed of RBF-based KANs is only marginally higher than for MLPs, making them viable alternatives. Code available at https://github.com/RomanBresson/KAGNN.

cs.LG

Uplift Modeling Under Limited Supervision

Estimating causal effects in e-commerce tends to involve costly treatment assignments which can be impractical in large-scale settings. Leveraging machine learning to predict such treatment effects without actual intervention is a standard practice to diminish the risk. However, existing methods for treatment effect prediction tend to rely on training sets of substantial size, which are built from real experiments and are thus inherently risky to create. In this work we propose a graph neural network to diminish the required training set size, relying on graphs that are common in e-commerce data. Specifically, we view the problem as node regression with a restricted number of labeled instances, develop a two-model neural architecture akin to previous causal effect estimators, and test varying message-passing layers for encoding. Furthermore, as an extra step, we combine the model with an acquisition function to guide the creation of the training set in settings with extremely low experimental budget. The framework is flexible since each step can be used separately with other models or treatment policies. The experiments on real large-scale networks indicate a clear advantage of our methodology over the state of the art, which in many cases performs close to random, underlining the need for models that can generalize with limited supervision to reduce experimental risks.

cs.LG

Maximizing Influence with Graph Neural Networks

Finding the seed set that maximizes the influence spread over a network is a well-known NP-hard problem. Though a greedy algorithm can provide near-optimal solutions, the subproblem of influence estimation renders the solutions inefficient. In this work, we propose \textsc{Glie}, a graph neural network that learns how to estimate the influence spread of the independent cascade. \textsc{Glie} relies on a theoretical upper bound that is tightened through supervised training. Experiments indicate that it provides accurate influence estimation for real graphs up to 10 times larger than the train set. Subsequently, we incorporate it into two influence maximization techniques. We first utilize Cost Effective Lazy Forward optimization substituting Monte Carlo simulations with \textsc{Glie}, surpassing the benchmarks albeit with a computational overhead. To improve computational efficiency we develop a provably submodular influence spread based on \textsc{Glie}'s representations, to rank nodes while building the seed set adaptively. The proposed algorithms are inductive, meaning they are trained on graphs with less than 300 nodes and up to 5 seeds, and tested on graphs with millions of nodes and up to 200 seeds. The final method exhibits the most promising combination of time efficiency and influence quality, outperforming several baselines.

cs.LG

Exploratory Analysis of Academic Collaborations between French and US

International academic collaborations cultivate diversity in the research landscape and facilitate multiperspective methods, as the scope of each country's science depends on its needs, history, wealth etc. Moreover the quality of science differ significantly amongst nations\cite{king2004scientific}, which renders international collaborations a potential source to understand the dynamics between countries and their advancements. Analyzing these collaborations can reveal sharing expertise between two countries in different fields, the most well-known institutions of a nation, the overall success of collaborative efforts compared to local ones etc. Such analysis were initially performed using statistical metrics \cite{melin1996studying}, but network analysis has later proven much more expressive \cite{wagner2005mapping,gonzalez2008coauthorship}. In this exploratory analysis, we aim to examine the collaboration patterns between French and US institutions. Towards this, we capitalize on the Microsoft Academic Graph MAG \cite{sinha2015overview}, the largest open bibliographic dataset that contains detailed information for authors, publications and institutions. We use the coordinates of the world map to tally affiliations to France or USA. In cases where the coordinates of an affiliation were absent, we used its Wikipedia url and named entity recognition to identify the country of its address in the Wikipedia page. We need to stress that institute names have been volatile (due to University federations created) in the last decade in France, so this is a best effort trial. The results indicate an intensive and increasing scientific production in with , with certain institutions such as Harvard, MIT and CNRS standing out.

cs.DL

Perturbative study of the Gluino-Glue operator in SYM

We investigate the renormalization of the Gluino-Glue operator, using both Lattice Perturbation Theory (LPT) and a Gauge Invariant Renormalization Scheme (GIRS). The latter scheme involves gauge-invariant Green's functions of two operators at different space-time points, which can be also computed via numerical simulations. There is no need to fix a gauge and the mixing with gauge noninvariant operators is inconsequential. We calculate perturbatively the conversion factor relating GIRS with the Modified Minimal Subtraction scheme. On the other hand, the Gluino-Glue operator being mixes with several gauge noninvariant operators which have the same quantum numbers. The determination of the mixing matrix on the lattice demands the calculation of 2-pt and 3-pt Green's functions with external gluon, gluino and ghost fields using LPT. We compute at one-loop order the renormalization of the Gluino-Glue operator and all operator mixing coefficients.

hep-lat

PyTorch Geometric Temporal: Spatiotemporal Signal Processing with Neural Machine Learning Models

We present PyTorch Geometric Temporal a deep learning framework combining state-of-the-art machine learning algorithms for neural spatiotemporal signal processing. The main goal of the library is to make temporal geometric deep learning available for researchers and machine learning practitioners in a unified easy-to-use framework. PyTorch Geometric Temporal was created with foundations on existing libraries in the PyTorch eco-system, streamlined neural network layer definitions, temporal snapshot generators for batching, and integrated benchmark datasets. These features are illustrated with a tutorial-like case study. Experiments demonstrate the predictive performance of the models implemented in the library on real world problems such as epidemiological forecasting, ridehail demand prediction and web-traffic management. Our sensitivity analysis of runtime shows that the framework can potentially operate on web-scale datasets with rich temporal features and spatial structure.

cs.LG

Transfer Graph Neural Networks for Pandemic Forecasting

The recent outbreak of COVID-19 has affected millions of individuals around the world and has posed a significant challenge to global healthcare. From the early days of the pandemic, it became clear that it is highly contagious and that human mobility contributes significantly to its spread. In this paper, we study the impact of population movement on the spread of COVID-19, and we capitalize on recent advances in the field of representation learning on graphs to capture the underlying dynamics. Specifically, we create a graph where nodes correspond to a country's regions and the edge weights denote human mobility from one region to another. Then, we employ graph neural networks to predict the number of future cases, encoding the underlying diffusion patterns that govern the spread into our learning model. Furthermore, to account for the limited amount of training data, we capitalize on the pandemic's asynchronous outbreaks across countries and use a model-agnostic meta-learning based method to transfer knowledge from one country's model to another's. We compare the proposed approach against simple baselines and more traditional forecasting techniques in 3 European countries. Experimental results demonstrate the superiority of our method, highlighting the usefulness of GNNs in epidemiological prediction. Transfer learning provides the best model, highlighting its potential to improve the accuracy of the predictions in case of secondary waves, if data from past/parallel outbreaks is utilized.

cs.SI

Can Author Collaboration Reveal Impact? The Case of h-index

Scientific impact has been the center of extended debate regarding its accuracy and reliability. From hiring committees in academic institutions to governmental agencies that distribute funding, an author's scientific success as measured by the h-index is a vital point to their career. The objective of this work is to investigate whether the collaboration patterns of an author are good predictors of the author's future $h$-index. Although not directly related to each other, a more intense collaboration can result into increased productivity which can potentially have an impact on the author's future $h$-index. In this paper, we capitalize on recent advances in graph neural networks and we examine the possibility of predicting the $h$-index relying solely on the author's collaboration and the textual content of a subset of their papers. We perform our experiments on a large-scale network consisting of more than $1$ million authors that have published papers in computer science venues and more than $37$ million edges. The task is a six-months-ahead forecast, i.e. what the $h$-index of each author will be after six months. Our experiments indicate that there is indeed some relationship between the future $h$-index of an author and their structural role in the co-authorship network. Furthermore, we found that the proposed method outperforms standard machine learning techniques based on simple graph metrics along with node representations learned from the textual content of the author's papers.

cs.SI

Gauge-invariant Renormalization of the Gluino-Glue operator

We study the Gluino-Glue operator in the context of Supersymmetric ${\cal N}{=}1$ Yang-Mills (SYM) theory. This composite operator is gauge invariant, and it is directly connected to light bound states of the theory; its renormalization is very important as a necessary step for the study of low-lying bound states via numerical simulations. We make use of a Gauge-Invariant Renormalization Scheme (GIRS). This requires the calculation of the Green's function of a product of two Gluino-Glue operators, situated at distinct space-time points. Within this scheme, the mixing with non-gauge invariant operators which have the same quantum numbers is inconsequential. We compute the one-loop conversion factor relating the GIRS scheme to $\overline{\rm MS}$. This conversion factor can be used in order to convert to $\overline{\rm MS}$ Green's functions which are obtained via lattice simulations and are renormalized nonperturbatively in GIRS.

hep-lat

Two-loop renormalization and mixing of gluon and quark energy-momentum tensor operators

In this paper, we present one- and two-loop results for the renormalization of the gluon and quark gauge-invariant operators which appear in the definition of the QCD energy-momentum tensor, in dimensional regularization. To this end, we consider a variety of Green's functions with different incoming momenta. We identify the set of twist-2 symmetric traceless and flavor singlet operators which mix among themselves and we calculate the corresponding mixing coefficients for the nondiagonal components. We also provide results for some appropriate regularization-independent (RI')-like schemes, which address this mixing, and we discuss their application to nonperturbative studies via lattice simulations. Finally, we extract the one- and two-loop expressions of the conversion factors between the proposed RI' and the MSbar schemes. From our results regarding the MSbar-renormalized Green's functions, one can easily derive conversion factors relating numerous variants of RI'-like schemes to MSbar. To make our results easily accessible, we also provide them as Supplemental Material, in the form of a Mathematica input file and, also, an equivalent text file.

hep-lat

Multi-task Learning for Influence Estimation and Maximization

We address the problem of influence maximization when the social network is accompanied by diffusion cascades. In prior works, such information is used to compute influence probabilities, which is utilized by stochastic diffusion models in influence maximization. Motivated by the recent criticism on the effectiveness of diffusion models as well as the galloping advancements in influence learning, we propose IMINFECTOR (Influence Maximization with INFluencer vECTORs), a unified approach that uses representations learned from diffusion cascades to perform model-independent influence maximization that scales in real-world datasets. The first part of our methodology is a multi-task neural network that learns embeddings of nodes that initiate cascades (influencer vectors) and embeddings of nodes that participate in them (susceptible vectors). The norm of an influencer vector captures the ability of the node to create lengthy cascades and is used to estimate the expected influence spread and reduce the number of candidate seeds. In addition, the combination of influencer and susceptible vectors form the diffusion probabilities between nodes. These are used to reformulate the network as a bipartite graph and propose a greedy solution to influence maximization that retains the theoretical guarantees.We a pply our method in three sizable networks with diffusion cascades and evaluate it using cascades from future time steps. IMINFECTOR is able to scale in all of them and outperforms various competitive algorithms and metrics from the diverse landscape of influence maximization in terms of efficiency and seed set quality.

cs.SI

A new branch of inflationary speed limits

We present a new mechanism for inflation which exhibits a speed limit on scalar motion, generating accelerated expansion even on a steep potential. This arises from explicitly integrating out the short modes of additional fields coupled to the inflaton $ϕ$ via a dimension six operator, yielding an expression for the effective action which includes a nontrivial (logarithmic) function of $(\partialϕ)^2$. The speed limit appears at the branch cut of this logarithm arising in a large flavor expansion, similarly to the square root branch cut in DBI inflation arising in a large color expansion. Finally, we describe observational constraints on the parameters of this model.

hep-th