Md Tauhidul Islam

Saleh Afroogh, Seyd Ishtiaque Ahmed, Petra Ahrweiler et al. · cmu

This study provides a cross-disciplinary examination of Explainable Artificial Intelligence (XAI) approaches-focusing on deep neural networks (DNNs) and large language models (LLMs)-and identifies empirical and conceptual limitations in current XAI. We discuss critical symptoms that stem from deeper root causes (i.e., two paradoxes, two conceptual confusions, and five false assumptions). These fundamental problems within the current XAI research field reveal three insights: experimentally, XAI exhibits significant flaws; conceptually, it is paradoxical; and pragmatically, further attempts to reform the paradoxical XAI might exacerbate its confusion-demanding fundamental shifts and new research directions. To move beyond XAI's limitations, we propose a four-pronged synthesized paradigm shift toward reliable and certified AI development. These four components include: verification-focused Interactive AI (IAI) to establish scientific community protocols for certifying AI system performance rather than attempting post-hoc explanations, AI Epistemology for rigorous scientific foundations, User-Sensible AI to create context-aware systems tailored to specific user communities, and Model-Centered Interpretability for faithful technical analysis-together offering comprehensive post-XAI research directions.

Charles Huang, Varun Vasudevan, Oscar Pastor-Serrano et al.

Objective: Knowledge based planning (KBP) typically involves training an end-to-end deep learning model to predict dose distributions. However, training end-to-end methods may be associated with practical limitations due to the limited size of medical datasets that are often used. To address these limitations, we propose a content based image retrieval (CBIR) method for retrieving dose distributions of previously planned patients based on anatomical similarity. Approach: Our proposed CBIR method trains a representation model that produces latent space embeddings of a patient's anatomical information. The latent space embeddings of new patients are then compared against those of previous patients in a database for image retrieval of dose distributions. All source code for this project is available on github. Main Results: The retrieval performance of various CBIR methods is evaluated on a dataset consisting of both publicly available plans and clinical plans from our institution. This study compares various encoding methods, ranging from simple autoencoders to more recent Siamese networks like SimSiam, and the best performance was observed for the multitask Siamese network. Significance: Applying CBIR to inform subsequent treatment planning potentially addresses many limitations associated with end-to-end KBP. Our current results demonstrate that excellent image retrieval performance can be obtained through slight changes to previously developed Siamese networks. We hope to integrate CBIR into automated planning workflow in future works, potentially through methods like the MetaPlanner framework.

Sakib Mostafa, Tarik Massoud, Maximilian Diehn et al.

Tabular data are central to biomedical research, from liquid biopsy and bulk and single-cell transcriptomics to electronic health records and phenotypic profiling. Unlike images or sequences, however, tabular datasets lack intrinsic spatial organization: features are treated as unordered dimensions, and their relationships must be inferred implicitly by the model. This limits the ability of vision architectures to exploit local structure and higher-order feature interactions in non-spatial biomedical data. Here we introduce Dynamic Feature Mapping (Dynomap), an end-to-end deep learning framework that learns a task-optimized spatial topology of features directly from data. Dynomap jointly optimizes feature placement and prediction through a fully differentiable rendering mechanism, without relying on heuristics, predefined groupings, or external priors. By transforming high-dimensional tabular vectors into learned feature maps, Dynomap enables vision-based models to operate effectively on unordered biomedical inputs. Across multiple clinical and biological datasets, Dynomap consistently outperformed classical machine learning, modern deep tabular models, and existing vector-to-image approaches. In liquid biopsy data, Dynomap organized clinically relevant gene signatures into coherent spatial patterns and improved multiclass cancer subtype prediction accuracy by up to 18%. In a Parkinson disease voice dataset, it clustered disease-associated acoustic descriptors and improved accuracy by up to 8%. Similar gains and interpretable feature organization were observed in additional biomedical datasets. These results establish Dynomap as a general strategy for bridging tabular and vision-based deep learning and for uncovering structured, clinically relevant patterns in high-dimensional biomedical data.

Chulong Zhang, Yuming Jiang, Na Li et al.

Pathologists need to combine information from differently stained pathology slices for accurate diagnosis. Deformable image registration is a necessary technique for fusing multi-modal pathology slices. This paper proposes a hybrid deep feature-based deformable image registration framework for stained pathology samples. We first extract dense feature points via the detector-based and detector-free deep learning feature networks and perform points matching. Then, to further reduce false matches, an outlier detection method combining the isolation forest statistical model and the local affine correction model is proposed. Finally, the interpolation method generates the deformable vector field for pathology image registration based on the above matching points. We evaluate our method on the dataset of the Non-rigid Histology Image Registration (ANHIR) challenge, which is co-organized with the IEEE ISBI 2019 conference. Our technique outperforms the traditional approaches by 17% with the Average-Average registration target error (rTRE) reaching 0.0034. The proposed method achieved state-of-the-art performance and ranked 1st in evaluating the test dataset. The proposed hybrid deep feature-based registration method can potentially become a reliable method for pathology image registration.

Rui Yan, Xiaohan Xing, Xun Wang et al.

Cellular identity and function are linked to both their intrinsic genomic makeup and extrinsic spatial context within the tissue microenvironment. Spatial transcriptomics (ST) offers an unprecedented opportunity to study this, providing in situ gene expression profiles at single-cell resolution and illuminating the spatial and functional organization of cells within tissues. However, a significant hurdle remains: ST data is inherently noisy, large, and structurally complex. This complexity makes it intractable for existing computational methods to effectively capture the interplay between spatial interactions and intrinsic genomic relationships, thus limiting our ability to discern critical biological patterns. Here, we present CellScape, a deep learning framework designed to overcome these limitations for high-performance ST data analysis and pattern discovery. CellScape jointly models cellular interactions in tissue space and genomic relationships among cells, producing comprehensive representations that seamlessly integrate spatial signals with underlying gene regulatory mechanisms. This technique uncovers biologically informative patterns that improve spatial domain segmentation and supports comprehensive spatial cellular analyses across diverse transcriptomics datasets, offering an accurate and versatile framework for deep analysis and interpretation of ST data.w

Mingjie Li, Yizheng Chen, Md Tauhidul Islam et al.

U-Net architectures have been instrumental in advancing biomedical image segmentation (BIS) but often struggle with capturing long-range information. One reason is the conventional down-sampling techniques that prioritize computational efficiency at the expense of information retention. This paper introduces a simple but effective strategy, we call it Stair Pooling, which moderates the pace of down-sampling and reduces information loss by leveraging a sequence of concatenated small and narrow pooling operations in varied orientations. Specifically, our method modifies the reduction in dimensionality within each 2D pooling step from $\frac{1}{4}$ to $\frac{1}{2}$. This approach can also be adapted for 3D pooling to preserve even more information. Such preservation aids the U-Net in more effectively reconstructing spatial details during the up-sampling phase, thereby enhancing its ability to capture long-range information and improving segmentation accuracy. Extensive experiments on three BIS benchmarks demonstrate that the proposed Stair Pooling can increase both 2D and 3D U-Net performance by an average of 3.8\% in Dice scores. Moreover, we leverage the transfer entropy to select the optimal down-sampling paths and quantitatively show how the proposed Stair Pooling reduces the information loss.

Koushik Howlader, Md Tauhidul Islam, Wei Le

Accurate prediction of cancer progression remains a challenge due to the high heterogeneity of molecular omics data across patients. While biologically informed models have improved the interpretability of these predictions, a persistent limitation lies in how they encode individual genes to construct pathway representations. Existing hierarchical models typically derive gene features by directly mapping raw molecular inputs, whereas integration frameworks often rely on simple statistical aggregations of patient-level signals. These approaches often fail to explicitly learn a shared base representation for each gene, thereby limiting the expressiveness and biological accuracy of downstream pathway embeddings. To address this, we introduce PATH, a modulation-based, patient-conditioned gene embedding strategy. PATH represents a paradigm shift by starting from a shared base embedding for each gene, preserving a stable biological identity across the population, and then dynamically adapting it using patient-specific copy number variation (CNV) and mutation signals. This allows the model to capture subtle individual molecular variations while maintaining a consistent latent understanding of the gene itself. We integrate PATH into a graph transformer framework that models interactions among biologically connected pathways through pathway-guided attention. Across pancancer metastasis prediction, PATH achieves an F1 score of 0.8766, representing an 8.8 percent improvement over the current SOTA multi-omics benchmarks. Beyond superior predictive accuracy, our approach identifies biologically meaningful pathways and, crucially, reveals disease-state-specific pathway rewiring, offering new insights into the evolving pathway-pathway interactions that drive cancer progression.

Zixia Zhou, Junyan Liu, Wei Emma Wu et al.

Dynamic brain data, teeming with biological and functional insights, are becoming increasingly accessible through advanced measurements, providing a gateway to understanding the inner workings of the brain in living subjects. However, the vast size and intricate complexity of the data also pose a daunting challenge in reliably extracting meaningful information across various data sources. This paper introduces a generalizable unsupervised deep manifold learning for exploration of neurocognitive and behavioral patterns. Unlike existing methods that extract patterns directly from the input data as in the existing methods, the proposed Brain-dynamic Convolutional-Network-based Embedding (BCNE) seeks to capture the brain-state trajectories by deciphering the temporospatial correlations within the data and subsequently applying manifold learning to this correlative representation. The performance of BCNE is showcased through the analysis of several important dynamic brain datasets. The results, both visual and quantitative, reveal a diverse array of intriguing and interpretable patterns. BCNE effectively delineates scene transitions, underscores the involvement of different brain regions in memory and narrative processing, distinguishes various stages of dynamic learning processes, and identifies differences between active and passive behaviors. BCNE provides an effective tool for exploring general neuroscience inquiries or individual-specific patterns.

Ridvan Yesiloglu, Wei Peng, Md Tauhidul Islam et al.

Brain aging synthesis is a critical task with broad applications in clinical and computational neuroscience. The ability to predict the future structural evolution of a subject's brain from an earlier MRI scan provides valuable insights into aging trajectories. Yet, the high-dimensionality of data, subtle changes of structure across ages, and subject-specific patterns constitute challenges in the synthesis of the aging brain. To overcome these challenges, we propose NeuroAR, a novel brain aging simulation model based on generative autoregressive transformers. NeuroAR synthesizes the aging brain by autoregressively estimating the discrete token maps of a future scan from a convenient space of concatenated token embeddings of a previous and future scan. To guide the generation, it concatenates into each scale the subject's previous scan, and uses its acquisition age and the target age at each block via cross-attention. We evaluate our approach on both the elderly population and adolescent subjects, demonstrating superior performance over state-of-the-art generative models, including latent diffusion models (LDM) and generative adversarial networks, in terms of image fidelity. Furthermore, we employ a pre-trained age predictor to further validate the consistency and realism of the synthesized images with respect to expected aging patterns. NeuroAR significantly outperforms key models, including LDM, demonstrating its ability to model subject-specific brain aging trajectories with high fidelity.

Md Tauhidul Islam, Wu Da-Wen, Tang Qing-Qing et al.

Retinal blood vessel segmentation is crucial for diagnosing ocular and cardiovascular diseases. Although the introduction of U-Net in 2015 by Olaf Ronneberger significantly advanced this field, yet issues like limited training data, imbalance data distribution, and inadequate feature extraction persist, hindering both the segmentation performance and optimal model generalization. Addressing these critical issues, the DEFFA-Unet is proposed featuring an additional encoder to process domain-invariant pre-processed inputs, thereby improving both richer feature encoding and enhanced model generalization. A feature filtering fusion module is developed to ensure the precise feature filtering and robust hybrid feature fusion. In response to the task-specific need for higher precision where false positives are very costly, traditional skip connections are replaced with the attention-guided feature reconstructing fusion module. Additionally, innovative data augmentation and balancing methods are proposed to counter data scarcity and distribution imbalance, further boosting the robustness and generalization of the model. With a comprehensive suite of evaluation metrics, extensive validations on four benchmark datasets (DRIVE, CHASEDB1, STARE, and HRF) and an SLO dataset (IOSTAR), demonstrate the proposed method's superiority over both baseline and state-of-the-art models. Particularly the proposed method significantly outperforms the compared methods in cross-validation model generalization.

Md Tauhidul Islam, Lei Xing

Advancements in deep learning are revolutionizing science and engineering. The immense success of deep learning is largely due to its ability to extract essential high-dimensional (HD) features from input data and make inference decisions based on this information. However, current deep neural network (DNN) models face several challenges, such as the requirements of extensive amounts of data and computational resources. Here, we introduce a new learning scheme, referred to as deep-and-wide learning (DWL), to systematically capture features not only within individual input data (intra-data features) but also across the data (inter-data features). Furthermore, we propose a dual-interactive-channel network (D-Net) to realize the DWL, which leverages our Bayesian formulation of low-dimensional (LD) inter-data feature extraction and its synergistic interaction with the conventional HD representation of the dataset, for substantially enhanced computational efficiency and inference. The proposed technique has been applied to data across various disciplines for both classification and regression tasks. Our results demonstrate that DWL surpasses state-of-the-art DNNs in accuracy by a substantial margin with limited training data and improves the computational efficiency by order(s) of magnitude. The proposed DWL strategy dramatically alters the data-driven learning techniques, including emerging large foundation models, and sheds significant insights into the evolving field of AI.

Varun Vasudevan, Maxime Bassenne, Md Tauhidul Islam et al.

Prior studies using graph neural networks (GNNs) for image classification have focused on graphs generated from a regular grid of pixels or similar-sized superpixels. In the latter, a single target number of superpixels is defined for an entire dataset irrespective of differences across images and their intrinsic multiscale structure. On the contrary, this study investigates image classification using graphs generated from an image-specific number of multiscale superpixels. We propose WaveMesh, a new wavelet-based superpixeling algorithm, where the number and sizes of superpixels in an image are systematically computed based on its content. WaveMesh superpixel graphs are structurally different from similar-sized superpixel graphs. We use SplineCNN, a state-of-the-art network for image graph classification, to compare WaveMesh and similar-sized superpixels. Using SplineCNN, we perform extensive experiments on three benchmark datasets under three local-pooling settings: 1) no pooling, 2) GraclusPool, and 3) WavePool, a novel spatially heterogeneous pooling scheme tailored to WaveMesh superpixels. Our experiments demonstrate that SplineCNN learns from multiscale WaveMesh superpixels on-par with similar-sized superpixels. In all WaveMesh experiments, GraclusPool performs poorer than no pooling / WavePool, indicating that poor choice of pooling can result in inferior performance while learning from multiscale superpixels.

Xiaomeng Li, Mengyu Jia, Md Tauhidul Islam et al.

The automatic diagnosis of various retinal diseases from fundus images is important to support clinical decision-making. However, developing such automatic solutions is challenging due to the requirement of a large amount of human-annotated data. Recently, unsupervised/self-supervised feature learning techniques receive a lot of attention, as they do not need massive annotations. Most of the current self-supervised methods are analyzed with single imaging modality and there is no method currently utilize multi-modal images for better results. Considering that the diagnostics of various vitreoretinal diseases can greatly benefit from another imaging modality, e.g., FFA, this paper presents a novel self-supervised feature learning method by effectively exploiting multi-modal data for retinal disease diagnosis. To achieve this, we first synthesize the corresponding FFA modality and then formulate a patient feature-based softmax embedding objective. Our objective learns both modality-invariant features and patient-similarity features. Through this mechanism, the neural network captures the semantically shared information across different modalities and the apparent visual similarity between patients. We evaluate our method on two public benchmark datasets for retinal disease diagnosis. The experimental results demonstrate that our method clearly outperforms other self-supervised feature learning methods and is comparable to the supervised baseline.

Masoud Badiei Khuzani, Hongyi Ren, Md Tauhidul Islam et al.

We propose a novel data-driven method to learn a mixture of multiple kernels with random features that is certifiabaly robust against adverserial inputs. Specifically, we consider a distributionally robust optimization of the kernel-target alignment with respect to the distribution of training samples over a distributional ball defined by the Kullback-Leibler (KL) divergence. The distributionally robust optimization problem can be recast as a min-max optimization whose objective function includes a log-sum term. We develop a mini-batch biased stochastic primal-dual proximal method to solve the min-max optimization. To debias the minibatch algorithm, we use the Gumbel perturbation technique to estimate the log-sum term. We establish theoretical guarantees for the performance of the proposed multiple kernel learning method. In particular, we prove the consistency, asymptotic normality, stochastic equicontinuity, and the minimax rate of the empirical estimators. In addition, based on the notion of Rademacher and Gaussian complexities, we establish distributionally robust generalization bounds that are tighter than previous known bounds. More specifically, we leverage matrix concentration inequalities to establish distributionally robust generalization bounds. We validate our kernel learning approach for classification with the kernel SVMs on synthetic dataset generated by sampling multvariate Gaussian distributions with differernt variance structures. We also apply our kernel learning approach to the MNIST data-set and evaluate its robustness to perturbation of input images under different adversarial models. More specifically, we examine the robustness of the proposed kernel model selection technique against FGSM, PGM, C\&W, and DDN adversarial perturbations, and compare its performance with alternative state-of-the-art multiple kernel learning paradigms.

Md Tauhidul Islam, Udoy Saha, K. T. Shahid et al.

In this paper, a speech enhancement method based on noise compensation performed on short time magnitude as well phase spectra is presented. Unlike the conventional geometric approach (GA) to spectral subtraction (SS), here the noise estimate to be subtracted from the noisy speech spectrum is proposed to be determined by exploiting the low frequency regions of current frame of noisy speech rather than depending only on the initial silence frames. This approach gives the capability of tracking non-stationary noise thus resulting in a non-stationary noise-driven geometric approach of spectral subtraction for speech enhancement. The noise compensated magnitude spectrum from the GA step is then recombined with unchanged phase of noisy speech spectrum and used in phase compensation to obtain an enhanced complex spectrum, which is used to produce an enhanced speech frame. Extensive simulations are carried out using speech files available in the NOIZEUS database shows that the proposed method consistently outperforms some of the recent methods of speech enhancement when employed on the noisy speeches corrupted by street or babble noise at different levels of SNR in terms of objective measures, spectrogram analysis and formal subjective listening tests.

Md Tauhidul Islam, Celia Shahnaz

This paper presents a speech enhancement method, where an adaptive threshold is statistically determined based on Gaussian modeling of Teager energy (TE) operated perceptual wavelet packet (PWP) coefficients of noisy speech. In order to obtain an enhanced speech, the threshold thus derived is applied upon the PWP coefficients by employing a Gaussian pdf dependent custom thresholding function, which is designed based on a combination of modified hard and semisoft thresholding functions. The effectiveness of the proposed method is evaluated for car and multi-talker babble noise corrupted speech signals through performing extensive simulations using the NOIZEUS database. The proposed method is found to outperform some of the state-of-the-art speech enhancement methods not only at at high but also at low levels of SNRs in the sense of standard objective measures and subjective evaluations including formal listening tests.

Md Tauhidul Islam, Asaduzzaman, Celia Shahnaz et al.

A two-step enhancement method based on spectral subtraction and phase spectrum compensation is presented in this paper for noisy speeches in adverse environments involving non-stationary noise and medium to low levels of SNR. The magnitude of the noisy speech spectrum is modified in the first step of the proposed method by a spectral subtraction approach, where a new noise estimation method based on the low frequency information of the noisy speech is introduced. We argue that this method of noise estimation is capable of estimating the non-stationary noise accurately. The phase spectrum of the noisy speech is modified in the second step consisting of phase spectrum compensation, where an SNR-dependent approach is incorporated to determine the amount of compensation to be imposed on the phase spectrum. A modified complex spectrum is obtained by aggregating the magnitude from the spectral subtraction step and modified phase spectrum from the phase compensation step, which is found to be a better representation of enhanced speech spectrum. Speech files available in the NOIZEUS database are used to carry extensive simulations for evaluation of the proposed method.

Md Tauhidul Islam, Celia Shahnaz, Wei-Ping Zhu et al.

A speech enhancement method based on probabilistic geometric approach to spectral subtraction (PGA) performed on short time magnitude spectrum is presented in this paper. A confidence parameter of noise estimation is introduced in the gain function of the proposed method to prevent subtraction of the overestimated and underestimated noise, which not only removes the noise efficiently but also prevents the speech distortion. The noise compensated magnitude spectrum is then recombined with the unchanged phase spectrum to produce a modified complex spectrum prior to synthesize an enhanced frame. Extensive simulations are carried out using the speech files available in the NOIZEUS database in order to evaluate the performance of the proposed method.

Md Tauhidul Islam, Celia Shahnaz, Wei-Ping Zhu et al.

In this paper, for real time enhancement of noisy speech, a method of threshold determination based on modeling of Teager energy (TE) operated perceptual wavelet packet (PWP) coefficients of the noisy speech and noise by an Erlang-2 PDF is presented. The proposed method is computationally much faster than the existing wavelet packet based thresholding methods. A custom thresholding function based on a combination of mu-law and semisoft thresholding functions is designed and exploited to apply the statistically derived threshold upon the PWP coefficients. The proposed custom thresholding function works as a mu-law or a semisoft thresholding function or their combination based on the probability of speech presence and absence in a subband of the PWP transformed noisy speech. By using the speech files available in NOIZEUS database, a number of simulations are performed to evaluate the performance of the proposed method for speech signals in the presence of Gaussian white and street noises. The proposed method outperforms some of the state-of-the-art speech enhancement methods both at high and low levels of SNRs in terms of standard objective measures and subjective evaluations including formal listening tests.

Md Tauhidul Islam, Celia Shahnaz, Wei-Ping Zhu et al.

A divide and conquer strategy for enhancement of noisy speeches in adverse environments involving lower levels of SNR is presented in this paper, where the total system of speech enhancement is divided into two separate steps. The first step is based on noise compensation on short time magnitude and the second step is based on phase compensation. The magnitude spectrum is compensated based on a modified spectral subtraction method where the cross-terms containing spectra of noise and clean speech are taken into consideration, which are neglected in the traditional spectral subtraction methods. By employing the modified magnitude and unchanged phase, a procedure is formulated to compensate the overestimation or underestimation of noise by phase compensation method based on the probability of speech presence. A modified complex spectrum based on these two steps are obtained to synthesize a musical noise free enhanced speech. Extensive simulations are carried out using the speech files available in the NOIZEUS database in order to evaluate the performance of the proposed method. It is shown in terms of the objective measures, spectrogram analysis and formal subjective listening tests that the proposed method consistently outperforms some of the state-of-the-art methods of speech enhancement for noisy speech corrupted by street or babble noise at very low as well as medium levels of SNR.