Md Osman Gani

Uzma Hasan, Emam Hossain, Md Osman Gani

The ability to understand causality from data is one of the major milestones of human-level intelligence. Causal Discovery (CD) algorithms can identify the cause-effect relationships among the variables of a system from related observational data with certain assumptions. Over the years, several methods have been developed primarily based on the statistical properties of data to uncover the underlying causal mechanism. In this study, we present an extensive discussion on the methods designed to perform causal discovery from both independent and identically distributed (I.I.D.) data and time series data. For this purpose, we first introduce the common terminologies used in causal discovery literature and then provide a comprehensive discussion of the algorithms designed to identify causal relations in different settings. We further discuss some of the benchmark datasets available for evaluating the algorithmic performance, off-the-shelf tools or software packages to perform causal discovery readily, and the common metrics used to evaluate these methods. We also evaluate some widely used causal discovery algorithms on multiple benchmark datasets and compare their performances. Finally, we conclude by discussing the research challenges and the applications of causal discovery algorithms in multiple areas of interest.

Riddhiman Adib, Md Mobasshir Arshed Naved, Chih-Hao Fang et al.

Structural causal models (SCMs) provide a principled approach to identifying causation from observational and experimental data in disciplines ranging from economics to medicine. However, SCMs, which is typically represented as graphical models, cannot rely only on data, rather require support of domain knowledge. A key challenge in this context is the absence of a methodological framework for encoding priors (background knowledge) into causal models in a systematic manner. We propose an abstraction called causal knowledge hierarchy (CKH) for encoding priors into causal models. Our approach is based on the foundation of "levels of evidence" in medicine, with a focus on confidence in causal information. Using CKH, we present a methodological framework for encoding causal priors from various information sources and combining them to derive an SCM. We evaluate our approach on a simulated dataset and demonstrate overall performance compared to the ground truth causal model with sensitivity analysis.

Riddhiman Adib, Md Osman Gani, Sheikh Iqbal Ahamed et al.

Delirium occurs in about 80% cases in the Intensive Care Unit (ICU) and is associated with a longer hospital stay, increased mortality and other related issues. Delirium does not have any biomarker-based diagnosis and is commonly treated with antipsychotic drugs (APD). However, multiple studies have shown controversy over the efficacy or safety of APD in treating delirium. Since randomized controlled trials (RCT) are costly and time-expensive, we aim to approach the research question of the efficacy of APD in the treatment of delirium using retrospective cohort analysis. We plan to use the Causal inference framework to look for the underlying causal structure model, leveraging the availability of large observational data on ICU patients. To explore safety outcomes associated with APD, we aim to build a causal model for delirium in the ICU using large observational data sets connecting various covariates correlated with delirium. We utilized the MIMIC III database, an extensive electronic health records (EHR) dataset with 53,423 distinct hospital admissions. Our null hypothesis is: there is no significant difference in outcomes for delirium patients under different drug-group in the ICU. Through our exploratory, machine learning based and causal analysis, we had findings such as: mean length-of-stay and max length-of-stay is higher for patients in Haloperidol drug group, and haloperidol group has a higher rate of death in a year compared to other two-groups. Our generated causal model explicitly shows the functional relationships between different covariates. For future work, we plan to do time-varying analysis on the dataset.

Sourajit Saha, Shaswati Saha, Md Osman Gani et al.

Learning High-Resolution representations is essential for semantic segmentation. Convolutional neural network (CNN)architectures with downstream and upstream propagation flow are popular for segmentation in medical diagnosis. However, due to performing spatial downsampling and upsampling in multiple stages, information loss is inexorable. On the contrary, connecting layers densely on high spatial resolution is computationally expensive. In this work, we devise a Loose Dense Connection Strategy to connect neurons in subsequent layers with reduced parameters. On top of that, using a m-way Tree structure for feature propagation we propose Receptive Field Chain Network (RFC-Net) that learns high resolution global features on a compressed computational space. Our experiments demonstrates that RFC-Net achieves state-of-the-art performance on Kvasir and CVC-ClinicDB benchmarks for Polyp segmentation.

Uzma Hasan, Md Osman Gani

Learning causal relationships solely from observational data often fails to reveal the underlying causal mechanisms due to the vast search space of possible causal graphs, which can grow exponentially, especially for greedy algorithms using score-based approaches. Leveraging prior causal information, such as the presence or absence of causal edges, can help restrict and guide the score-based discovery process, leading to a more accurate search. In the healthcare domain, prior knowledge is abundant from sources like medical journals, electronic health records (EHRs), and clinical intervention outcomes. This study introduces a knowledge-guided causal structure search (KGS) approach that utilizes observational data and structural priors (such as causal edges) as constraints to learn the causal graph. KGS leverages prior edge information between variables, including the presence of a directed edge, the absence of an edge, and the presence of an undirected edge. We extensively evaluate KGS in multiple settings using synthetic and benchmark real-world datasets, as well as in a real-life healthcare application related to oxygen therapy treatment. To obtain causal priors, we use GPT-4 to retrieve relevant literature information. Our results show that structural priors of any type and amount enhance the search process, improving performance and optimizing causal discovery. This guided strategy ensures that the discovered edges align with established causal knowledge, enhancing the trustworthiness of findings while expediting the search process. It also enables a more focused exploration of causal mechanisms, potentially leading to more effective and personalized healthcare solutions.

Sahara Ali, Uzma Hasan, Xingyan Li et al.

This survey paper covers the breadth and depth of time-series and spatiotemporal causality methods, and their applications in Earth Science. More specifically, the paper presents an overview of causal discovery and causal inference, explains the underlying causal assumptions, and enlists evaluation techniques and key terminologies of the domain area. The paper elicits the various state-of-the-art methods introduced for time-series and spatiotemporal causal analysis along with their strengths and limitations. The paper further describes the existing applications of several methods for answering specific Earth Science questions such as extreme weather events, sea level rise, teleconnections etc. This survey paper can serve as a primer for Data Science researchers interested in data-driven causal study as we share a list of resources, such as Earth Science datasets (synthetic, simulated and observational data) and open source tools for causal analysis. It will equally benefit the Earth Science community interested in taking an AI-driven approach to study the causality of different dynamic and thermodynamic processes as we present the open challenges and opportunities in performing causality-based Earth Science study.

Muhammad Hasan Ferdous, Uzma Hasan, Md Osman Gani

Time series data are found in many areas of healthcare such as medical time series, electronic health records (EHR), measurements of vitals, and wearable devices. Causal discovery, which involves estimating causal relationships from observational data, holds the potential to play a significant role in extracting actionable insights about human health. In this study, we present a novel constraint-based causal discovery approach for autocorrelated and non-stationary time series data (CDANs). Our proposed method addresses several limitations of existing causal discovery methods for autocorrelated and non-stationary time series data, such as high dimensionality, the inability to identify lagged causal relationships, and overlooking changing modules. Our approach identifies lagged and instantaneous/contemporaneous causal relationships along with changing modules that vary over time. The method optimizes the conditioning sets in a constraint-based search by considering lagged parents instead of conditioning on the entire past that addresses high dimensionality. The changing modules are detected by considering both contemporaneous and lagged parents. The approach first detects the lagged adjacencies, then identifies the changing modules and contemporaneous adjacencies, and finally determines the causal direction. We extensively evaluated our proposed method on synthetic and real-world clinical datasets, and compared its performance with several baseline approaches. The experimental results demonstrate the effectiveness of the proposed method in detecting causal relationships and changing modules for autocorrelated and non-stationary time series data.

Muhammad Hasan Ferdous, Uzma Hasan, Md Osman Gani

Conventional temporal causal discovery (CD) methods suffer from high dimensionality, fail to identify lagged causal relationships, and often ignore dynamics in relations. In this study, we present a novel constraint-based CD approach for autocorrelated and non-stationary time series data (eCDANs) capable of detecting lagged and contemporaneous causal relationships along with temporal changes. eCDANs addresses high dimensionality by optimizing the conditioning sets while conducting conditional independence (CI) tests and identifies the changes in causal relations by introducing a surrogate variable to represent time dependency. Experiments on synthetic and real-world data show that eCDANs can identify time influence and outperform the baselines.

Emam Hossain, Muhammad Hasan Ferdous, Jianwu Wang et al.

Traditional machine learning and deep learning techniques rely on correlation-based learning, often failing to distinguish spurious associations from true causal relationships, which limits robustness, interpretability, and generalizability. To address these challenges, we propose a causality-driven deep learning framework that integrates Multivariate Granger Causality (MVGC) and PCMCI+ causal discovery algorithms with a hybrid deep learning architecture. Using 43 years (1979-2021) of daily and monthly Arctic Sea Ice Extent (SIE) and ocean-atmospheric datasets, our approach identifies causally significant factors, prioritizes features with direct influence, reduces feature overhead, and improves computational efficiency. Experiments demonstrate that integrating causal features enhances the deep learning model's predictive accuracy and interpretability across multiple lead times. Beyond SIE prediction, the proposed framework offers a scalable solution for dynamic, high-dimensional systems, advancing both theoretical understanding and practical applications in predictive modeling.

Muhammad Hasan Ferdous, Emam Hossain, Md Osman Gani

Robust causal discovery in time series datasets depends on reliable benchmark datasets with known ground-truth causal relationships. However, such datasets remain scarce, and existing synthetic alternatives often overlook critical temporal properties inherent in real-world data, including nonstationarity driven by trends and seasonality, irregular sampling intervals, and the presence of unobserved confounders. To address these challenges, we introduce TimeGraph, a comprehensive suite of synthetic time-series benchmark datasets that systematically incorporates both linear and nonlinear dependencies while modeling key temporal characteristics such as trends, seasonal effects, and heterogeneous noise patterns. Each dataset is accompanied by a fully specified causal graph featuring varying densities and diverse noise distributions and is provided in two versions: one including unobserved confounders and one without, thereby offering extensive coverage of real-world complexity while preserving methodological neutrality. We further demonstrate the utility of TimeGraph through systematic evaluations of state-of-the-art causal discovery algorithms including PCMCI+, LPCMCI, and FGES across a diverse array of configurations and metrics. Our experiments reveal significant variations in algorithmic performance under realistic temporal conditions, underscoring the need for robust synthetic benchmarks in the fair and transparent assessment of causal discovery methods. The complete TimeGraph suite, including dataset generation scripts, evaluation metrics, and recommended experimental protocols, is freely available to facilitate reproducible research and foster community-driven advancements in time-series causal discovery.

Emam Hossain, Md Osman Gani

Conventional machine learning and deep learning models typically rely on correlation-based learning, which often fails to distinguish genuine causal relationships from spurious associations, limiting their robustness, interpretability, and ability to generalize. To overcome these limitations, we introduce a causality-aware deep learning framework that integrates Multivariate Granger Causality (MVGC) and PCMCI+ for causal feature selection within a hybrid neural architecture. Leveraging 43 years (1979-2021) of Arctic Sea Ice Extent (SIE) data and associated ocean-atmospheric variables at daily and monthly resolutions, the proposed method identifies causally influential predictors, prioritizes direct causes of SIE dynamics, reduces unnecessary features, and enhances computational efficiency. Experimental results show that incorporating causal inputs leads to improved prediction accuracy and interpretability across varying lead times. While demonstrated on Arctic SIE forecasting, the framework is broadly applicable to other dynamic, high-dimensional domains, offering a scalable approach that advances both the theoretical foundations and practical performance of causality-informed predictive modeling.

Siyuan Wang, James R. Foulds, Md Osman Gani et al.

In this paper, we introduce CIBER (Claim Investigation Based on Evidence Retrieval), an extension of the Retrieval-Augmented Generation (RAG) framework designed to identify corroborating and refuting documents as evidence for scientific claim verification. CIBER addresses the inherent uncertainty in Large Language Models (LLMs) by evaluating response consistency across diverse interrogation probes. By focusing on the behavioral analysis of LLMs without requiring access to their internal information, CIBER is applicable to both white-box and black-box models. Furthermore, CIBER operates in an unsupervised manner, enabling easy generalization across various scientific domains. Comprehensive evaluations conducted using LLMs with varying levels of linguistic proficiency reveal CIBER's superior performance compared to conventional RAG approaches. These findings not only highlight the effectiveness of CIBER but also provide valuable insights for future advancements in LLM-based scientific claim verification.

Muhammad Hasan Ferdous, Md Osman Gani

Multivariate time series in domains such as finance, climate science, and healthcare often exhibit long-term trends, seasonal patterns, and short-term fluctuations, complicating causal inference under non-stationarity and autocorrelation. Existing causal discovery methods typically operate on raw observations, making them vulnerable to spurious edges and misattributed temporal dependencies. We introduce a decomposition-based causal discovery framework that separates each time series into trend, seasonal, and residual components and performs component-specific causal analysis. Trend components are assessed using stationarity tests, seasonal components using kernel-based dependence measures, and residual components using constraint-based causal discovery. The resulting component-level graphs are integrated into a unified multi-scale causal structure. This approach isolates long- and short-range causal effects, reduces spurious associations, and improves interpretability. Across extensive synthetic benchmarks and real-world climate data, our framework more accurately recovers ground-truth causal structure than state-of-the-art baselines, particularly under strong non-stationarity and temporal autocorrelation.

Emam Hossain, Muhammad Hasan Ferdous, Devon Dunmire et al.

Causal modeling offers a principled foundation for uncovering stable, invariant relationships in time-series data, thereby improving robustness and generalization under distribution shifts. Yet its potential is underutilized in spatiotemporal Earth observation, where models often depend on purely correlational features that fail to transfer across heterogeneous domains. We propose RIC-TSC, a regionally-informed causal time-series classification framework that embeds lag-aware causal discovery directly into sequence modeling, enabling both predictive accuracy and scientific interpretability. Using multi-modal satellite and reanalysis data-including Sentinel-1 microwave backscatter, Sentinel-2 and Landsat-8 optical reflectance, and CARRA meteorological variables-we leverage Joint PCMCI+ (J-PCMCI+) to identify region-specific and invariant predictors of supraglacial lake evolution in Greenland. Causal graphs are estimated globally and per basin, with validated predictors and their time lags supplied to lightweight classifiers. On a balanced benchmark of 1000 manually labeled lakes from two contrasting melt seasons (2018-2019), causal models achieve up to 12.59% higher accuracy than correlation-based baselines under out-of-distribution evaluation. These results show that causal discovery is not only a means of feature selection but also a pathway to generalizable and mechanistically grounded models of dynamic Earth surface processes.

Md Osman Gani, Somenath Kuiry, Alaka Das et al.

Object detection in natural scenes can be a challenging task. In many real-life situations, the visible spectrum is not suitable for traditional computer vision tasks. Moving outside the visible spectrum range, such as the thermal spectrum or the near-infrared (NIR) images, is much more beneficial in low visibility conditions, NIR images are very helpful for understanding the object's material quality. In this work, we have taken images with both the Thermal and NIR spectrum for the object detection task. As multi-spectral data with both Thermal and NIR is not available for the detection task, we needed to collect data ourselves. Data collection is a time-consuming process, and we faced many obstacles that we had to overcome. We train the YOLO v3 network from scratch to detect an object from multi-spectral images. Also, to avoid overfitting, we have done data augmentation and tune hyperparameters.

Md Osman Gani, Shravan Kethireddy, Marvi Bikak et al.

Recent advances in causal inference techniques, more specifically, in the theory of structural causal models, provide the framework for identification of causal effects from observational data in the cases where the causal graph is identifiable, i.e., the data generating mechanism can be recovered from the joint distribution. However, no such studies have been done to demonstrate this concept with a clinical example. We present a complete framework to estimate the causal effect from observational data by augmenting expert knowledge in the model development phase and with a practical clinical application. Our clinical application entails a timely and important research question, i.e., the effect of oxygen therapy intervention in the intensive care unit (ICU); the result of this project is useful in a variety of disease conditions, including severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) patients in the ICU. We used data from the MIMIC III database, a standard database in the machine learning community that contains 58,976 admissions from an ICU in Boston, MA, for estimating the oxygen therapy effect on morality. We also identified the covariate-specific effect to oxygen therapy from the model for more personalized intervention.