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Hamid Alinejad-Rokny

Publications and source records attributed to Hamid Alinejad-Rokny.

At least 19 recordsLinked to original sources
arXiv2026

How to Use Parallel Data for Multilingual Pretraining

High-quality human-translated parallel corpora can improve cross-lingual transfer, but are typically too small for large-scale pretraining. Machine-translated web corpora help overcome this limitation, making parallel data available at pretraining scale. Standard multilingual pretraining, however, samples source documents and their translations independently, without explicitly using their parallel structure. We investigate how to use the parallel structure of the data to improve multilingual pretraining by concatenating each document with its translation in the same training sequence. We compare this parallel pretraining (PPT) approach with standard pretraining (SPT), training models from scratch at matched token budgets. Surprisingly, despite the benefits of parallel data reported in prior cross-lingual work, PPT alone does not consistently improve language understanding over SPT. Our further analysis suggests that although PPT builds a strong cross-lingual foundation, as shown by its better use of shared information across languages, the mismatch between parallel training contexts and single-language task inputs limits its gains in general language understanding. This finding motivates a two-stage approach following the pretraining-fine-tuning paradigm: we first use PPT to build a cross-lingual foundation, then continue with SPT to adapt it to standard language modeling. In both high-resource and low-resource settings, the two-stage approach consistently improves general language understanding and cross-lingual task performance over standard pretraining alone at matched training budgets.

cs.CL↗
arXiv2026

Revolutionizing Genomics with Reinforcement Learning Techniques

In recent years, Reinforcement Learning (RL) has emerged as a powerful tool for solving a wide range of problems, including decision-making and genomics. The exponential growth of raw genomic data over the past two decades has exceeded the capacity of manual analysis, leading to a growing interest in automatic data analysis and processing. RL algorithms are capable of learning from experience with minimal human supervision, making them well-suited for genomic data analysis and interpretation. One of the key benefits of using RL is the reduced cost associated with collecting labeled training data, which is required for supervised learning. While there have been numerous studies examining the applications of Machine Learning (ML) in genomics, this survey focuses exclusively on the use of RL in various genomics research fields, including gene regulatory networks (GRNs), genome assembly, and sequence alignment. We present a comprehensive technical overview of existing studies on the application of RL in genomics, highlighting the strengths and limitations of these approaches. We then discuss potential research directions that are worthy of future exploration, including the development of more sophisticated reward functions as RL heavily depends on the accuracy of the reward function, the integration of RL with other machine learning techniques, and the application of RL to new and emerging areas in genomics research. Finally, we present our findings and conclude by summarizing the current state of the field and the future outlook for RL in genomics.

q-bio.GN↗
arXiv2026

Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability

Immune checkpoint inhibitors (ICIs) have transformed cancer therapy; yet substantial proportion of patients exhibit intrinsic or acquired resistance, making accurate pre-treatment response prediction a critical unmet need. Transcriptomics-based biomarkers derived from bulk and single-cell RNA sequencing (scRNA-seq) offer a promising avenue for capturing tumour-immune interactions, yet the cross-cohort generalisability of existing prediction models remains unclear.We systematically benchmark nine state-of-the-art transcriptomic ICI response predictors, five bulk RNA-seq-based models (COMPASS, IRNet, NetBio, IKCScore, and TNBC-ICI) and four scRNA-seq-based models (PRECISE, DeepGeneX, Tres and scCURE), using publicly available independent datasets unseen during model development. Overall, predictive performance was modest: bulk RNA-seq models performed at or near chance level across most cohorts, while scRNA-seq models showed only marginal improvements. Pathway-level analyses revealed sparse and inconsistent biomarker signals across models. Although scRNA-seq-based predictors converged on immune-related programs such as allograft rejection, bulk RNA-seq-based models exhibited little reproducible overlap. PRECISE and NetBio identified the most coherent immune-related themes, whereas IRNet predominantly captured metabolic pathways weakly aligned with ICI biology. Together, these findings demonstrate the limited cross-cohort robustness and biological consistency of current transcriptomic ICI prediction models, underscoring the need for improved domain adaptation, standardised preprocessing, and biologically grounded model design.

q-bio.GN↗
arXiv2026

Large Language Model Agents for Evidence Based Genetic Disease Severity Classification

Disease severity classification for genetic conditions is subjective and labor-intensive, creating bottlenecks in genomic screening, where commercial panels vary widely in size and overlap. We developed an autonomous AI agent integrating Reasoning and Acting (ReAct) with Retrieval-Augmented Generation (RAG) to classify 10,211 Human Phenotype Ontology terms. It uses American College of Medical Genetics (ACMG)-endorsed severity guidelines and American College of Obstetricians and Gynecologists (ACOG) quality-of-life criteria to retrieve PubMed literature, generate interpretable reasoning chains, and independently verify claims. At the phenotype level, using expert-curated cohorts, the agent achieved 93.55% accuracy (MCC 0.9237) with 82.6% to 91.4% of claims supported by direct evidence or valid inferences. Gene-level severity was aggregated across 8,738 pairs, identifying 3,283 autosomal recessive pairs with severe or profound presentations. External validation showed 95.2% concordance with Mackenzie's Mission gene list. This system enables standardized panel design by providing reliable, automated classification supported by direct evidence.

q-bio.GN↗
arXiv2026

Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation

Single-cell and spatial foundation models promise transferable biological representations, yet their generality remains largely untested across modalities, biological domains and analytical tasks. We benchmarked six representative models, Nicheformer, CellPLM, scGPT-spatial, GenePT, scELMo and Novae, using a harmonised framework spanning scRNA-seq, spatial transcriptomics and Perturb-seq. We evaluated zero-shot and continually pretrained clustering, supervised annotation, marker-gene concordance and perturbation prediction. Model performance was strongly conditional: expression-trained cell-level transformers best resolved many cell-identity tasks, spatial and graph-aware models better preserved tissue architecture, and language-derived gene embeddings were competitive for selected perturbation-response metrics. No model dominated across tasks, and rankings shifted with modality, preprocessing, tokenisation, biological prior, domain shift and metric choice. This benchmark provides practical guidance for model selection and argues that future models should be judged by biological generalisation, interpretability and perturbation-grounded validity, not by scale or leaderboard performance alone.

q-bio.GN↗
arXiv2026

Breaking the Block: Preserving Data Continuity to Train Superior SAEs for Instruct Models

Sparse Autoencoders (SAEs) are a cornerstone of mechanistic interpretability. Existing training methods inherit the Block Training paradigm from LLM pre-training, which introduces destructive gradient noise in instruct models due to attention leakage from unrelated contexts. Using GSNR analysis, we theoretically characterize this issue and propose Finetuning-aligned Sequential Training (FAST), a sequential training paradigm specifically designed for instruct models. FAST aligns SAE training with the data distribution and activation patterns of instruct models, substantially improving both reconstruction fidelity and feature interpretability. Experimental results show that FAST achieves higher GSNR, a significantly lower log-scaled MSE of 0.6468 compared to the baseline's 5.1985, and a near-zero Delta Loss (-0.51\% to 0.37\%). Moreover, on Llama-3.2-3B-it, FAST produces 21.1\% high-quality features, substantially outperforming baseline methods that achieve 7.0\% and 10.2\%. We further find that intervening on special token activations through SAEs can improve generation quality, revealing new opportunities for fine-grained control. Our codes are available as open source at https://github.com/Geaming2002/FAST.

cs.CL↗
arXiv2026

Multi-Hypothesis Test-Time Adaptation to Mitigate Underspecification

Test-Time Adaptation (TTA) seeks to improve model robustness under distribution shifts by adapting parameters using unlabeled target data. However, in the absence of supervision, entropy-based adaptation is fundamentally underconstrained: multiple distinct parameter updates can achieve similarly low entropy while inducing drastically different decision boundaries. This phenomenon, known as underspecification, renders standard TTA brittle and prone to collapse into spurious modes. In this work, we reinterpret TTA through a posterior-inspired lens induced by entropy minimization, where low-entropy solutions define a pseudo-likelihood over parameters. Instead of committing to a single point estimate, we introduce a particle-based diversification framework that explores multiple plausible adaptation trajectories simultaneously. Our method can be viewed as a structured exploration of multiple plausible adaptation solutions, implemented through multi-level diversification at the output, parameter, optimizer, and input levels. Crucially, the framework acts as a plug-and-play wrapper compatible with existing TTA methods. Extensive experiments on challenging benchmarks demonstrate consistent gains in stability and robustness, achieving improvements of 3-4% under mixed shifts, 2-3% with batch size one, and 1-2.5% under label shifts, outperforming state-of-the-art baselines. Our results suggest that treating TTA as a multi-hypothesis inference problem, rather than a single-point optimization task, is key to mitigating underspecification and enabling reliable real-world deployment.

cs.CV↗
arXiv2026

SrDetection: A Self-Referential Framework for Data Leakage Detection in Code Large Language Models

Evaluating code large language models (Code LLMs) requires reliable detection of data leakage, where benchmark performance is artificially inflated by exposure to benchmark data during pre-training. Existing approaches either assume access to proprietary training corpora, rely on brittle heuristics such as timestamp filtering, or use external reference sets with manually tuned, non-generalizable thresholds. To address these limitations, we introduce \textbf{SrDetection}, a unified \textbf{s}elf-\textbf{r}eferential leakage detection framework for both gray-box (access to model logits) and black-box (access to model outputs) settings. SrDetection generates semantically equivalent variants of a benchmark sample and detects leakage by contrasting the model's behavior on the original versus its variants, flagging cases where the original is disproportionately easier for the model. We further design a controlled leakage detection testbed and evaluate SrDetection in this environment. Across different models and training stages, SrDetection improves average F1 by 21.52 points in the gray-box setting and 14.46 points in the black-box setting over strong baselines, demonstrating robust, threshold-independent leakage detection. Finally, a gray-box study of 15 widely used Code LLMs on four popular benchmarks reveals benchmark-specific leakage patterns beyond prior overlap-based analyses\footnote{\footnotesize Source code and data are available at https://github.com/SMinL/SrDetectionCode

cs.CL↗
arXiv2026

MS-DKC: A Dataset Knowledge Card Framework for Designing and Adapting Medical Image Segmentation Models

Medical image segmentation is often framed as a search for stronger architectures, but this can obscure a more fundamental question: what does the dataset require from the model? In medical imaging, this requirement is shaped by foreground occupancy, morphology, boundary ambiguity, topology sensitivity, annotation quality, acquisition variation, and operating point. This paper introduces the Medical Segmentation Dataset Knowledge Card (MS-DKC), a framework for making these factors explicit. MS-DKC records dataset evidence through image/acquisition, morphology, supervision, context-dependence, and deployment-risk descriptors. These descriptors are mapped to failure modes, design priors, and risk-aligned criteria, making segmentation design more traceable than architecture-first comparison. We evaluate MS-DKC on DRIVE, ISIC2018, and ACDC, representing distinct regimes. DRIVE contains sparse, thin, branching vessels, favoring detail-preserving models, sensitivity-aware optimization, threshold analysis, and topology-aware metrics. DKC-TNet-v2 achieved Dice 0.8044 and IoU 0.6730 with 35103 parameters, while SA-UNetv2-DKC-AmbRef reached Dice 0.8141, IoU 0.6865, sensitivity 0.8265, specificity 0.9804, and AUC 0.9853. ISIC2018 involves compact but appearance-variable lesions; validation-constrained score-function selection on Att-Next-Topo/ATTNext produced MS-DKC-AttNextTopo-VCSF-NoAug with Dice 0.8872, IoU 0.8214, precision 0.9173, Boundary F1 0.4878, and ASSD 4.13, while plausible additions failed to improve the risk-aligned profile. ACDC provides a multi-class cardiac case, where MS-DKC recommends four-class softmax segmentation, class-balanced Dice/CE supervision, and class-wise surface evaluation. Overall, the results support dataset-conditioned design: different datasets require different priors, operating points, and evidence before a model can be judged appropriate.

cs.CV↗
arXiv2026

EVADE-Bench: Multimodal Benchmark for Evaluating and Enhancing Evasive Content Detection

E-commerce platforms increasingly rely on Large Language Models (LLMs) and Vision Language Models (VLMs) to detect illicit or misleading product content. However, these models remain vulnerable to evasive content, which refers to inputs that have been deliberately modified through techniques such as word splitting, euphemistic language, or image cropping to conceal policy violations while still conveying prohibited claims. Crucially, detecting such content requires a model to simultaneously master two capabilities: accurately comprehending complex rules, and correctly inferring the true intent behind deliberately obfuscated multimodal inputs. While prior work has separately explored LLM reasoning over complex rules and LLM-based detection of evasive content, no existing benchmark combines both within a unified evaluation framework. This gap is particularly consequential in e-commerce, where accurate moderation demands that both capabilities operate in concert. To address this gap, we introduce EVADE-Bench, the first expert-curated Chinese multimodal benchmark specifically designed to evaluate LLMs and VLMs on evasive content detection in real-world e-commerce scenarios. Our comprehensive evaluation of 26 open- and closed-source LLMs and VLMs reveals that even state-of-the-art models frequently misclassify evasive samples. We further demonstrate that clearer rule categorization significantly improves model prediction consistency and reduces false predictions, highlighting the critical role of benchmark design in enabling reliable evaluation. To explore paths for performance improvement, we investigate the feasibility of multi-agent decomposition for multimodal reasoning, wherein visual description and logical inference are decoupled into separate agents, and find that this strategy yields notable accuracy gains.

cs.CL↗
arXiv2026

PatRe: A Full-Stage Office Action and Rebuttal Generation Benchmark for Patent Examination

Patent examination is a complex, multi-stage process requiring both technical expertise and legal reasoning, increasingly challenged by rising application volumes. Prior benchmarks predominantly view patent examination as discriminative classification or static extraction, failing to capture its inherently interactive and iterative nature, similar to the peer review and rebuttal process in academic publishing. In this paper, we introduce PatRe, the first benchmark that models the full patent examination lifecycle, including Office Action generation and applicant rebuttal. PatRe comprises 480 real-world cases and supports both oracle and retrieval-simulated evaluation settings. Our benchmark reframes patent examination as a dynamic, multi-turn process of justification and response. Extensive experiments across various LLMs reveal critical insights into model performance, including differences between proprietary and open-source models, as well as task asymmetries between examiner analysis and applicant-side rebuttal. These findings highlight both the potential and current limitations of LLMs in modeling complex, real-world legal reasoning and technical novelty judgment in patent examination. We release our code and dataset to facilitate future research on patent examination modeling.

cs.CL↗
arXiv2026

Focal Modulation and Bidirectional Feature Fusion Network for Medical Image Segmentation

Medical image segmentation is essential for clinical applications such as disease diagnosis, treatment planning, and disease development monitoring because it provides precise morphological and spatial information on anatomical structures that directly influence treatment decisions. Convolutional neural networks significantly impact image segmentation; however, since convolution operations are local, capturing global contextual information and long-range dependencies is still challenging. Their capacity to precisely segment structures with complicated borders and a variety of sizes is impacted by this restriction. Since transformers use self-attention methods to capture global context and long-range dependencies efficiently, integrating transformer-based architecture with CNNs is a feasible approach to overcoming these challenges. To address these challenges, we propose the Focal Modulation and Bidirectional Feature Fusion Network for Medical Image Segmentation, referred to as FM-BFF-Net in the remainder of this paper. The network combines convolutional and transformer components, employs a focal modulation attention mechanism to refine context awareness, and introduces a bidirectional feature fusion module that enables efficient interaction between encoder and decoder representations across scales. Through this design, FM-BFF-Net enhances boundary precision and robustness to variations in lesion size, shape, and contrast. Extensive experiments on eight publicly available datasets, including polyp detection, skin lesion segmentation, and ultrasound imaging, show that FM-BFF-Net consistently surpasses recent state-of-the-art methods in Jaccard index and Dice coefficient, confirming its effectiveness and adaptability for diverse medical imaging scenarios.

cs.CV↗
arXiv2026

InteractWeb-Bench: Can Multimodal Agent Escape Blind Execution in Interactive Website Generation?

With the advancement of multimodal large language models (MLLMs) and coding agents, the website development has shifted from manual programming to agent-based project-level code synthesis. Existing benchmarks rely on idealized assumptions, especially for well-structured, information-rich inputs and static execution settings. In contrast, real-world development is constrained by a critical bottleneck: the semantic misalignment between ambiguous, low-quality instructions from non-expert users and model understanding, which results in a failure mode that we term blind execution. To address this gap, we introduce InteractWeb-Bench, the first multimodal interactive benchmark for website generation under non-expert low-code user conditions. InteractWeb-Bench introduces four types of user agents and persona-driven instruction perturbations to systematically simulate diverse user behaviors, including ambiguity, redundancy, and contradiction, grounded in requirement engineering defect taxonomies. We develop an interactive execution environment for agents, featuring a unified action space comprising Clarify, Implement, Verify, and Submit, enabling iterative intent refinement, code synthesis, and visual feedback-based validation. Extensive experiments and analysis reveal that frontier MLLM-based agents remain trapped in blind execution, exposing limitations in intent recognition and adaptive interaction.

cs.AI↗
arXiv2026

PLOT: Enhancing Preference Learning via Optimal Transport

Preference learning in Large Language Models (LLMs) has advanced significantly, yet existing methods remain limited by modest performance gains, high computational costs, hyperparameter sensitivity, and insufficient modeling of global token-level relationships. We introduce PLOT, which enhances Preference Learning in fine-tuning-based alignment through a token-level loss derived from Optimal Transport. By formulating preference learning as an Optimal Transport Problem, PLOT aligns model outputs with human preferences while preserving the original distribution of LLMs, ensuring stability and robustness. Furthermore, PLOT leverages token embeddings to capture semantic relationships, enabling globally informed optimization. Experiments across two preference categories - Human Values and Logic & Problem Solving - spanning seven subpreferences demonstrate that PLOT consistently improves alignment performance while maintaining fluency and coherence. These results substantiate optimal transport as a principled methodology for preference learning, establishing a theoretically grounded framework that provides new insights for preference learning of LLMs.

cs.CL↗
arXiv2026

FlowPIE: Test-Time Scientific Idea Evolution with Flow-Guided Literature Exploration

Scientific idea generation (SIG) is critical to AI-driven autonomous research, yet existing approaches are often constrained by a static retrieval-then-generation paradigm, leading to homogeneous and insufficiently divergent ideas. In this work, we propose FlowPIE, a tightly coupled retrieval-generation framework that treats literature exploration and idea generation as a co-evolving process. FlowPIE expands literature trajectories via a flow-guided Monte Carlo Tree Search (MCTS) inspired by GFlowNets, using the quality of current ideas assessed by an LLM-based generative reward model (GRM) as a supervised signal to guide adaptive retrieval and construct a diverse, high-quality initial population. Based on this population, FlowPIE models idea generation as a test-time idea evolution process, applying selection, crossover, and mutation with the isolation island paradigm and GRM-based fitness computation to incorporate cross-domain knowledge. It effectively mitigates the information cocoons arising from over-reliance on parametric knowledge and static literature. Extensive evaluations demonstrate that FlowPIE consistently produces ideas with higher novelty, feasibility and diversity compared to strong LLM-based and agent-based frameworks, while enabling reward scaling during test time.

cs.AI↗
arXiv2026

Automatic Paper Reviewing with Heterogeneous Graph Reasoning over LLM-Simulated Reviewer-Author Debates

Existing paper review methods often rely on superficial manuscript features or directly on large language models (LLMs), which are prone to hallucinations, biased scoring, and limited reasoning capabilities. Moreover, these methods often fail to capture the complex argumentative reasoning and negotiation dynamics inherent in reviewer-author interactions. To address these limitations, we propose ReViewGraph (Reviewer-Author Debates Graph Reasoner), a novel framework that performs heterogeneous graph reasoning over LLM-simulated multi-round reviewer-author debates. In our approach, reviewer-author exchanges are simulated through LLM-based multi-agent collaboration. Diverse opinion relations (e.g., acceptance, rejection, clarification, and compromise) are then explicitly extracted and encoded as typed edges within a heterogeneous interaction graph. By applying graph neural networks to reason over these structured debate graphs, ReViewGraph captures fine-grained argumentative dynamics and enables more informed review decisions. Extensive experiments on three datasets demonstrate that ReViewGraph outperforms strong baselines with an average relative improvement of 15.73%, underscoring the value of modeling detailed reviewer-author debate structures.

cs.CL↗
arXiv2026

CoTJudger: A Graph-Driven Framework for Automatic Evaluation of Chain-of-Thought Efficiency and Redundancy in LRMs

Large Reasoning Models (LRMs) have demonstrated strong performance by producing extended Chain-of-Thought (CoT) traces before answering. However, this paradigm often induces over-reasoning: redundant calculations and circular self-verification that increase computational cost without improving outcomes. Existing evaluations largely emphasize final accuracy or coarse token counts, and lack automated tools to separate essential logic from structural redundancy. We introduce CoTJudger, a graph-driven framework that quantifies reasoning efficiency by converting free-form CoTs into directed dependency graphs and extracting the Shortest Effective Path (SEP) needed to reach a correct solution. This yields an interpretable efficiency signal -- how much of a CoT is necessary versus structurally redundant -- that is comparable across models and tasks. Evaluating 21 LRMs, CoTJudger reveals pervasive redundancy and surfaces recurring failure modes, including verification obsession and compensatory redundancy. These results provide a practical metric for disentangling reasoning ability from computational waste, enabling more targeted evaluation and diagnosis of LRM efficiency.

cs.AI↗
arXiv2026

RuCL: Stratified Rubric-Based Curriculum Learning for Multimodal Large Language Model Reasoning

Reinforcement Learning with Verifiable Rewards (RLVR) has emerged as a prevailing paradigm for enhancing reasoning in Multimodal Large Language Models (MLLMs). However, relying solely on outcome supervision risks reward hacking, where models learn spurious reasoning patterns to satisfy final answer checks. While recent rubric-based approaches offer fine-grained supervision signals, they suffer from high computational costs of instance-level generation and inefficient training dynamics caused by treating all rubrics as equally learnable. In this paper, we propose Stratified Rubric-based Curriculum Learning (RuCL), a novel framework that reformulates curriculum learning by shifting the focus from data selection to reward design. RuCL generates generalized rubrics for broad applicability and stratifies them based on the model's competence. By dynamically adjusting rubric weights during training, RuCL guides the model from mastering foundational perception to tackling advanced logical reasoning. Extensive experiments on various visual reasoning benchmarks show that RuCL yields a remarkable +7.83% average improvement over the Qwen2.5-VL-7B model, achieving a state-of-the-art accuracy of 60.06%.

cs.CL↗