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arXiv:2505.12392공식 코드 · Papers with Code

SLOT: Sample-specific Language Model Optimization at Test-time

We propose SLOT (Sample-specific Language Model Optimization at Test-time), a novel and parameter-efficient test-time inference approach that enhances a language model's ability to more accurately respond to individual prompts. Existing Large Language Models (LLMs) often struggle with complex instructions, leading to poor performances on those not well represented among general samples. To address this, SLOT conducts few optimization steps at test-time to update a light-weight sample-specific parameter vector. It is added to the final hidden layer before the output head, and enables efficient adaptation by caching the last layer features during per-sample optimization. By minimizing the cross-entropy loss on the input prompt only, SLOT helps the model better aligned with and follow each given instruction. In experiments, we demonstrate that our method outperforms the compared models across multiple benchmarks and LLMs. For example, Qwen2.5-7B with SLOT achieves an accuracy gain of 8.6% on GSM8K from 57.54% to 66.19%, while DeepSeek-R1-Distill-Llama-70B with SLOT achieves a SOTA accuracy of 68.69% on GPQA among 70B-level models. Our code is available at https://github.com/maple-research-lab/SLOT.

arXiv:2505.09331공식 코드 · Papers with Code

MUST: Multi-Scale Structural-Temporal Link Prediction Model for UAV Ad Hoc Networks

Link prediction in unmanned aerial vehicle (UAV) ad hoc networks (UANETs) aims to predict the potential formation of future links between UAVs. In adversarial environments where the route information of UAVs is unavailable, predicting future links must rely solely on the observed historical topological information of UANETs. However, the highly dynamic and sparse nature of UANET topologies presents substantial challenges in effectively capturing meaningful structural and temporal patterns for accurate link prediction. Most existing link prediction methods focus on temporal dynamics at a single structural scale while neglecting the effects of sparsity, resulting in insufficient information capture and limited applicability to UANETs. In this paper, we propose a multi-scale structural-temporal link prediction model (MUST) for UANETs. Specifically, we first employ graph attention networks (GATs) to capture structural features at multiple levels, including the individual UAV level, the UAV community level, and the overall network level. Then, we use long short-term memory (LSTM) networks to learn the temporal dynamics of these multi-scale structural features. Additionally, we address the impact of sparsity by introducing a sophisticated loss function during model optimization. We validate the performance of MUST using several UANET datasets generated through simulations. Extensive experimental results demonstrate that MUST achieves state-of-the-art link prediction performance in highly dynamic and sparse UANETs.

arXiv:2505.06698공식 코드 · Papers with Code

From Rankings to Insights: Evaluation Should Shift Focus from Leaderboard to Feedback

Automatic evaluation benchmarks such as MT-Bench, Arena-Hard, and Auto-Arena are seeing growing adoption for the evaluation of Large Language Models (LLMs). Existing research has primarily focused on approximating human-based model rankings using limited data and LLM-as-a-Judge. However, the fundamental premise of these studies, which attempts to replicate human rankings, is flawed. Specifically, these benchmarks typically offer only overall scores, limiting their utility to leaderboard rankings, rather than providing feedback that can guide model optimization and support model profiling. Therefore, we advocate for an evaluation paradigm shift from approximating human-based model rankings to providing feedback with analytical value. To this end, we introduce \textbf{Feedbacker}, an evaluation framework that provides comprehensive and fine-grained results, thereby enabling thorough identification of a model's specific strengths and weaknesses. Such feedback not only supports the targeted optimization of the model but also enhances the understanding of its behavior. Feedbacker comprises three key components: an extensible tree-based query taxonomy builder, an automated query synthesis scheme, and a suite of visualization and analysis tools. Furthermore, we propose a novel LLM-as-a-Judge method: PC$^{2}$ (Pre-Comparison-derived Criteria) pointwise evaluation. This method derives evaluation criteria by pre-comparing the differences between several auxiliary responses, achieving the accuracy of pairwise evaluation while maintaining the time complexity of pointwise evaluation. Finally, leveraging the evaluation results of 17 mainstream LLMs, we demonstrate the usage of Feedbacker and highlight its effectiveness and potential. Our project homepage and dataset are available at https://liudan193.github.io/Feedbacker.

arXiv:2505.05880

Combining Abstract Argumentation and Machine Learning for Efficiently Analyzing Low-Level Process Event Streams

Monitoring and analyzing process traces is a critical task for modern companies and organizations. In scenarios where there is a gap between trace events and reference business activities, this entails an interpretation problem, amounting to translating each event of any ongoing trace into the corresponding step of the activity instance. Building on a recent approach that frames the interpretation problem as an acceptance problem within an Abstract Argumentation Framework (AAF), one can elegantly analyze plausible event interpretations (possibly in an aggregated form), as well as offer explanations for those that conflict with prior process knowledge. Since, in settings where event-to-activity mapping is highly uncertain (or simply under-specified) this reasoning-based approach may yield lowly-informative results and heavy computation, one can think of discovering a sequencetagging model, trained to suggest highly-probable candidate event interpretations in a context-aware way. However, training such a model optimally may require using a large amount of manually-annotated example traces. Considering the urgent need of developing Green AI solutions enabling environmental and societal sustainability (with reduced labor/computational costs and carbon footprint), we propose a data/computation-efficient neuro-symbolic approach to the problem, where the candidate interpretations returned by the example-driven sequence tagger is refined by the AAF-based reasoner. This allows us to also leverage prior knowledge to compensate for the scarcity of example data, as confirmed by experimental results; clearly, this property is particularly useful in settings where data annotation and model optimization costs are subject to stringent constraints.

arXiv:2504.15299

D$^{2}$MoE: Dual Routing and Dynamic Scheduling for Efficient On-Device MoE-based LLM Serving

The mixture of experts (MoE) model is a sparse variant of large language models (LLMs), designed to hold a better balance between intelligent capability and computational overhead. Despite its benefits, MoE is still too expensive to deploy on resource-constrained edge devices, especially with the demands of on-device inference services. Recent research efforts often apply model compression techniques, such as quantization, pruning and merging, to restrict MoE complexity. Unfortunately, due to their predefined static model optimization strategies, they cannot always achieve the desired quality-overhead trade-off when handling multiple requests, finally degrading the on-device quality of service. These limitations motivate us to propose the D$^2$MoE, an algorithm-system co-design framework that matches diverse task requirements by dynamically allocating the most proper bit-width to each expert. Specifically, inspired by the nested structure of matryoshka dolls, we propose the matryoshka weight quantization (MWQ) to progressively compress expert weights in a bit-nested manner and reduce the required runtime memory. On top of it, we further optimize the I/O-computation pipeline and design a heuristic scheduling algorithm following our hottest-expert-bit-first (HEBF) principle, which maximizes the expert parallelism between I/O and computation queue under constrained memory budgets, thus significantly reducing the idle temporal bubbles waiting for the experts to load. Evaluations on real edge devices show that D$^2$MoE improves the overall inference throughput by up to 1.39$\times$ and reduces the peak memory footprint by up to 53% over the latest on-device inference frameworks, while still preserving comparable serving accuracy as its INT8 counterparts.

arXiv:2505.01821

Edge-Cloud Collaborative Computing on Distributed Intelligence and Model Optimization: A Survey

Edge-cloud collaborative computing (ECCC) has emerged as a pivotal paradigm for addressing the computational demands of modern intelligent applications, integrating cloud resources with edge devices to enable efficient, low-latency processing. Recent advancements in AI, particularly deep learning and large language models (LLMs), have dramatically enhanced the capabilities of these distributed systems, yet introduce significant challenges in model deployment and resource management. In this survey, we comprehensive examine the intersection of distributed intelligence and model optimization within edge-cloud environments, providing a structured tutorial on fundamental architectures, enabling technologies, and emerging applications. Additionally, we systematically analyze model optimization approaches, including compression, adaptation, and neural architecture search, alongside AI-driven resource management strategies that balance performance, energy efficiency, and latency requirements. We further explore critical aspects of privacy protection and security enhancement within ECCC systems and examines practical deployments through diverse applications, spanning autonomous driving, healthcare, and industrial automation. Performance analysis and benchmarking techniques are also thoroughly explored to establish evaluation standards for these complex systems. Furthermore, the review identifies critical research directions including LLMs deployment, 6G integration, neuromorphic computing, and quantum computing, offering a roadmap for addressing persistent challenges in heterogeneity management, real-time processing, and scalability. By bridging theoretical advancements and practical deployments, this survey offers researchers and practitioners a holistic perspective on leveraging AI to optimize distributed computing environments, fostering innovation in next-generation intelligent systems.

arXiv:2504.12359

Unveiling Hidden Collaboration within Mixture-of-Experts in Large Language Models

Mixture-of-Experts based large language models (MoE LLMs) have shown significant promise in multitask adaptability by dynamically routing inputs to specialized experts. Despite their success, the collaborative mechanisms among experts are still not well understood, limiting both the interpretability and optimization of these models. In this paper, we focus on two critical issues: (1) identifying expert collaboration patterns, and (2) optimizing MoE LLMs through expert pruning. To address the first issue, we propose a hierarchical sparse dictionary learning (HSDL) method that uncovers the collaboration patterns among experts. For the second issue, we introduce the Contribution-Aware Expert Pruning (CAEP) algorithm, which effectively prunes low-contribution experts. Our extensive experiments demonstrate that expert collaboration patterns are closely linked to specific input types and exhibit semantic significance across various tasks. Moreover, pruning experiments show that our approach improves overall performance by 2.5\% on average, outperforming existing methods. These findings offer valuable insights into enhancing the efficiency and interpretability of MoE LLMs, offering a clearer understanding of expert interactions and improving model optimization.

arXiv:2504.07856

2D-Curri-DPO: Two-Dimensional Curriculum Learning for Direct Preference Optimization

Aligning large language models with human preferences is crucial for their safe deployment. While Direct Preference Optimization (DPO) offers an efficient alternative to reinforcement learning from human feedback, traditional DPO methods are limited by their reliance on single preference pairs. Recent work like Curriculum-DPO integrates multiple pairs using a one-dimensional difficulty curriculum based on pairwise distinguishability (PD), but overlooks the complexity of the input prompt itself. To address this, we propose 2D-Curri-DPO, a novel framework employing a two-dimensional curriculum that jointly models Prompt Complexity (PC) and Pairwise Distinguishability. This framework introduces dual difficulty metrics to quantify prompt semantic complexity and response preference clarity, defines a curriculum strategy space encompassing multiple selectable strategies for task adaptation, and incorporates a KL-divergence-based adaptive mechanism for dynamic reference model updates to enhance training stability. Comprehensive experiments demonstrate that 2D-Curri-DPO significantly outperforms standard DPO and prior curriculum methods across multiple benchmarks, including MT-Bench, Vicuna Bench, and WizardLM. Our approach achieves state-of-the-art performance on challenging test sets like UltraFeedback. Ablation studies confirm the benefits of the 2D structure and adaptive mechanisms, while analysis provides guidance for strategy selection. These findings demonstrate that effective alignment requires modeling both prompt complexity and pairwise distinguishability, establishing adaptive, multi-dimensional curriculum learning as a powerful and interpretable new paradigm for preference-based language model optimization.

arXiv:2504.07397

MicroNAS: An Automated Framework for Developing a Fall Detection System

This work presents MicroNAS, an automated neural architecture search tool specifically designed to create models optimized for microcontrollers with small memory resources. The ESP32 microcontroller, with 320 KB of memory, is used as the target platform. The artificial intelligence contribution lies in a novel method for optimizing convolutional neural network and gated recurrent unit architectures by considering the memory size of the target microcontroller as a guide. A comparison is made between memory-driven model optimization and traditional two-stage methods, which use pruning, to show the effectiveness of the proposed framework. To demonstrate the engineering application of MicroNAS, a fall detection system (FDS) for lower-limb amputees is developed as a pilot study. A critical challenge in fall detection studies, class imbalance in the dataset, is addressed. The results show that MicroNAS models achieved higher F1-scores than alternative approaches, such as ensemble methods and H2O Automated Machine Learning, presenting a significant step forward in real-time FDS development. Biomechanists using body-worn sensors for activity detection can adopt the open-source code to design machine learning models tailored for microcontroller platforms with limited memory.

arXiv:2504.02280

LLM-Guided Evolution: An Autonomous Model Optimization for Object Detection

In machine learning, Neural Architecture Search (NAS) requires domain knowledge of model design and a large amount of trial-and-error to achieve promising performance. Meanwhile, evolutionary algorithms have traditionally relied on fixed rules and pre-defined building blocks. The Large Language Model (LLM)-Guided Evolution (GE) framework transformed this approach by incorporating LLMs to directly modify model source code for image classification algorithms on CIFAR data and intelligently guide mutations and crossovers. A key element of LLM-GE is the "Evolution of Thought" (EoT) technique, which establishes feedback loops, allowing LLMs to refine their decisions iteratively based on how previous operations performed. In this study, we perform NAS for object detection by improving LLM-GE to modify the architecture of You Only Look Once (YOLO) models to enhance performance on the KITTI dataset. Our approach intelligently adjusts the design and settings of YOLO to find the optimal algorithms against objective such as detection accuracy and speed. We show that LLM-GE produced variants with significant performance improvements, such as an increase in Mean Average Precision from 92.5% to 94.5%. This result highlights the flexibility and effectiveness of LLM-GE on real-world challenges, offering a novel paradigm for automated machine learning that combines LLM-driven reasoning with evolutionary strategies.

arXiv:2503.23370

Map Feature Perception Metric for Map Generation Quality Assessment and Loss Optimization

In intelligent cartographic generation tasks empowered by generative models, the authenticity of synthesized maps constitutes a critical determinant. Concurrently, the selection of appropriate evaluation metrics to quantify map authenticity emerges as a pivotal research challenge. Current methodologies predominantly adopt computer vision-based image assessment metrics to compute discrepancies between generated and reference maps. However, conventional visual similarity metrics-including L1, L2, SSIM, and FID-primarily operate at pixel-level comparisons, inadequately capturing cartographic global features and spatial correlations, consequently inducing semantic-structural artifacts in generated outputs. This study introduces a novel Map Feature Perception Metric designed to evaluate global characteristics and spatial congruence between synthesized and target maps. Diverging from pixel-wise metrics, our approach extracts elemental-level deep features that comprehensively encode cartographic structural integrity and topological relationships. Experimental validation demonstrates MFP's superior capability in evaluating cartographic semantic features, with classification-enhanced implementations outperforming conventional loss functions across diverse generative frameworks. When employed as optimization objectives, our metric achieves performance gains ranging from 2% to 50% across multiple benchmarks compared to traditional L1, L2, and SSIM baselines. This investigation concludes that explicit consideration of cartographic global attributes and spatial coherence substantially enhances generative model optimization, thereby significantly improving the geographical plausibility of synthesized maps.

arXiv:2503.23796공식 코드 · Papers with Code

On-device Sora: Enabling Training-Free Diffusion-based Text-to-Video Generation for Mobile Devices

We present On-device Sora, the first model training-free solution for diffusion-based on-device text-to-video generation that operates efficiently on smartphone-grade devices. To address the challenges of diffusion-based text-to-video generation on computation- and memory-limited mobile devices, the proposed On-device Sora applies three novel techniques to pre-trained video generative models. First, Linear Proportional Leap (LPL) reduces the excessive denoising steps required in video diffusion through an efficient leap-based approach. Second, Temporal Dimension Token Merging (TDTM) minimizes intensive token-processing computation in attention layers by merging consecutive tokens along the temporal dimension. Third, Concurrent Inference with Dynamic Loading (CI-DL) dynamically partitions large models into smaller blocks and loads them into memory for concurrent model inference, effectively addressing the challenges of limited device memory. We implement On-device Sora on the iPhone 15 Pro, and the experimental evaluations show that it is capable of generating high-quality videos on the device, comparable to those produced by high-end GPUs. These results show that On-device Sora enables efficient and high-quality video generation on resource-constrained mobile devices. We envision the proposed On-device Sora as a significant first step toward democratizing state-of-the-art generative technologies, enabling video generation on commodity mobile and embedded devices without resource-intensive re-training for model optimization (compression). The code implementation is available at a GitHub repository(https://github.com/eai-lab/On-device-Sora).

arXiv:2503.21500공식 코드 · Papers with Code

OpenHuEval: Evaluating Large Language Model on Hungarian Specifics

We introduce OpenHuEval, the first benchmark for LLMs focusing on the Hungarian language and specifics. OpenHuEval is constructed from a vast collection of Hungarian-specific materials sourced from multiple origins. In the construction, we incorporated the latest design principles for evaluating LLMs, such as using real user queries from the internet, emphasizing the assessment of LLMs' generative capabilities, and employing LLM-as-judge to enhance the multidimensionality and accuracy of evaluations. Ultimately, OpenHuEval encompasses eight Hungarian-specific dimensions, featuring five tasks and 3953 questions. Consequently, OpenHuEval provides the comprehensive, in-depth, and scientifically accurate assessment of LLM performance in the context of the Hungarian language and its specifics. We evaluated current mainstream LLMs, including both traditional LLMs and recently developed Large Reasoning Models. The results demonstrate the significant necessity for evaluation and model optimization tailored to the Hungarian language and specifics. We also established the framework for analyzing the thinking processes of LRMs with OpenHuEval, revealing intrinsic patterns and mechanisms of these models in non-English languages, with Hungarian serving as a representative example. We will release OpenHuEval at https://github.com/opendatalab/OpenHuEval .

arXiv:2503.21620공식 코드 · Papers with Code

UI-R1: Enhancing Efficient Action Prediction of GUI Agents by Reinforcement Learning

The recent DeepSeek-R1 has showcased the emergence of reasoning capabilities in LLMs through reinforcement learning (RL) with rule-based rewards. Despite its success in language models, its application in multi-modal domains, particularly in graphic user interface (GUI) agent tasks, remains under-explored. To address this issue, we propose UI-R1, the first framework to explore how rule-based RL can enhance the reasoning capabilities of multimodal large language models (MLLMs) for GUI action prediction tasks. Specifically, UI-R1 introduces a novel rule-based action reward, enabling model optimization via policy-based algorithms such as Group Relative Policy Optimization (GRPO). For efficient training, we curate a small yet high-quality dataset of 136 challenging tasks, encompassing five common action types on mobile devices. Experimental results demonstrate that our proposed UI-R1-3B achieves significant improvements over the base model (i.e. Qwen2.5-VL-3B) on both in-domain (ID) and out-of-domain (OOD) tasks, with average accuracy gains of 22.1% on ScreenSpot, 6.0% on ScreenSpot-Pro, and 12.7% on ANDROIDCONTROL. Furthermore, UI-R1-3B delivers competitive performance compared to larger models (e.g., OS-Atlas-7B) trained via supervised fine-tuning (SFT) on 76K samples. We additionally develop an optimized version, UI-R1-E-3B, which significantly improves both grounding efficiency and accuracy. These results underscore the potential of rule-based reinforcement learning to advance GUI understanding and control, paving the way for future research in this domain. Code website: https://github.com/lll6gg/UI-R1.

arXiv:2503.16328

Knowledge-guided machine learning for county-level corn yield prediction under drought

Remote sensing (RS) technique, enabling the non-contact acquisition of extensive ground observations, is a valuable tool for crop yield predictions. Traditional process-based models struggle to incorporate large volumes of RS data, and most users lack understanding of crop growth mechanisms. In contrast, machine learning (ML) models are often criticized as "black boxes" due to their limited interpretability. To address these limitations, we utilized Knowledge-Guided Machine Learning (KGML), a framework that leverages the strengths of both process-based and ML models. Existing works have either overlooked the role of soil moisture in corn growth or did not embed this effect into their models. To bridge this gap, we developed the Knowledge-Guided Machine Learning with Soil Moisture (KGML-SM) framework, treating soil moisture as an intermediate variable in corn growth to emphasize its key role in plant development. Additionally, based on the prior knowledge that the model may overestimate under drought conditions, we designed a drought-aware loss function that penalized predicted yield in drought-affected areas. Our experiments showed that the KGML-SM model outperformed other traditional ML models. We explored the relationships between drought, soil moisture, and corn yield prediction by assessing the importance of different features within the model, and analyzing how soil moisture impacts predictions across different regions and time periods. Finally we provided interpretability for prediction errors to guide future model optimization.

arXiv:2503.14110공식 코드 · Papers with Code

A Comprehensive Survey on Cross-Domain Recommendation: Taxonomy, Progress, and Prospects

Recommender systems (RS) have become crucial tools for information filtering in various real world scenarios. And cross domain recommendation (CDR) has been widely explored in recent years in order to provide better recommendation results in the target domain with the help of other domains. The CDR technology has developed rapidly, yet there is a lack of a comprehensive survey summarizing recent works. Therefore, in this paper, we will summarize the progress and prospects based on the main procedure of CDR, including Cross Domain Relevance, Cross Domain Interaction, Cross Domain Representation Enhancement and Model Optimization. To help researchers better understand and engage in this field, we also organize the applications and resources, and highlight several current important challenges and future directions of CDR. More details of the survey articles are available at https://github.com/USTCAGI/Awesome-Cross-Domain Recommendation-Papers-and-Resources.

arXiv:2503.13862

HySurvPred: Multimodal Hyperbolic Embedding with Angle-Aware Hierarchical Contrastive Learning and Uncertainty Constraints for Survival Prediction

Multimodal learning that integrates histopathology images and genomic data holds great promise for cancer survival prediction. However, existing methods face key limitations: 1) They rely on multimodal mapping and metrics in Euclidean space, which cannot fully capture the hierarchical structures in histopathology (among patches from different resolutions) and genomics data (from genes to pathways). 2) They discretize survival time into independent risk intervals, which ignores its continuous and ordinal nature and fails to achieve effective optimization. 3) They treat censorship as a binary indicator, excluding censored samples from model optimization and not making full use of them. To address these challenges, we propose HySurvPred, a novel framework for survival prediction that integrates three key modules: Multimodal Hyperbolic Mapping (MHM), Angle-aware Ranking-based Contrastive Loss (ARCL) and Censor-Conditioned Uncertainty Constraint (CUC). Instead of relying on Euclidean space, we design the MHM module to explore the inherent hierarchical structures within each modality in hyperbolic space. To better integrate multimodal features in hyperbolic space, we introduce the ARCL module, which uses ranking-based contrastive learning to preserve the ordinal nature of survival time, along with the CUC module to fully explore the censored data. Extensive experiments demonstrate that our method outperforms state-of-the-art methods on five benchmark datasets. The source code is to be released.

arXiv:2503.12852

ACT360: An Efficient 360-Degree Action Detection and Summarization Framework for Mission-Critical Training and Debriefing

Effective training and debriefing are critical in high-stakes, mission-critical environments such as disaster response, military simulations, and industrial safety, where precision and minimizing errors are paramount. The traditional post-training analysis relies on manually reviewing 2D videos, a time-consuming process that lacks comprehensive situational awareness. To address these limitations, we introduce ACT360, a system that leverages 360-degree videos and machine learning for automated action detection and structured debriefing. ACT360 integrates 360YOWO, an enhanced You Only Watch Once (YOWO) model with spatial attention and equirectangular-aware convolution (EAC) to mitigate panoramic video distortions. To enable deployment in resource-constrained environments, we apply quantization and model pruning, reducing the model size by 74% while maintaining robust accuracy (mAP drop of only 1.5%, from 0.865 to 0.850) and improving inference speed. We validate our approach on a publicly available dataset of 55 labeled 360-degree videos covering seven key operational actions, recorded across various real-world training sessions and environmental conditions. Additionally, ACT360 integrates 360AIE (Action Insight Explorer), a web-based interface for automatic action detection, retrieval, and textual summarization using large language models (LLMs), significantly enhancing post-incident analysis efficiency. ACT360 serves as a generalized framework for mission-critical debriefing, incorporating EAC, spatial attention, summarization, and model optimization. These innovations apply to any training environment requiring lightweight action detection and structured post-exercise analysis.

arXiv:2503.08916

Robust Unsupervised Fault Diagnosis For High-Dimensional Nonlinear Noisy Data

Traditional fault diagnosis methods struggle to handle fault data, with complex data characteristics such as high dimensions and large noise. Deep learning is a promising solution, which typically works well only when labeled fault data are available. To address these problems, a robust unsupervised fault diagnosis using machine learning is proposed in this paper. First, a special dimension reduction method for the high-dimensional fault data is designed. Second, the extracted features are enhanced by incorporating nonlinear information through the learning of a graph structure. Third, to alleviate the problem of reduced fault-diagnosis accuracy attributed to noise and outliers, $l_{2,1}$-norm and typicality-aware constraints are introduced from the perspective of model optimization, respectively. Finally, this paper provides comprehensive theoretical and experimental evidence supporting the effectiveness and robustness of the proposed method. The experiments on both the benchmark Tennessee-Eastman process and a real hot-steel milling process show that the proposed method exhibits better robustness compared to other methods, maintaining high diagnostic accuracy even in the presence of outliers or noise.

arXiv:2503.09085

Differentiable Folding for Nearest Neighbor Model Optimization

The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains $\approx13,000$ underlying thermodynamic parameters, and fitting these to both experimental and structural data is computationally challenging. Here, we leverage recent advances in $\textit{differentiable folding}$, a method for directly computing gradients of the RNA folding algorithms, to devise an efficient, scalable, and flexible means of parameter optimization that uses known RNA structures and thermodynamic experiments. Our method yields a significantly improved parameter set that outperforms existing baselines on all metrics, including an increase in the average predicted probability of ground-truth sequence-structure pairs for a single RNA family by over 23 orders of magnitude. Our framework provides a path towards drastically improved RNA models, enabling the flexible incorporation of new experimental data, definition of novel loss terms, large training sets, and even treatment as a module in larger deep learning pipelines. We make available a new database, RNAometer, with experimentally-determined stabilities for small RNA model systems.