Md Atik Ahamed

Md Atik Ahamed, Mihir Parmar, Palash Goyal et al.

We introduce TFRBench, the first benchmark designed to evaluate the reasoning capabilities of forecasting systems. Traditionally, time-series forecasting has been evaluated solely on numerical accuracy, treating foundation models as ``black boxes.'' Unlike existing benchmarks, TFRBench provides a protocol for evaluating the reasoning generated by forecasting systems--specifically their analysis of cross-channel dependencies, trends, and external events. To enable this, we propose a systematic multi-agent framework that utilizes an iterative verification loop to synthesize numerically grounded reasoning traces. Spanning ten datasets across five domains, our evaluation confirms that this reasoning is causally effective; useful for evaluation; and prompting LLMs with our generated traces significantly improves forecasting accuracy compared to direct numerical prediction (e.g., avg. $\sim40.2\%\to56.6\%)$, validating the quality of our reasoning. Conversely, benchmarking experiments reveal that off-the-shelf LLMs consistently struggle with both reasoning (lower LLM-as-a-Judge scores) and numerical forecasting, frequently failing to capture domain-specific dynamics. TFRBench thus establishes a new standard for interpretable, reasoning-based evaluation in time-series forecasting. Our benchmark is available at: https://tfrbench.github.io

Tyler Ward, Xiaoqin Wang, Braxton McFarland et al.

Complete removal of cancer tumors with a negative specimen margin during lumpectomy is essential in reducing breast cancer recurrence. However, 2D specimen radiography (SR), the current method used to assess intraoperative specimen margin status, has limited accuracy, resulting in nearly a quarter of patients requiring additional surgery. To address this, we propose a novel deep learning framework combining the Segment Anything Model (SAM) with Forward-Forward Contrastive Learning (FFCL), a pre-training strategy leveraging both local and global contrastive learning for patch-level classification of SR images. After annotating SR images with regions of known maligancy, non-malignant tissue, and pathology-confirmed margins, we pre-train a ResNet-18 backbone with FFCL to classify margin status, then reconstruct coarse binary masks to prompt SAM for refined tumor margin segmentation. Our approach achieved an AUC of 0.8455 for margin classification and segmented margins with a 27.4% improvement in Dice similarity over baseline models, while reducing inference time to 47 milliseconds per image. These results demonstrate that FFCL-SAM significantly enhances both the speed and accuracy of intraoperative margin assessment, with strong potential to reduce re-excision rates and improve surgical outcomes in breast cancer treatment. Our code is available at https://github.com/tbwa233/FFCL-SAM/.

Md Atik Ahamed, Qiang Cheng

Long-term time-series forecasting remains challenging due to the difficulty in capturing long-term dependencies, achieving linear scalability, and maintaining computational efficiency. We introduce TimeMachine, an innovative model that leverages Mamba, a state-space model, to capture long-term dependencies in multivariate time series data while maintaining linear scalability and small memory footprints. TimeMachine exploits the unique properties of time series data to produce salient contextual cues at multi-scales and leverage an innovative integrated quadruple-Mamba architecture to unify the handling of channel-mixing and channel-independence situations, thus enabling effective selection of contents for prediction against global and local contexts at different scales. Experimentally, TimeMachine achieves superior performance in prediction accuracy, scalability, and memory efficiency, as extensively validated using benchmark datasets. Code availability: https://github.com/Atik-Ahamed/TimeMachine

Md Atik Ahamed, Mihir Parmar, Palash Goyal et al.

Time Series Foundation Models (TSFMs) excel at numerical forecasting but operate as black boxes lacking qualitative reasoning. Conversely, applying LLMs directly to temporal data introduces a modality gap: text tokenizers fragment continuous numerical values, degrading mathematical relationships and exploding sequence lengths, leading to computational overhead. To resolve this, we introduce STRIDE (Strategic Time-series Reasoning Injected via Distilled Embeddings), a novel framework natively integrating LLM reasoning into the continuous embedding space of TSFMs. Instead of discrete tokens, STRIDE distills reasoning traces into a lightweight LLM, dynamically projecting its mean-pooled hidden states as a cross-modal prior into the target numerical encoder. The architecture is jointly optimized using cross-entropy and quantile losses. Evaluations demonstrate STRIDE establishes state-of-the-art numerical forecasting on GIFT-Eval (0.674 MASE, 0.454 CRPS) compared to TSFMs and exhibits superior in-domain and out-of-domain numerical as well as reasoning performance on TFRBench. Specifically, STRIDE acts as a plug-and-play enhancement, consistently improving diverse TSFMs (e.g., Chronos-2, Timer-S1) across various LLM configurations. Thus, injecting semantic reasoning as a continuous prior equips TSFMs with human-interpretable reasoning while fundamentally improving predictive accuracy.

Rabeya Tus Sadia, Md Atik Ahamed, Qiang Cheng

The integration of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data is crucial for understanding gene expression in spatial context. Existing methods for such integration have limited performance, with structural similarity often below 60\%, We attribute this limitation to the failure to consider causal relationships between genes. We present CausalGeD, which combines diffusion and autoregressive processes to leverage these relationships. By generalizing the Causal Attention Transformer from image generation to gene expression data, our model captures regulatory mechanisms without predefined relationships. Across 10 tissue datasets, CausalGeD outperformed state-of-the-art baselines by 5- 32\% in key metrics, including Pearson's correlation and structural similarity, advancing both technical and biological insights.

Md Atik Ahamed, Qiang Ye, Qiang Cheng

Molecular generation conditioned on textual descriptions is a fundamental task in computational chemistry and drug discovery. Existing methods often struggle to simultaneously ensure high-quality, diverse generation and fast inference. In this work, we propose a novel causality-aware framework that addresses these challenges through two key innovations. First, we introduce a Causality-Aware Transformer (CAT) that jointly encodes molecular graph tokens and text instructions while enforcing causal dependencies during generation. Second, we develop a Variational Mean Flow (VMF) framework that generalizes existing flow-based methods by modeling the latent space as a mixture of Gaussians, enhancing expressiveness beyond unimodal priors. VMF enables efficient one-step inference while maintaining strong generation quality and diversity. Extensive experiments on four standard molecular benchmarks demonstrate that our model outperforms state-of-the-art baselines, achieving higher novelty (up to 74.5\%), diversity (up to 70.3\%), and 100\% validity across all datasets. Moreover, VMF requires only one number of function evaluation (NFE) during conditional generation and up to five NFEs for unconditional generation, offering substantial computational efficiency over diffusion-based methods.

Md Atik Ahamed, Qiang Ye, Qiang Cheng

Missing values in high-dimensional, mixed-type datasets pose significant challenges for data imputation, particularly under Missing Not At Random (MNAR) mechanisms. Existing methods struggle to integrate local and global data characteristics, limiting performance in MNAR and high-dimensional settings. We propose an innovative framework, RefiDiff, combining local machine learning predictions with a novel Mamba-based denoising network efficiently capturing long-range dependencies among features and samples with low computational complexity. RefiDiff bridges the predictive and generative paradigms of imputation, leveraging pre-refinement for initial warm-up imputations and post-refinement to polish results, enhancing stability and accuracy. By encoding mixed-type data into unified tokens, RefiDiff enables robust imputation without architectural or hyperparameter tuning. RefiDiff outperforms state-of-the-art (SOTA) methods across missing-value settings, demonstrating strong performance in MNAR settings and superior out-of-sample generalization. Extensive evaluations on nine real-world datasets demonstrate its robustness, scalability, and effectiveness in handling complex missingness patterns.

Md Atik Ahamed, Qiang Ye, Qiang Cheng

The design of novel molecules with desired properties is a key challenge in drug discovery and materials science. Traditional methods rely on trial-and-error, while recent deep learning approaches have accelerated molecular generation. However, existing models struggle with generating molecules based on specific textual descriptions. We introduce Mol-CADiff, a novel diffusion-based framework that uses causal attention mechanisms for text-conditional molecular generation. Our approach explicitly models the causal relationship between textual prompts and molecular structures, overcoming key limitations in existing methods. We enhance dependency modeling both within and across modalities, enabling precise control over the generation process. Our extensive experiments demonstrate that Mol-CADiff outperforms state-of-the-art methods in generating diverse, novel, and chemically valid molecules, with better alignment to specified properties, enabling more intuitive language-driven molecular design.

Md Atik Ahamed, Andrew Cheng, Qiang Ye et al.

Graph Neural Networks (GNNs) have demonstrated remarkable success in various applications, yet they often struggle to capture long-range dependencies (LRD) effectively. This paper introduces GraphMinNet, a novel GNN architecture that generalizes the idea of minimal Gated Recurrent Units to graph-structured data. Our approach achieves efficient LRD modeling with linear computational complexity while maintaining permutation equivariance and stability. The model incorporates both structural and positional information through a unique combination of feature and positional encodings, leading to provably stronger expressiveness than the 1-WL test. Theoretical analysis establishes that GraphMinNet maintains non-decaying gradients over long distances, ensuring effective long-range information propagation. Extensive experiments on ten diverse datasets, including molecular graphs, image graphs, and synthetic networks, demonstrate that GraphMinNet achieves state-of-the-art performance while being computationally efficient. Our results show superior performance on 6 out of 10 datasets and competitive results on the others, validating the effectiveness of our approach in capturing both local and global graph structures.

Md Atik Ahamed, Qiang Cheng

Multivariate time series classification (TSC) is critical for various applications in fields such as healthcare and finance. While various approaches for TSC have been explored, important properties of time series, such as shift equivariance and inversion invariance, are largely underexplored by existing works. To fill this gap, we propose a novel multi-view approach to capture patterns with properties like shift equivariance. Our method integrates diverse features, including spectral, temporal, local, and global features, to obtain rich, complementary contexts for TSC. We use continuous wavelet transform to capture time-frequency features that remain consistent even when the input is shifted in time. These features are fused with temporal convolutional or multilayer perceptron features to provide complex local and global contextual information. We utilize the Mamba state space model for efficient and scalable sequence modeling and capturing long-range dependencies in time series. Moreover, we introduce a new scanning scheme for Mamba, called tango scanning, to effectively model sequence relationships and leverage inversion invariance, thereby enhancing our model's generalization and robustness. Experiments on two sets of benchmark datasets (10+20 datasets) demonstrate our approach's effectiveness, achieving average accuracy improvements of 4.01-6.45\% and 7.93\% respectively, over leading TSC models such as TimesNet and TSLANet.

Md Atik Ahamed, Qiang Cheng

Despite the prevalence of images and texts in machine learning, tabular data remains widely used across various domains. Existing deep learning models, such as convolutional neural networks and transformers, perform well however demand extensive preprocessing and tuning limiting accessibility and scalability. This work introduces an innovative approach based on a structured state-space model (SSM), MambaTab, for tabular data. SSMs have strong capabilities for efficiently extracting effective representations from data with long-range dependencies. MambaTab leverages Mamba, an emerging SSM variant, for end-to-end supervised learning on tables. Compared to state-of-the-art baselines, MambaTab delivers superior performance while requiring significantly fewer parameters, as empirically validated on diverse benchmark datasets. MambaTab's efficiency, scalability, generalizability, and predictive gains signify it as a lightweight, "plug-and-play" solution for diverse tabular data with promise for enabling wider practical applications.