A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

Task Allocation for Autonomous Machines using Computational Intelligence and Deep Reinforcement Learning

Enabling multiple autonomous machines to perform reliably requires the development of efficient cooperative control algorithms. This paper presents a survey of algorithms that have been developed for controlling and coordinating autonomous machines in complex environments. We especially focus on task allocation methods using computational intelligence (CI) and deep reinforcement learning (RL). The advantages and disadvantages of the surveyed methods are analysed thoroughly. We also propose and discuss in detail various future research directions that shed light on how to improve existing algorithms or create new methods to enhance the employability and performance of autonomous machines in real-world applications. The findings indicate that CI and deep RL methods provide viable approaches to addressing complex task allocation problems in dynamic and uncertain environments. The recent development of deep RL has greatly contributed to the literature on controlling and coordinating autonomous machines, and it has become a growing trend in this area. It is envisaged that this paper will provide researchers and engineers with a comprehensive overview of progress in machine learning research related to autonomous machines. It also highlights underexplored areas, identifies emerging methodologies, and suggests new avenues for exploration in future research within this domain.

How Effectively Can Large Language Models Connect SNP Variants and ECG Phenotypes for Cardiovascular Risk Prediction?

Cardiovascular disease (CVD) prediction remains a tremendous challenge due to its multifactorial etiology and global burden of morbidity and mortality. Despite the growing availability of genomic and electrophysiological data, extracting biologically meaningful insights from such high-dimensional, noisy, and sparsely annotated datasets remains a non-trivial task. Recently, LLMs has been applied effectively to predict structural variations in biological sequences. In this work, we explore the potential of fine-tuned LLMs to predict cardiac diseases and SNPs potentially leading to CVD risk using genetic markers derived from high-throughput genomic profiling. We investigate the effect of genetic patterns associated with cardiac conditions and evaluate how LLMs can learn latent biological relationships from structured and semi-structured genomic data obtained by mapping genetic aspects that are inherited from the family tree. By framing the problem as a Chain of Thought (CoT) reasoning task, the models are prompted to generate disease labels and articulate informed clinical deductions across diverse patient profiles and phenotypes. The findings highlight the promise of LLMs in contributing to early detection, risk assessment, and ultimately, the advancement of personalized medicine in cardiac care.

Dual-Stage Value-Guided Inference with Margin-Based Reward Adjustment for Fast and Faithful VLM Captioning

Despite significant advances in inference-time search for vision-language models (VLMs), existing approaches remain both computationally expensive and prone to unpenalized, low-confidence generations which often lead to persistent hallucinations. We introduce \textbf{Value-guided Inference with Margin-based Reward (ViMaR)}, a two-stage inference framework that improves both efficiency and output fidelity by combining a temporal-difference value model with a margin-aware reward adjustment. In the first stage, we perform a single pass to identify the highest-value caption among diverse candidates. In the second stage, we selectively refine only those segments that were overlooked or exhibit weak visual grounding, thereby eliminating frequently rewarded evaluations. A calibrated margin-based penalty discourages low-confidence continuations while preserving descriptive richness. Extensive experiments across multiple VLM architectures demonstrate that ViMaR generates captions that are significantly more reliable, factually accurate, detailed, and explanatory, while achieving over 4$\times$ speedup compared to existing value-guided methods. Specifically, we show that ViMaR trained solely on LLaVA Mistral-7B, \textit{generalizes effectively to guide decoding in a stronger unseen model}. To further validate this, we adapt the ViMaR to steer generation in LLaVA-OneVision-Qwen2-7B, leading to consistent improvements in caption quality and demonstrating robust cross-model guidance. This cross-model generalization highlights ViMaR's flexibility and modularity, positioning it as a scalable and transferable inference-time decoding strategy. Furthermore, when ViMaR-generated captions are used for self-training, the underlying models achieve substantial gains across a broad suite of visual comprehension benchmarks, underscoring the potential of fast, accurate, and self-improving VLM pipelines.

PAL: Probing Audio Encoders via LLMs -- A Study of Information Transfer from Audio Encoders to LLMs

The integration of audio perception capabilities into Large Language Models (LLMs) has enabled significant advances in Audio-LLMs. Although application-focused developments, particularly in curating training data for specific capabilities e.g., audio reasoning, have progressed rapidly, the underlying mechanisms that govern efficient transfer of rich semantic representations from audio encoders to LLMs remain under-explored. We conceptualize effective audio-LLM interaction as the LLM's ability to proficiently probe the audio encoder representations to satisfy textual queries. This paper presents a systematic investigation on how architectural design choices can affect that. Beginning with a standard Pengi/LLaVA-style audio-LLM architecture, we propose and evaluate several modifications guided by hypotheses derived from mechanistic interpretability studies and LLM operational principles. Our experiments demonstrate that: (1) delaying audio integration until the LLM's initial layers establish textual context that enhances its ability to probe the audio representations for relevant information; (2) the LLM can proficiently probe audio representations exclusively through LLM layer's attention submodule, without requiring propagation to its Feed-Forward Network (FFN) submodule; (3) an efficiently integrated ensemble of diverse audio encoders provides richer, complementary representations, thereby broadening the LLM's capacity to probe a wider spectrum of audio information. All hypotheses are evaluated using an identical three-stage training curriculum on a dataset of 5.6 million audio-text pairs, ensuring controlled comparisons. Our final architecture, which incorporates all proposed modifications, achieves relative improvements from 10\% to 60\% over the baseline, validating our approach to optimizing cross-modal information transfer in audio-LLMs. Project page: https://ta012.github.io/PAL/

Flick: Few Labels Text Classification using K-Aware Intermediate Learning in Multi-Task Low-Resource Languages

Training deep learning networks with minimal supervision has gained significant research attention due to its potential to reduce reliance on extensive labelled data. While self-training methods have proven effective in semi-supervised learning, they remain vulnerable to errors from noisy pseudo labels. Moreover, most recent approaches to the few-label classification problem are either designed for resource-rich languages such as English or involve complex cascading models that are prone to overfitting. To address the persistent challenge of few-label text classification in truly low-resource linguistic contexts, where existing methods often struggle with noisy pseudo-labels and domain adaptation, we propose Flick. Unlike prior methods that rely on generic multi-cluster pseudo-labelling or complex cascading architectures, Flick leverages the fundamental insight that distilling high-confidence pseudo-labels from a broader set of initial clusters can dramatically improve pseudo-label quality, particularly for linguistically diverse, low-resource settings. Flick introduces a novel pseudo-label refinement component, a departure from traditional pseudo-labelling strategies by identifying and leveraging top-performing pseudo-label clusters. This component specifically learns to distil highly reliable pseudo-labels from an initial broad set by focusing on single-cluster cohesion and leveraging an adaptive top-k selection mechanism. This targeted refinement process is crucial for mitigating the propagation of errors inherent in low-resource data, allowing for robust fine-tuning of pre-trained language models with only a handful of true labels. We demonstrate Flick's efficacy across 14 diverse datasets, encompassing challenging low-resource languages such as Arabic, Urdu, and Setswana, alongside English, showcasing its superior performance and adaptability.

SAM-aware Test-time Adaptation for Universal Medical Image Segmentation

Universal medical image segmentation using the Segment Anything Model (SAM) remains challenging due to its limited adaptability to medical domains. Existing adaptations, such as MedSAM, enhance SAM's performance in medical imaging but at the cost of reduced generalization to unseen data. Therefore, in this paper, we propose SAM-aware Test-Time Adaptation (SAM-TTA), a fundamentally different pipeline that preserves the generalization of SAM while improving its segmentation performance in medical imaging via a test-time framework. SAM-TTA tackles two key challenges: (1) input-level discrepancies caused by differences in image acquisition between natural and medical images and (2) semantic-level discrepancies due to fundamental differences in object definition between natural and medical domains (e.g., clear boundaries vs. ambiguous structures). Specifically, our SAM-TTA framework comprises (1) Self-adaptive Bezier Curve-based Transformation (SBCT), which adaptively converts single-channel medical images into three-channel SAM-compatible inputs while maintaining structural integrity, to mitigate the input gap between medical and natural images, and (2) Dual-scale Uncertainty-driven Mean Teacher adaptation (DUMT), which employs consistency learning to align SAM's internal representations to medical semantics, enabling efficient adaptation without auxiliary supervision or expensive retraining. Extensive experiments on five public datasets demonstrate that our SAM-TTA outperforms existing TTA approaches and even surpasses fully fine-tuned models such as MedSAM in certain scenarios, establishing a new paradigm for universal medical image segmentation. Code can be found at https://github.com/JianghaoWu/SAM-TTA.

DeepChest: Dynamic Gradient-Free Task Weighting for Effective Multi-Task Learning in Chest X-ray Classification

While Multi-Task Learning (MTL) offers inherent advantages in complex domains such as medical imaging by enabling shared representation learning, effectively balancing task contributions remains a significant challenge. This paper addresses this critical issue by introducing DeepChest, a novel, computationally efficient and effective dynamic task-weighting framework specifically designed for multi-label chest X-ray (CXR) classification. Unlike existing heuristic or gradient-based methods that often incur substantial overhead, DeepChest leverages a performance-driven weighting mechanism based on effective analysis of task-specific loss trends. Given a network architecture (e.g., ResNet18), our model-agnostic approach adaptively adjusts task importance without requiring gradient access, thereby significantly reducing memory usage and achieving a threefold increase in training speed. It can be easily applied to improve various state-of-the-art methods. Extensive experiments on a large-scale CXR dataset demonstrate that DeepChest not only outperforms state-of-the-art MTL methods by 7% in overall accuracy but also yields substantial reductions in individual task losses, indicating improved generalization and effective mitigation of negative transfer. The efficiency and performance gains of DeepChest pave the way for more practical and robust deployment of deep learning in critical medical diagnostic applications. The code is publicly available at https://github.com/youssefkhalil320/DeepChest-MTL

The Role of AI in Early Detection of Life-Threatening Diseases: A Retinal Imaging Perspective

Retinal imaging has emerged as a powerful, non-invasive modality for detecting and quantifying biomarkers of systemic diseases-ranging from diabetes and hypertension to Alzheimer's disease and cardiovascular disorders but current insights remain dispersed across platforms and specialties. Recent technological advances in optical coherence tomography (OCT/OCTA) and adaptive optics (AO) now deliver ultra-high-resolution scans (down to 5 {\mu}m ) with superior contrast and spatial integration, allowing early identification of microvascular abnormalities and neurodegenerative changes. At the same time, AI-driven and machine learning (ML) algorithms have revolutionized the analysis of large-scale retinal datasets, increasing sensitivity and specificity; for example, deep learning models achieve > 90 \% sensitivity for diabetic retinopathy and AUC = 0.89 for the prediction of cardiovascular risk from fundus photographs. The proliferation of mobile health technologies and telemedicine platforms further extends access, reduces costs, and facilitates community-based screening and longitudinal monitoring. Despite these breakthroughs, translation into routine practice is hindered by heterogeneous imaging protocols, limited external validation of AI models, and integration challenges within clinical workflows. In this review, we systematically synthesize the latest OCT/OCT and AO developments, AI/ML approaches, and mHealth/Tele-ophthalmology initiatives and quantify their diagnostic performance across disease domains. Finally, we propose a roadmap for multicenter protocol standardization, prospective validation trials, and seamless incorporation of retinal screening into primary and specialty care pathways-paving the way for precision prevention, early intervention, and ongoing treatment of life-threatening systemic diseases.

Navigating loss manifolds via rigid body dynamics: A promising avenue for robustness and generalisation

Training large neural networks through gradient-based optimization requires navigating high-dimensional loss landscapes, which often exhibit pathological geometry, leading to undesirable training dynamics. In particular, poor generalization frequently results from convergence to sharp minima that are highly sensitive to input perturbations, causing the model to overfit the training data while failing to generalize to unseen examples. Furthermore, these optimization procedures typically display strong dependence on the fine structure of the loss landscape, leading to unstable training dynamics, due to the fractal-like nature of the loss surface. In this work, we propose an alternative optimizer that simultaneously reduces this dependence, and avoids sharp minima, thereby improving generalization. This is achieved by simulating the motion of the center of a ball rolling on the loss landscape. The degree to which our optimizer departs from the standard gradient descent is controlled by a hyperparameter, representing the radius of the ball. Changing this hyperparameter allows for probing the loss landscape at different scales, making it a valuable tool for understanding its geometry.