arXiv subjects

Hamid Alinejad-Rokny

Publications and source records attributed to Hamid Alinejad-Rokny.

At least 37 records · Page 2Linked to original sources

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

Structuring Reasoning for Complex Rules Beyond Flat Representations

Large language models (LLMs) face significant challenges when processing complex rule systems, as they typically treat interdependent rules as unstructured textual data rather than as logically organized frameworks. This limitation results in reasoning divergence, where models often overlook critical rule dependencies essential for accurate interpretation. Although existing approaches such as Chain-of-Thought (CoT) reasoning have shown promise, they lack systematic methodologies for structured rule processing and are particularly susceptible to error propagation through sequential reasoning chains. To address these limitations, we propose the Dynamic Adjudication Template (DAT), a novel framework inspired by expert human reasoning processes. DAT structures the inference mechanism into three methodical stages: qualitative analysis, evidence gathering, and adjudication. During the qualitative analysis phase, the model comprehensively evaluates the contextual landscape. The subsequent evidence gathering phase involves the targeted extraction of pertinent information based on predefined template elements ([placeholder]), followed by systematic verification against applicable rules. Finally, in the adjudication phase, the model synthesizes these validated components to formulate a comprehensive judgment. Empirical results demonstrate that DAT consistently outperforms conventional CoT approaches in complex rule-based tasks. Notably, DAT enables smaller language models to match, and in some cases exceed, the performance of significantly larger LLMs, highlighting its efficiency and effectiveness in managing intricate rule systems.

cs.AI↗

arXiv2026

ToolRM: Towards Agentic Tool-Use Reward Modeling

Reward models (RMs) play a critical role in aligning large language models (LLMs) with human preferences. Yet in the domain of tool learning, the lack of RMs specifically designed for function-calling tasks has limited progress toward more capable agentic AI. We introduce ToolRM, a family of lightweight reward models tailored for general tool-use scenarios. To build these models, we propose a novel pipeline that constructs high-quality pairwise preference data using rule-based scoring and multidimensional sampling. This yields ToolPref-Pairwise-30K, a diverse, balanced, and challenging preference dataset that supports both generative and discriminative reward modeling. We also introduce TRBench$_{BFCL}$, a benchmark built on the agent evaluation suite BFCL to evaluate RMs on tool calling tasks. Trained on our constructed data, models from the Qwen3-4B/8B series achieve up to 17.94% higher accuracy, substantially outperforming frontier LLMs and RMs in pairwise reward judgments. Beyond training objectives, generative ToolRM generalizes to broader critique tasks, including Best-of-N sampling and self-correction. Experiments on ACEBench highlight its effectiveness and efficiency, enabling inference-time scaling while reducing output token usage by over 66%. Its support for downstream RL training further validates its practical utility. We release data to facilitate future research.

cs.AI↗

arXiv2026

Expanding before Inferring: Enhancing Factuality in Large Language Models through Premature Layers Interpolation

Large Language Models (LLMs) demonstrate remarkable capabilities in text understanding and generation. However, their tendency to produce factually inconsistent outputs, commonly referred to as ''hallucinations'', remains a critical challenge. Existing approaches, such as retrieval-based and inference-time correction methods, primarily address this issue at the input or output level, often overlooking the intrinsic information refinement process and the role of premature layers. Meanwhile, alignment- and fine-tuning-based methods are resource-intensive. In this paper, we propose PLI (Premature Layers Interpolation), a novel, training-free, and plug-and-play intervention designed to enhance factuality. PLI mitigates hallucinations by inserting premature layers formed through mathematical interpolation with adjacent layers. Inspired by stable diffusion and sampling steps, PLI extends the depth of information processing and transmission in LLMs, improving factual coherence. Experiments on four publicly available datasets demonstrate that PLI effectively reduces hallucinations while outperforming existing baselines in most cases. Further analysis suggests that the success of layer interpolation is closely linked to LLMs' internal mechanisms. Our dataset and code are available at https://github.com/CuSO4-Chen/PLI.

cs.CL↗

arXiv2026

Act-Adaptive Margin: Dynamically Calibrating Reward Models for Subjective Ambiguity

Currently, most reinforcement learning tasks focus on domains like mathematics and programming, where verification is relatively straightforward. However, in subjective tasks such as role-playing, alignment techniques struggle to make progress, primarily because subjective reward modeling using the Bradley-Terry model faces significant challenges when dealing with ambiguous preferences. To improve reward modeling in subjective tasks, this paper proposes AAM (\textbf{\underline{A}}ct-\textbf{\underline{A}}daptive \textbf{\underline{M}}argin), which enhances reward modeling by dynamically calibrating preference margins using the model's internal parameter knowledge. We design two versions of AAM that efficiently generate contextually-appropriate preference gaps without additional human annotation. This approach fundamentally improves how reward models handle subjective rewards by better integrating generative understanding with preference scoring. To validate AAM's effectiveness in subjective reward modeling, we conduct evaluations on RewardBench, JudgeBench, and challenging role-playing tasks. Results show that AAM significantly improves subjective reward modeling performance, enhancing Bradley-Terry reward models by 2.95\% in general tasks and 4.85\% in subjective role-playing tasks. Furthermore, reward models trained with AAM can help downstream alignment tasks achieve better results. Our test results show that applying rewards generated by AAM-Augmented RM to preference learning techniques (e.g., GRPO) achieves state-of-the-art results on CharacterEval and Charm. Code and dataset are available at https://github.com/calubkk/AAM.

cs.CL↗

arXiv2025

RxSafeBench: Identifying Medication Safety Issues of Large Language Models in Simulated Consultation

Numerous medical systems powered by Large Language Models (LLMs) have achieved remarkable progress in diverse healthcare tasks. However, research on their medication safety remains limited due to the lack of real world datasets, constrained by privacy and accessibility issues. Moreover, evaluation of LLMs in realistic clinical consultation settings, particularly regarding medication safety, is still underexplored. To address these gaps, we propose a framework that simulates and evaluates clinical consultations to systematically assess the medication safety capabilities of LLMs. Within this framework, we generate inquiry diagnosis dialogues with embedded medication risks and construct a dedicated medication safety database, RxRisk DB, containing 6,725 contraindications, 28,781 drug interactions, and 14,906 indication-drug pairs. A two-stage filtering strategy ensures clinical realism and professional quality, resulting in the benchmark RxSafeBench with 2,443 high-quality consultation scenarios. We evaluate leading open-source and proprietary LLMs using structured multiple choice questions that test their ability to recommend safe medications under simulated patient contexts. Results show that current LLMs struggle to integrate contraindication and interaction knowledge, especially when risks are implied rather than explicit. Our findings highlight key challenges in ensuring medication safety in LLM-based systems and provide insights into improving reliability through better prompting and task-specific tuning. RxSafeBench offers the first comprehensive benchmark for evaluating medication safety in LLMs, advancing safer and more trustworthy AI-driven clinical decision support.

cs.AI↗

arXiv2025

IPBench: Benchmarking the Knowledge of Large Language Models in Intellectual Property

Intellectual Property (IP) is a highly specialized domain that integrates technical and legal knowledge, making it inherently complex and knowledge-intensive. Recent advancements in LLMs have demonstrated their potential to handle IP-related tasks, enabling more efficient analysis, understanding, and generation of IP-related content. However, existing datasets and benchmarks focus narrowly on patents or cover limited aspects of the IP field, lacking alignment with real-world scenarios. To bridge this gap, we introduce IPBench, the first comprehensive IP task taxonomy and a large-scale bilingual benchmark encompassing 8 IP mechanisms and 20 distinct tasks, designed to evaluate LLMs in real-world IP scenarios. We benchmark 17 main LLMs, ranging from general purpose to domain-specific, including chat-oriented and reasoning-focused models, under zero-shot, few-shot, and chain-of-thought settings. Our results show that even the top-performing model, DeepSeek-V3, achieves only 75.8% accuracy, indicating significant room for improvement. Notably, open-source IP and law-oriented models lag behind closed-source general-purpose models. To foster future research, we publicly release IPBench, and will expand it with additional tasks to better reflect real-world complexities and support model advancements in the IP domain. We provide the data and code in the supplementary URLs.

cs.CL↗

arXiv2025

OpenOmni: Advancing Open-Source Omnimodal Large Language Models with Progressive Multimodal Alignment and Real-Time Self-Aware Emotional Speech Synthesis

Recent advancements in omnimodal learning have significantly improved understanding and generation across images, text, and speech, yet these developments remain predominantly confined to proprietary models. The lack of high-quality omnimodal datasets and the challenges of real-time emotional speech synthesis have notably hindered progress in open-source research. To address these limitations, we introduce \name, a two-stage training framework that integrates omnimodal alignment and speech generation to develop a state-of-the-art omnimodal large language model. In the alignment phase, a pre-trained speech model undergoes further training on text-image tasks, enabling (near) zero-shot generalization from vision to speech, outperforming models trained on tri-modal datasets. In the speech generation phase, a lightweight decoder is trained on speech tasks with direct preference optimization, enabling real-time emotional speech synthesis with high fidelity. Experiments show that \name surpasses state-of-the-art models across omnimodal, vision-language, and speech-language benchmarks. It achieves a 4-point absolute improvement on OmniBench over the leading open-source model VITA, despite using 5x fewer training samples and a smaller model size (7B vs. 7x8B). Additionally, \name achieves real-time speech generation with <1s latency at non-autoregressive mode, reducing inference time by 5x compared to autoregressive methods, and improves emotion classification accuracy by 7.7\%

cs.CL↗

arXiv2025

AgentCourt: Simulating Court with Adversarial Evolvable Lawyer Agents

Current research in LLM-based simulation systems lacks comprehensive solutions for modeling real-world court proceedings, while existing legal language models struggle with dynamic courtroom interactions. We present AgentCourt, a comprehensive legal simulation framework that addresses these challenges through adversarial evolution of LLM-based agents. Our AgentCourt introduces a new adversarial evolutionary approach for agents called AdvEvol, which performs dynamic knowledge learning and evolution through structured adversarial interactions in a simulated courtroom program, breaking the limitations of the traditional reliance on static knowledge bases or manual annotations. By simulating 1,000 civil cases, we construct an evolving knowledge base that enhances the agents' legal reasoning abilities. The evolved lawyer agents demonstrated outstanding performance on our newly introduced CourtBench benchmark, achieving a 12.1% improvement in performance compared to the original lawyer agents. Evaluations by professional lawyers confirm the effectiveness of our approach across three critical dimensions: cognitive agility, professional knowledge, and logical rigor. Beyond outperforming specialized legal models in interactive reasoning tasks, our findings emphasize the importance of adversarial learning in legal AI and suggest promising directions for extending simulation-based legal reasoning to broader judicial and regulatory contexts. The project's code is available at: https://github.com/relic-yuexi/AgentCourt

cs.CL↗

arXiv2025

SemanticST: Spatially Informed Semantic Graph Learning for Clustering, Integration, and Scalable Analysis of Spatial Transcriptomics

Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with noisy data, limited scalability, and inadequate modelling of complex cellular relationships. We present SemanticST, a biologically informed, graph-based deep learning framework that models diverse cellular contexts through multi-semantic graph construction. SemanticST builds multiple context-specific graphs capturing spatial proximity, gene expression similarity, and tissue domain structure, and learns disentangled embeddings for each. These are fused using an attention-inspired strategy to yield a unified, biologically meaningful representation. A community-aware min-cut loss improves robustness over contrastive learning, particularly in sparse ST data. SemanticST supports mini-batch training, making it the first graph neural network scalable to large-scale datasets such as Xenium (500,000 cells). Benchmarking across four platforms (Visium, Slide-seq, Stereo-seq, Xenium) and multiple human and mouse tissues shows consistent 20 percentage gains in ARI, NMI, and trajectory fidelity over DeepST, GraphST, and IRIS. In re-analysis of breast cancer Xenium data, SemanticST revealed rare and clinically significant niches, including triple receptor-positive clusters, spatially distinct DCIS-to-IDC transition zones, and FOXC2 tumour-associated myoepithelial cells, suggesting non-canonical EMT programs with stem-like features. SemanticST thus provides a scalable, interpretable, and biologically grounded framework for spatial transcriptomics analysis, enabling robust discovery across tissue types and diseases, and paving the way for spatially resolved tissue atlases and next-generation precision medicine.

q-bio.GN↗

arXiv2025

Lower Layers Matter: Alleviating Hallucination via Multi-Layer Fusion Contrastive Decoding with Truthfulness Refocused

Large Language Models (LLMs) have demonstrated exceptional performance across various natural language processing tasks. However, they occasionally generate inaccurate and counterfactual outputs, a phenomenon commonly referred to as "hallucinations''. To tackle this issue, recent studies have explored contrastive decoding between the original model and an amateur model with induced hallucination, showing promising results. Nevertheless, this approach can disrupt the original LLM's output distribution due to coarse contrast and simple subtraction operations, potentially leading to errors. In this paper, we introduce a novel contrastive decoding framework, termed LOL (LOwer Layer Matters). Unlike prior methods that focus solely on the final layer, our approach integrates contrastive information from lower layers to enable multi-layer fusion during contrastive decoding. Additionally, we incorporate a truthfulness refocused module that leverages instruction guidance to further improve truthfulness in contrastive decoding. Extensive experiments on four publicly available datasets demonstrate that the LOL framework significantly mitigates hallucination while outperforming existing baselines in most cases. For reproducibility, we will release our code and data upon acceptance.

cs.CL↗

arXiv2025

STORYTELLER: An Enhanced Plot-Planning Framework for Coherent and Cohesive Story Generation

Stories are central to human culture, serving to share ideas, preserve traditions, and foster connections. Automatic story generation, a key advancement in artificial intelligence (AI), offers new possibilities for creating personalized content, exploring creative ideas, and enhancing interactive experiences. However, existing methods struggle to maintain narrative coherence and logical consistency. This disconnect compromises the overall storytelling experience, underscoring the need for substantial improvements. Inspired by human cognitive processes, we introduce Storyteller, a novel approach that systemically improves the coherence and consistency of automatically generated stories. Storyteller introduces a plot node structure based on linguistically grounded subject verb object (SVO) triplets, which capture essential story events and ensure a consistent logical flow. Unlike previous methods, Storyteller integrates two dynamic modules, the STORYLINE and narrative entity knowledge graph (NEKG),that continuously interact with the story generation process. This integration produces structurally sound, cohesive and immersive narratives. Extensive experiments demonstrate that Storyteller significantly outperforms existing approaches, achieving an 84.33% average win rate through human preference evaluation. At the same time, it is also far ahead in other aspects including creativity, coherence, engagement, and relevance.

cs.CL↗

arXiv2025

CLaSp: In-Context Layer Skip for Self-Speculative Decoding

Speculative decoding (SD) is a promising method for accelerating the decoding process of Large Language Models (LLMs). The efficiency of SD primarily hinges on the consistency between the draft model and the verify model. However, existing drafting approaches typically require additional modules to be trained, which can be challenging to implement and ensure compatibility across various LLMs. In this paper, we propose CLaSp, an in-context layer-skipping strategy for self-speculative decoding. Unlike prior methods, CLaSp does not require additional drafting modules or extra training. Instead, it employs a plug-and-play mechanism by skipping intermediate layers of the verify model to construct a compressed draft model. Specifically, we develop a dynamic programming algorithm that optimizes the layer-skipping process by leveraging the complete hidden states from the last verification stage as an objective. This enables CLaSp to dynamically adjust its layer-skipping strategy after each verification stage, without relying on pre-optimized sets of skipped layers. Experimental results across diverse downstream tasks demonstrate that CLaSp achieves a speedup of 1.3x ~ 1.7x on LLaMA3 series models without altering the original distribution of the generated text.

cs.CL↗

arXiv2025

Enhancing Monte Carlo Dropout Performance for Uncertainty Quantification

Knowing the uncertainty associated with the output of a deep neural network is of paramount importance in making trustworthy decisions, particularly in high-stakes fields like medical diagnosis and autonomous systems. Monte Carlo Dropout (MCD) is a widely used method for uncertainty quantification, as it can be easily integrated into various deep architectures. However, conventional MCD often struggles with providing well-calibrated uncertainty estimates. To address this, we introduce innovative frameworks that enhances MCD by integrating different search solutions namely Grey Wolf Optimizer (GWO), Bayesian Optimization (BO), and Particle Swarm Optimization (PSO) as well as an uncertainty-aware loss function, thereby improving the reliability of uncertainty quantification. We conduct comprehensive experiments using different backbones, namely DenseNet121, ResNet50, and VGG16, on various datasets, including Cats vs. Dogs, Myocarditis, Wisconsin, and a synthetic dataset (Circles). Our proposed algorithm outperforms the MCD baseline by 2-3% on average in terms of both conventional accuracy and uncertainty accuracy while achieving significantly better calibration. These results highlight the potential of our approach to enhance the trustworthiness of deep learning models in safety-critical applications.

cs.CV↗

arXiv2025

Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

q-bio.GN↗

arXiv2025

PersonaMath: Boosting Mathematical Reasoning via Persona-Driven Data Augmentation

While closed-source Large Language Models (LLMs) demonstrate strong mathematical problem-solving abilities, open-source models still face challenges with such tasks. To bridge this gap, we propose a data augmentation approach and introduce PersonaMathQA, a dataset derived from MATH and GSM8K, on which we train the PersonaMath models. Our approach consists of two stages: the first stage focuses on learning from Persona Diversification, and the second stage emphasizes learning from Reflection. In the first stage, we regenerate detailed chain-of-thought (CoT) solutions as instructions using a closed-source LLM and introduce a persona-driven data augmentation technique. This technique innovatively classifies personas based on occupations, significantly enhancing the dataset's diversity and quality. In the second stage, we incorporate reflection to fully leverage more challenging and valuable questions. Evaluation of our PersonaMath models on MATH and GSM8K reveals that the PersonaMath-7B model (based on Qwen2.5-7B) achieves an accuracy of 61.2% on MATH and 87.8% on GSM8K, surpassing all baseline methods and achieving state-of-the-art performance. Notably, our dataset contains only 128.9K data points-merely 32.6% of MetaMathQA and 49.5% of MathInstruct-yet our model outperforms these baselines, demonstrating the high quality and diversity of our dataset, which enables more efficient model training. We open-source the PersonaMathQA dataset, PersonaMath models, and our code for public usage.

cs.CL↗

arXiv2025

Bayesian Low-Rank LeArning (Bella): A Practical Approach to Bayesian Neural Networks

Computational complexity of Bayesian learning is impeding its adoption in practical, large-scale tasks. Despite demonstrations of significant merits such as improved robustness and resilience to unseen or out-of-distribution inputs over their non- Bayesian counterparts, their practical use has faded to near insignificance. In this study, we introduce an innovative framework to mitigate the computational burden of Bayesian neural networks (BNNs). Our approach follows the principle of Bayesian techniques based on deep ensembles, but significantly reduces their cost via multiple low-rank perturbations of parameters arising from a pre-trained neural network. Both vanilla version of ensembles as well as more sophisticated schemes such as Bayesian learning with Stein Variational Gradient Descent (SVGD), previously deemed impractical for large models, can be seamlessly implemented within the proposed framework, called Bayesian Low-Rank LeArning (Bella). In a nutshell, i) Bella achieves a dramatic reduction in the number of trainable parameters required to approximate a Bayesian posterior; and ii) it not only maintains, but in some instances, surpasses the performance of conventional Bayesian learning methods and non-Bayesian baselines. Our results with large-scale tasks such as ImageNet, CAMELYON17, DomainNet, VQA with CLIP, LLaVA demonstrate the effectiveness and versatility of Bella in building highly scalable and practical Bayesian deep models for real-world applications.

cs.LG↗

arXiv2025

Quantification of Large Language Model Distillation

Model distillation is a fundamental technique in building large language models (LLMs), transferring knowledge from a teacher model to a student model. However, distillation can lead to model homogenization, reducing diversity among models and impairing their ability to robustly handle complex or novel tasks. These limitations underscore the need to systematically quantify the distillation process and its impact. In this work, we propose a framework to evaluate and quantify model distillation. Our method addresses two key aspects: (1) Identifying identity cognition contradictions to assess discrepancies in how models perceive and represent identity-related information, and (2) Analyzing multi-granularity response similarities across models to measure the extent of homogenization. Experimental results demonstrate two key insights: (1) Well-known closed-source and open-source LLMs usually exhibit high distillation degrees, except for Claude, Doubao, and Gemini. (2) Base LLMs show higher distillation degrees compared to aligned LLMs. By offering a systematic approach to improve the transparency of LLM data distillation, we call for LLMs with more independent development and more transparent technical reports to improve LLMs' robustness and safety. The code and data are available under https://github.com/Aegis1863/LLMs-Distillation-Quantification.

cs.CL↗