arXiv subjects

Imran Razzak

Publications and source records attributed to Imran Razzak.

At least 19 recordsLinked to original sources

arXiv2026

TaxoMFM: A Taxonomy-Aware Foundation Model for the Human Gut Microbiome

Existing gut microbiome foundation models typically use flat taxon representations, limiting their ability to exploit known taxonomic hierarchies. We introduce TaxoMFM, a microbiome foundation model that integrates taxonomic structure into self-supervised learning. TaxoMFM jointly learns abundance patterns across taxonomic ranks and relative proportions within groups through taxonomy-aware encoding and hierarchical compositional reconstruction. We further construct TaxoGut-HPP, comprising 100,806 gut microbiome profiles from 231 source cohorts and covering 40 classification and 8 regression tasks. TaxoMFM achieves competitive performance across disease, gut health, host trait, and liver ultrasound phenotype prediction. In cross-cohort zero-shot transfer, where target cohorts are excluded from both pretraining and downstream adaptation, TaxoMFM achieves AUROCs of 0.838, 0.736, and 0.722 for colorectal cancer, type 2 diabetes, and inflammatory bowel disease, respectively. Further analyses show that TaxoMFM recovers community changes across taxonomic scales, while preserving community information and producing consistent representations under database updates and species-vocabulary shifts. Our code is available at https://anonymous.4open.science/r/TaxoMFM-F16D/.

cs.LG↗

arXiv2026

DoAtlas-2: A Foundation for Self-Evolving Causal Biomedical Discovery

We introduce DoAtlas-2, a foundation for self-evolving causal biomedical discovery that organizes knowledge around causal mechanisms and advances through external evidence from human populations. DoAtlas-2 integrates 771 research resources covering more than 720,000 participants in 48 countries, from longitudinal clinical phenotypes, medical imaging, and continuous physiological signals to eight molecular layers, together with an evidence network of approximately 4.7 million literature-derived records over 93,566 concepts and 149,383 candidate causal relations. DoAtlas-2 autonomously formulates research questions from evidence gaps and unresolved mechanisms, prespecifies their causal designs, and generates validated analyses. Supporting, challenging, and unresolved results continuously revise mechanistic interpretations, the causal evidence state, and the discovery frontier, so that DoAtlas-2 self-evolves within a closed loop of hypothesis generation, empirical testing, and renewed discovery. DoAtlas-2 has systematically evaluated 2,031 research questions. In the Human Phenotype Project (HPP), it formulated 4,014 candidate pathway questions across vascular, early-glycemic, and hepatic-metabolic systems, and screening of the first 1,079 yielded statistical support for 756. Representative studies identify blood pressure as a convergence node linking adiposity, hepatic, and lipid phenotypes to vascular outcomes, and show that an adiposity-inflammation-blood-pressure pathway is largely attenuated by joint adjustment for body mass index (BMI) and smoking. The discovered vascular network constitutes a completely interpretable predictive foundation, admitting exact attribution of every prediction and closed-form mediation effects. DoAtlas-2 thereby unifies causal mechanism discovery, population-evidence testing, and interpretable prediction within one continuously evolving foundation.

cs.AI↗

arXiv2026

Neither Over- nor Under-Constrained: Evaluating LLM Personalization under a Constraint Qualification Audit

Accurate evaluation of LLM personalization is hindered by current evaluation paradigms that over- or under-constrain the response space, yielding frequent false rejections and false acceptances. To reduce these false rates, we introduce ConQual-Audit, an audit-based framework that evaluates LLM personalization through a three-stage process: (1) extracting semantic constraints from user profiles and task-grounded reference; (2) qualifying constraints by pruning unnecessary constraints and recovering missing constraints; and (3) verifying candidate responses against the audited constraints via natural language inference. Across PrefEval and LaMP, ConQual-Audit outperforms nine baselines, attaining top AUCs (0.88 and 0.90) and the lowest false rate (0.21) on the leanest constraint sets at an amortizable audit cost. Crucially, this constraint audit is portable: integrating it into ExPerT and PREF helps revise smaller, higher-quality constraint sets to reduce their evaluation false rates.

cs.AI↗

arXiv2026

Mixture-of-Memories: Low-Overhead Language Modeling with Modular Knowledge Injection

Large language models store substantial factual knowledge in their parameters, yet this knowledge is difficult to control, update, and reliably elicit at inference time. Existing memory-augmented approaches typically rely on a single auxiliary mechanism, such as retrieval, parameter updates, or neural memory, and therefore apply the same form of correction to tokens with very different knowledge demands. We propose Mixture-of-Memories (MoM), a memory-augmented language modeling framework that separates routed neural memory from writable factual memory. MoM combines a frozen base LM with two neural memory experts: a latent memory that provides low-latency hidden-state corrections and a lexical memory that provides a token-space knowledge pathway. A lightweight Budget Router sets per-token mixture weights from uncertainty and disagreement features, replacing the fixed interpolation of prior memory modules. For post-hoc updates, an external explicit memory stays outside the router, because a router trained before facts are written learns to down-weight it; new facts are appended without retraining any component and used only when an answer-level gate accepts the retrieved fact. Experiments across language modeling, factual QA, update analysis, and efficiency show that MoM improves both predictive accuracy and updateability while retaining low inference overhead.

cs.CL↗

arXiv2026

Beyond Reward Scoring: Online Multi-Agent Preference Learning for Multimodal Response Generation

Multimodal preference alignment often follows a score-based RLHF pipeline: a reward model is first trained to learn human preferences, then used to score on-policy responses and optimize the response model's generation. This turns preference supervision into a scalar signal for generation: a model may learn to produce answers with higher preference scores, but is rarely trained explicitly to learn the reasons underlying human preferences. We therefore ask whether making preference understanding an internal capability of the response model can improve its generation. To investigate this question, we propose \textbf{PrefMind}, an online dual-agent reinforcement learning framework with two trainable agents: a response Generator and a preference Critic. Given a pair of candidate responses, the agents analyze and discuss which response better aligns with human preference. Human labels supervise their judgments and corrections. For pairs on which both the Generator and revised Critic correctly identify the human-preferred response, the Generator produces an improved answer, and the Critic compares it against the original preferred response to provide a generation reward. Both agents are jointly updated from interactions sampled with their current policies. Through this process, \textbf{PrefMind} trains the Generator to understand human preferences via explicit judgment and correction, and to translate this understanding into better responses. Experiments across three model scales show improvements in both standalone preference judgment and downstream response generation.

cs.AI↗

arXiv2026

QuAnTS: Question Answering on Time Series

Text offers intuitive access to information. This can, in particular, complement the density of numerical time series, thereby enabling improved interactions with time series models to enhance accessibility and decision-making. While the creation of question-answering datasets and models has recently seen remarkable growth, most research focuses on question answering (QA) on vision and text, with time series receiving minute attention. To bridge this gap, we propose a challenging novel time series QA (TSQA) dataset, QuAnTS, for Question Answering on Time Series data. Specifically, we pose a wide variety of questions and answers about human motion in the form of tracked skeleton trajectories. We verify that the large-scale QuAnTS dataset is well-formed and comprehensive through extensive experiments. Thoroughly evaluating existing and newly proposed baselines then lays the groundwork for a deeper exploration of TSQA using QuAnTS. Additionally, we provide human performances as a key reference for gauging the practical usability of such models. We hope to encourage future research on interacting with time series models through text, enabling better decision-making and more transparent systems.

cs.LG↗

arXiv2026

MAGE: Multi-Agent Self-Evolution with Co-Evolutionary Knowledge Graphs

Self-evolving language-model agents must decide what to learn next and how to preserve what they have learned across iterations. Existing systems typically carry this cross-iteration knowledge as natural-language feedback, flat episodic memory, or implicit reinforcement signals, none of which cleanly supports a frozen weak backbone at inference time. This paper introduces MAGE (Multi-Agent Graph-guided Evolution), a framework that externalizes self-knowledge into a four-subgraph co-evolutionary knowledge graph. Its experience subgraph stores both teacher-written failure corrections and the learner's own past correct reasoning traces, which are retrieved as task-conditioned guidance for a frozen execution model. During evolution, the graph, a task-level search bandit, and a skill-level routing bandit are updated from the same reward stream, while the learner's backbone remains unchanged. We further provide structural analysis showing how append-only memory growth, bounded curriculum coverage, and task-filtered retrieval together support stable improvement of the retrieval substrate for frozen-learner evolution. Across nine benchmarks spanning mathematical reasoning, multi-hop and open-domain question answering, spatio-temporal analysis, financial numerical reasoning, medical multiple-choice, an open-world survival game, and web navigation, MAGE achieves strong performance against prompt-based frozen-backbone baselines. Ablations show that self-harvested success traces and teacher-written corrections are complementary, with success memories contributing most on reasoning-template-heavy tasks and corrective memories supporting harder composition and interaction settings. Code is available in https://github.com/RuiyiYang01/mage-alg

cs.AI↗

arXiv2026

GlucoPRISM: Protocol-Supervised Pretraining for Cross-Cohort Glucose Transfer

Continuous glucose monitoring (CGM) foundation models encode each day as one vector that mixes who the person is, what happened that day and how the sensor measured it, so measurement differences travel with the representation into new cohorts. We ask whether pretraining can place the measurement component that harms transfer in known coordinates, so that deployment drops them with a fixed projection and no target data. GlucoPRISM supervises a GlucoFM backbone with response contracts, rules for how each part of the representation should change when only the day or only the sensor changes: a 64-dimensional Trait band should change with neither, a 48-dimensional State band only across days, and a 16-dimensional Sensor band should track the device. Synthetic sensor views calibrated on paired Dexcom and Libre recordings, different-day pairs and glucose-summary targets supply this supervision without clinical labels. Across twelve cross-cohort directions, dropping the Sensor band from the same frozen encoder raises mean transfer AUROC from 68.75 to 73.57, against 69.3 for GlucoFM. The gain has two parts. Into CGMacros, the one target cohort recorded with two sensor types, filtering adds 11 to 19 points, and this holds when the generator is recalibrated on half of the participants and scored on the other half. On the other eight directions filtering is neutral and the encoder itself exceeds GlucoFM by 3.5 points. The device remains linearly decodable after filtering, so the filter removes a device-related component that harms transfer rather than all measurement information. The retained bands improve window AUROC on thirteen of fourteen public task--cohort cells (Holm-adjusted p=0.031) and correlation on fourteen of fifteen clinical endpoints in an external cohort of 9,303 participants.

cs.LG↗

arXiv2026

BARRAC: Adaptation of an English Aspect-based Sentiment Analysis Approach for Classification Tasks in Arabic Dialects

With the rapid growth of Arabic NLP, several models, datasets and benchmarks have been reported. This paper asks whether approaches developed for majority languages like English can be adapted to Arabic tasks. We adapt an English aspect-based sentiment analysis framework to Arabic classification tasks and present the adaptation as BARRAC: Brainstorming Alignment and Replaced Representation learning for ArabiC tasks. BARRAC replaces consumer-review attribute pools with Arabic linguistic devices and markers for dialectal sentiment, sarcasm, and dialect identification, and replaces noisy self-training with two-stage training. Evaluated on five Arabic dialect datasets, BARRAC achieves a mean macro-F1 of 63.93\%, outperforming the best few-label SOTA by 3\%, and outperforming GPT-4o on four out of five tasks. Error analysis provides insights into remaining challenges. These results demonstrate that adapting task-specific approaches is a promising direction for Arabic NLP alongside adapting models, datasets and benchmarks.

cs.CL↗

arXiv2026

What Makes Recurrence Effective in Looped Language Models?

Looped language models (LoopLMs) increase computational depth through parameter sharing, offering a path to scale inference computation without adding parameters. However, it remains unclear when additional recurrence is beneficial and how architectural choices affect its effectiveness. Through controlled experiments, we systematically examine (1) when recurrence helps, (2) where it should be applied, and (3) how its conditioning affects performance. Our evaluation covers inference budgets below, within, and beyond the training horizon under knowledge and reasoning tasks. (1) We find that recurrence can improve reasoning beyond the training horizon while degrading knowledge performance, but harder reasoning instances do not consistently benefit more. (2) Performance also depends on how distinct layers and recurrent iterations are allocated, showing that effective depth alone is insufficient to predict behavior. Non-recurrent output layers improve robustness to under-unrolling, while the preferred placement of input and output layers varies with inference budget. (3) Finally, we find that conventional initial-state injection offers limited robustness to varying recurrence depth. We therefore propose history-state injection as an alternative, and show that channel-wise history-state injection combined with timestep conditioning offers a low-cost and more effective design, better preserving knowledge under extended unrolling while improving robustness across inference budgets. Overall, our results clarify when recurrent computation helps, where it fails, and offer practical guidelines for designing LoopLMs across variable inference budgets.

cs.LG↗

arXiv2026

AMO: Operator-level Adaptive Muon Orthogonalization

Muon has recently emerged as a competitive alternative to AdamW for large-scale pre-training, with orthogonalization via Newton-Schulz (NS) iteration as its core operation. Standard Muon applies a uniform NS schedule to all parameter matrices, overlooking possible differences in orthogonalization difficulty and its impact on performance. Through a systematic empirical study, we show that this per-matrix heterogeneity is pervasive and strongly associated with matrix geometry, which evolves dynamically across operator types, training stages, and network depths. Therefore, uniform NS schedules can lead to uneven orthogonalization quality across the model. Motivated by these findings, we propose Operator-level Adaptive Muon Orthogonalization (AMO), an observe-then-commit method that measures weight geometry by operator type early in training and then uses these signals to allocate the NS budget for the remainder of training. AMO delivers consistent improvements over uniform-schedule Muon across standard, prolonged, and continual pre-training, surpassing the strongest baseline by +0.76 on Llama3.1-1.4B and +0.51 on Qwen3-1.7B in average downstream performance of 12 evaluation tasks, with gains persisting at Llama3.1-4B scale.

cs.LG↗

arXiv2026

Divide by Question, Conquer by Agent: SPLIT-RAG with Question-Driven Graph Partitioning

Retrieval-Augmented Generation (RAG) systems empower large language models (LLMs) with external knowledge, yet struggle with efficiency-accuracy trade-offs when scaling to large knowledge graphs. Existing approaches often rely on monolithic graph retrieval, incurring unnecessary latency for simple queries and fragmented reasoning for complex multi-hop questions. To address these challenges, this paper propose SPLIT-RAG, a multi-agent RAG framework that addresses these limitations with question-driven semantic graph partitioning and collaborative subgraph retrieval. The innovative framework first create Semantic Partitioning of Linked Information, then use the Type-Specialized knowledge base to achieve Multi-Agent RAG. The attribute-aware graph segmentation manages to divide knowledge graphs into semantically coherent subgraphs, ensuring subgraphs align with different query types, while lightweight LLM agents are assigned to partitioned subgraphs, and only relevant partitions are activated during retrieval, thus reduce search space while enhancing efficiency. Finally, a hierarchical merging module resolves inconsistencies across subgraph-derived answers through logical verifications. Extensive experimental validation demonstrates considerable improvements compared to existing approaches.

cs.AI↗

arXiv2026

MedRoundsQA: A Persona and Difficulty Aware Evaluation for Multi-Turn Medical Consultations

Medical benchmarks are dominated by single-turn, multiple-choice clinical cases that poorly reflect real consultations. Practically, clinicians elicit evidence interactively and patient communication varies widely. We introduce MedRoundsQA, a multi-turn diagnostic benchmark derived from 1,387 board-exam cases across 17 specialties. Each case is converted into a structured 24-slot clinical record, and then instantiated as controlled doctor-patient dual-agent dialogues under varying patient personas, with the underlying clinical content held fixed. We further classify cases by difficulty using model-based uncertainty to enable easy-to-hard analysis. Evaluations of fifteen LLM doctor agents show that (i) moving from a single-turn diagnosis on the standardized records to multi-turn consultations causes large degradations of roughly 13-39 points; (ii) more turns reliably improves question relevance, but diagnostic accuracy exhibits diminishing returns and typically plateaus after 6-12 turns; and (iii) patient persona differences can shift diagnosis accuracy by about 7-8 points (lowest to highest education), highlighting equity risks that single-turn benchmarks miss.

cs.AI↗

arXiv2026

LLM as GNN: Graph Vocabulary Learning for Text-Attributed Graph Foundation Models

Text-Attributed Graphs (TAGs), where each node is associated with text descriptions, are ubiquitous in real-world scenarios. They typically exhibit distinctive structure and domain-specific knowledge, motivating the development of a Graph Foundation Model (GFM) that generalizes across diverse graphs and tasks. Despite large efforts to integrate Large Language Models (LLMs) and Graph Neural Networks (GNNs) for TAGs, existing approaches suffer from decoupled architectures with two-stage alignment, limiting their synergistic potential. Even worse, existing methods assign out-of-vocabulary (OOV) tokens to graph nodes, leading to graph-specific semantics, token explosion, and incompatibility with task-oriented prompt templates, which hinders cross-graph and cross-task transferability. To address these challenges, we propose PromptGFM, a versatile GFM for TAGs grounded in graph vocabulary learning. PromptGFM comprises two key components: (1) Graph Understanding Module, which explicitly prompts LLMs to replicate the finest GNN workflow within the text space, facilitating seamless GNN-LLM integration and elegant graph-text alignment; (2) Graph Inference Module, which establishes a language-based graph vocabulary ensuring expressiveness, transferability, and scalability, enabling readable instructions for LLM fine-tuning. Extensive experiments demonstrate our superiority and transferability across diverse graphs and tasks. The code is available at this: https://github.com/agiresearch/PromptGFM.

cs.LG↗

arXiv2026

TopoBrick: Agentic Topology Sampling of Exogenous Variables for Zero-Shot Building IoT Forecasting

Building sensors are embedded in physical topology, spatial hierarchy, and operational context, yet existing forecasters often treat them as isolated time series or rely on fixed covariate sets. We present TopoBrick, a training-free framework for zero-shot building IoT (Internet-of-Things) forecasting. TopoBrick uses building knowledge graphs to construct a compact structural skeleton and employs an agentic topology sampler to select target-specific exogenous variables. The selected variables are organized by deployment-time availability, separating past-known sensor states from future-known calendar, schedule, and meteorological exogenous variables. Across three real-world buildings, TopoBrick outperforms strong zero-shot foundation-model baselines and remains competitive with fully trained building-specific models. Ablations show that topology-aware sampling is more reliable than random, ontology-only, or fixed-hop selection, especially for physically coupled HVAC and weather-driven sensing variables.

cs.AI↗

arXiv2026

MVC-Bench: Benchmarking Calibration of Medical Vision-Language Models

Reliable evaluation of vision-language models (VLMs) and medical vision-language models (Medical-VLMs) requires calibrated confidence, particularly under realistic clinical conditions. However, existing efforts mainly focused on improving accuracy, leaving calibration in the medical domain underexplored. To this end, we propose MVC-Bench, a calibration-centric benchmark for medical image classification with VLMs and Medical-VLMs. MVC-Bench assesses the calibration across three axes: (i) robustness to modality, backbone, and domain shift (ii) effectiveness of calibration strategies and prompt-tuning methods (iii) stability under prompt-template and random-seed variations. The benchmark covers eight different backbones, three medical modalities, including fundus imaging, histopathology, and chest X-ray under in-domain and domain shift settings. It compares post-hoc calibration, train-time calibration, and zero-shot inference methods, together with six prompt-tuning methods. Across more than 1638 controlled experiments, we report accuracy and Expected Calibration Error (ECE) as primary metrics, and further report results with complementary calibration measures, including Maximum Calibration Error (MCE) and Adaptive Calibration Error (ACE). We further investigate the underlying causes of miscalibration in VLMs and Medical-VLMs and propose a simple train-time calibration method, Multi-Class Margin (MCM) regularization, which achieves lowest ECE on 10 out of 12 settings in in-domain and remains competitive under domain shifts. Collectively, MVC-Bench provides a structured evaluation framework and actionable guidance for improving calibration in safety-critical medical workflows.

cs.CV↗

arXiv2026

Grounding Isn't Knowing: Do VLMs Need Object Localization for Spatial Reasoning?

Vision-language models (VLMs) can answer spatial questions, yet the mechanisms connecting object grounding to spatial reasoning remain poorly understood. It is underexplored whether spatial reasoning internally requires precise objects localization, or can bypass explicit localization through global layout cues. In this work, we investigate two representative model families, LLaVA-1.5 and Qwen2.5-VL, using a suite of mechanistic interpretability tools, including token ablation, layer-wise probing, attention knockout, and causal mediation analysis. We find that spatial relation prediction follows a staged grounding-to-reasoning process in which object-aligned tokens establish coarse target-reference anchors, while precise bounding-box boundaries are not required. Positional information becomes decodable before relation decisions emerge, and a small set of attention heads mediates the causal effects of both localization and spatial reasoning. The two tasks share early grounding-related processing but ultimately rely on partially distinct specialized pathways. Through rigorous experiments, we provide a token-, layer-, and head-level account of how VLMs transform object grounding into spatial relations, showing that knowing where objects are is not equivalent to knowing how they relate.

cs.CV↗

arXiv2026

Counterfactual Anatomy-guided Spatial-Temporal Decoding for Annotation-Free Hallucination Mitigation in Medical VLMs

Medical vision-language models (Med-VLMs) have demonstrated strong performance on medical visual question answering, yet they remain prone to hallucination, generating clinically unsupported statements that are insufficiently grounded in image evidence. Mitigation methods applied during decoding offer a practical solution, but they typically lack anatomical awareness or rely heavily on ground truth annotations, which limits their applicability. We propose Counterfactual Anatomy-guided Spatial-Temporal decoding (CAST), a framework that operates entirely during inference and requires no manual annotations for anatomically grounded hallucination mitigation. CAST automatically discovers anatomical regions relevant to the given query through broad medical segmentation. It then selects a compact, causally informative area using counterfactual intervention based on the drop in answer likelihood under occlusion. Guided by this chosen region, CAST performs a unified contrastive decoding process, combining classifier-free guidance to correct spatial attention with stepwise temporal contrast to regulate generation dynamics. Experiments on the SLAKE and MIMIC-CXR datasets across three Med-VLMs demonstrate that CAST consistently outperforms strong baselines and surpasses decoding strategies reliant on ground truth. Our results indicate that compact, automatically selected regions provide highly effective contrastive guidance without expert annotations, offering a practical and generalizable solution for improving spatial grounding and reducing hallucinations. Code is available at https://github.com/csyifan/CAST.

cs.CV↗