OpenRaiser/Intern-Atlas huggingface dataset:
Automated Neuron Labelling Enables Generative Steering and Interpretability in Protein Language Models
Venue: arXiv cs.LG 2025
Year: 2025

Protein language models (PLMs) encode rich biological information, yet their internal neuron representations are poorly understood. We introduce the first automated framework for labeling every neuron in a PLM with biologically grounded natural language descriptions. Unlike prior approaches relying on sparse autoencoders or manual annotation, our method scales to hundreds of thousands of neurons, revealing individual neurons are selectively sensitive to diverse biochemical and structural properties. We then develop a novel neuron activation-guided steering method to generate proteins with desired traits, enabling convergence to target biochemical properties like molecular weight and instability index as well as secondary and tertiary structural motifs, including alpha helices and canonical Zinc Fingers. We finally show that analysis of labeled neurons in different model sizes reveals PLM scaling laws and a structured neuron space distribution.
GR-LLMs: Recent Advances in Generative Recommendation Based on Large Language Models
Venue: arXiv cs.IR 2025
Year: 2025

In the past year, Generative Recommendations (GRs) have undergone substantial advancements, especially in leveraging the powerful sequence modeling and reasoning capabilities of Large Language Models (LLMs) to enhance overall recommendation performance. LLM-based GRs are forming a new paradigm that is distinctly different from discriminative recommendations, showing strong potential to replace traditional recommendation systems heavily dependent on complex hand-crafted features. In this paper, we provide a comprehensive survey aimed at facilitating further research of LLM-based GRs. Initially, we outline the general preliminaries and application cases of LLM-based GRs. Subsequently, we introduce the main considerations when LLM-based GRs are applied in real industrial scenarios. Finally, we explore promising directions for LLM-based GRs. We hope that this survey contributes to the ongoing advancement of the GR domain.
Prediction-Augmented Mechanism Design for Weighted Facility Location
Venue: arXiv cs.DS 2025
Year: 2025

Facility location is fundamental in operations research, mechanism design, and algorithmic game theory, with applications ranging from urban infrastructure planning to distributed systems. Recent research in this area has focused on augmenting classic strategyproof mechanisms with predictions to achieve an improved performance guarantee against the uncertainty under the strategic environment. Previous work has been devoted to address the trade-off obstacle of balancing the consistency (near-optimality under accurate predictions) and robustness (bounded inefficiency under poor predictions) primarily in the unweighted setting, assuming that all agents have the same importance. However, this assumption may not be true in some practical scenarios, leading to research of weighted facility location problems. The major contribution of the current work is to provide a prediction augmented algorithmic framework for balancing the consistency and robustness over strategic agents with non-uniform weights. In particular, through a reduction technique that identifies a subset of representative instances and maps the other given locations to the representative ones, we prove that there exists a strategyproof mechanism achieving a bounded consistency guarantee of $\frac{\sqrt{(1+c)^2W^2_{\min}+(1-c)^2W^2_{\max}}}{(1+c)W_{\min}}$ and a bounded robustness guarantee of $\frac{\sqrt{(1-c)^2W^2_{\min}+(1+c)^2W^2_{\max}}}{(1-c)W_{\min}}$ in weighted settings, where $c$ can be viewed as a parameter to make a trade-off between the consistency and robustness and $W_{\min}$ and $W_{\max}$ denote the minimum and maximum agents' weight. We also prove that there is no strategyproof deterministic mechanism that reach $1$-consistency and $O\left( n \cdot \frac{W_{\max}}{W_{\min}} \right)$-robustness in weighted FLP, even with fully predictions of all agents.
Direct Regret Optimization in Bayesian Optimization
Venue: arXiv cs.LG 2025
Year: 2025

Bayesian optimization (BO) is a powerful paradigm for optimizing expensive black-box functions. Traditional BO methods typically rely on separate hand-crafted acquisition functions and surrogate models for the underlying function, and often operate in a myopic manner. In this paper, we propose a novel direct regret optimization approach that jointly learns the optimal model and non-myopic acquisition by distilling from a set of candidate models and acquisitions, and explicitly targets minimizing the multi-step regret. Our framework leverages an ensemble of Gaussian Processes (GPs) with varying hyperparameters to generate simulated BO trajectories, each guided by an acquisition function chosen from a pool of conventional choices, until a Bayesian early stop criterion is met. These simulated trajectories, capturing multi-step exploration strategies, are used to train an end-to-end decision transformer that directly learns to select next query points aimed at improving the ultimate objective. We further adopt a dense training--sparse learning paradigm: The decision transformer is trained offline with abundant simulated data sampled from ensemble GPs and acquisitions, while a limited number of real evaluations refine the GPs online. Experimental results on synthetic and real-world benchmarks suggest that our method consistently outperforms BO baselines, achieving lower simple regret and demonstrating more robust exploration in high-dimensional or noisy settings.
Towards Designing Social Interventions For Online Climate Change Denialism Discussions
Venue: arXiv cs.HC 2025
Year: 2025

As conspiracy theories gain traction, it has become crucial to research effective intervention strategies that can foster evidence and science-based discussions in conspiracy theory communities online. This study presents a novel framework using insider language to contest conspiracy theory ideology in climate change denialism on Reddit. Focusing on discussions in two Reddit communities, our research investigates reactions to pro-social and evidence-based intervention messages for two cohorts of users: climate change deniers and climate change supporters. Specifically, we combine manual and generative AI-based methods to craft intervention messages and deploy the interventions as replies on Reddit posts and comments through transparently labeled bot accounts. On the one hand, we find that evidence-based interventions with neutral language foster positive engagement, encouraging open discussions among believers of climate change denialism. On the other, climate change supporters respond positively, actively participating and presenting additional evidence. Our study contributes valuable insights into the process and challenges of automatically delivering interventions in conspiracy theory communities on social media, and helps inform future research on social media interventions.
From Data-Centric to Sample-Centric: Enhancing LLM Reasoning via Progressive Optimization
Venue: arXiv cs.LG 2025
Year: 2025

Reinforcement learning with verifiable rewards (RLVR) has recently advanced the reasoning capabilities of large language models (LLMs). While prior work has emphasized algorithmic design, data curation, and reward shaping, we investigate RLVR from a sample-centric perspective and introduce LPPO (Learning-Progress and Prefix-guided Optimization), a framework of progressive optimization techniques. Our work addresses a critical question: how to best leverage a small set of trusted, high-quality demonstrations, rather than simply scaling up data volume. First, motivated by how hints aid human problem-solving, we propose prefix-guided sampling, an online data augmentation method that incorporates partial solution prefixes from expert demonstrations to guide the policy, particularly for challenging instances. Second, inspired by how humans focus on important questions aligned with their current capabilities, we introduce learning-progress weighting, a dynamic strategy that adjusts each training sample's influence based on model progression. We estimate sample-level learning progress via an exponential moving average of per-sample pass rates, promoting samples that foster learning and de-emphasizing stagnant ones. Experiments on mathematical-reasoning benchmarks demonstrate that our methods outperform strong baselines, yielding faster convergence and a higher performance ceiling.
Learning controllable dynamics through informative exploration
Venue: arXiv cs.LG 2025
Year: 2025

Environments with controllable dynamics are usually understood in terms of explicit models. However, such models are not always available, but may sometimes be learned by exploring an environment. In this work, we investigate using an information measure called "predicted information gain" to determine the most informative regions of an environment to explore next. Applying methods from reinforcement learning allows good suboptimal exploring policies to be found, and leads to reliable estimates of the underlying controllable dynamics. This approach is demonstrated by comparing with several myopic exploration approaches.
FuDoBa: Fusing Document and Knowledge Graph-based Representations with Bayesian Optimisation
Venue: arXiv cs.CL 2025
Year: 2025

Building on the success of Large Language Models (LLMs), LLM-based representations have dominated the document representation landscape, achieving great performance on the document embedding benchmarks. However, the high-dimensional, computationally expensive embeddings from LLMs tend to be either too generic or inefficient for domain-specific applications. To address these limitations, we introduce FuDoBa a Bayesian optimisation-based method that integrates LLM-based embeddings with domain-specific structured knowledge, sourced both locally and from external repositories like WikiData. This fusion produces low-dimensional, task-relevant representations while reducing training complexity and yielding interpretable early-fusion weights for enhanced classification performance. We demonstrate the effectiveness of our approach on six datasets in two domains, showing that when paired with robust AutoML-based classifiers, our proposed representation learning approach performs on par with, or surpasses, those produced solely by the proprietary LLM-based embedding baselines.
On the Convergence Speed of Spatially Coupled LDPC Ensembles Under Window Decoding
Venue: arXiv cs.IT 2025
Year: 2025

It is known that windowed decoding (WD) can effectively balance the performance and complexity of spatially coupled low-density parity-check (LDPC) codes. In this study, we show that information can propagate in a wave-like manner at a constant speed under WD. Additionally, we provide an upper bound for the information propagation speed on the binary erasure channel, which can assist in designing the number of iterations required within each window.
ClipGS: Clippable Gaussian Splatting for Interactive Cinematic Visualization of Volumetric Medical Data
Venue: arXiv cs.CV 2025
Year: 2025

The visualization of volumetric medical data is crucial for enhancing diagnostic accuracy and improving surgical planning and education. Cinematic rendering techniques significantly enrich this process by providing high-quality visualizations that convey intricate anatomical details, thereby facilitating better understanding and decision-making in medical contexts. However, the high computing cost and low rendering speed limit the requirement of interactive visualization in practical applications. In this paper, we introduce ClipGS, an innovative Gaussian splatting framework with the clipping plane supported, for interactive cinematic visualization of volumetric medical data. To address the challenges posed by dynamic interactions, we propose a learnable truncation scheme that automatically adjusts the visibility of Gaussian primitives in response to the clipping plane. Besides, we also design an adaptive adjustment model to dynamically adjust the deformation of Gaussians and refine the rendering performance. We validate our method on five volumetric medical data (including CT and anatomical slice data), and reach an average 36.635 PSNR rendering quality with 156 FPS and 16.1 MB model size, outperforming state-of-the-art methods in rendering quality and efficiency.
Deep Disentangled Representation Network for Treatment Effect Estimation
Venue: arXiv cs.LG 2025
Year: 2025

Estimating individual-level treatment effect from observational data is a fundamental problem in causal inference and has attracted increasing attention in the fields of education, healthcare, and public policy.In this work, we concentrate on the study of disentangled representation methods that have shown promising outcomes by decomposing observed covariates into instrumental, confounding, and adjustment factors. However, most of the previous work has primarily revolved around generative models or hard decomposition methods for covariates, which often struggle to guarantee the attainment of precisely disentangled factors. In order to effectively model different causal relationships, we propose a novel treatment effect estimation algorithm that incorporates a mixture of experts with multi-head attention and a linear orthogonal regularizer to softly decompose the pre-treatment variables, and simultaneously eliminates selection bias via importance sampling re-weighting techniques. We conduct extensive experiments on both public semi-synthetic and real-world production datasets. The experimental results clearly demonstrate that our algorithm outperforms the state-of-the-art methods focused on individual treatment effects.
Smartphone Exergames with Real-Time Markerless Motion Capture: Challenges and Trade-offs
Venue: arXiv cs.HC 2025
Year: 2025

Markerless Motion Capture (MoCap) using smartphone cameras is a promising approach to making exergames more accessible and cost-effective for health and rehabilitation. Unlike traditional systems requiring specialized hardware, recent advancements in AI-powered pose estimation enable movement tracking using only a mobile device. For an upcoming study, a mobile application with real-time exergames including markerless motion capture is being developed. However, implementing such technology introduces key challenges, including balancing accuracy and real-time responsiveness, ensuring proper user interaction. Future research should explore optimizing AI models for realtime performance, integrating adaptive gamification, and refining user-centered design principles. By overcoming these challenges, smartphone-based exergames could become powerful tools for engaging users in physical activity and rehabilitation, extending their benefits to a broader audience.
Heterogeneous Graph Neural Networks for Short-term State Forecasting in Power Systems across Domains and Time Scales: A Hydroelectric Power Plant Case Study
Venue: arXiv cs.LG 2025
Year: 2025

Accurate short-term state forecasting is essential for efficient and stable operation of modern power systems, especially in the context of increasing variability introduced by renewable and distributed energy resources. As these systems evolve rapidly, it becomes increasingly important to reliably predict their states in the short term to ensure operational stability, support control decisions, and enable interpretable monitoring of sensor and machine behavior. Modern power systems often span multiple physical domains - including electrical, mechanical, hydraulic, and thermal - posing significant challenges for modeling and prediction. Graph Neural Networks (GNNs) have emerged as a promising data-driven framework for system state estimation and state forecasting in such settings. By leveraging the topological structure of sensor networks, GNNs can implicitly learn inter-sensor relationships and propagate information across the network. However, most existing GNN-based methods are designed under the assumption of homogeneous sensor relationships and are typically constrained to a single physical domain. This limitation restricts their ability to integrate and reason over heterogeneous sensor data commonly encountered in real-world energy systems, such as those used in energy conversion infrastructure. In this work, we propose the use of Heterogeneous Graph Attention Networks to address these limitations. Our approach models both homogeneous intra-domain and heterogeneous inter-domain relationships among sensor data from two distinct physical domains - hydraulic and electrical - which exhibit fundamentally different temporal dynamics. Experimental results demonstrate that our method significantly outperforms conventional baselines on average by 35.5% in terms of normalized root mean square error, confirming its effectiveness in multi-domain, multi-rate power system state forecasting.
PromptTea: Let Prompts Tell TeaCache the Optimal Threshold
Venue: arXiv cs.CV 2025
Year: 2025

Despite recent progress in video generation, inference speed remains a major bottleneck. A common acceleration strategy involves reusing model outputs via caching mechanisms at fixed intervals. However, we find that such fixed-frequency reuse significantly degrades quality in complex scenes, while manually tuning reuse thresholds is inefficient and lacks robustness. To address this, we propose Prompt-Complexity-Aware (PCA) caching, a method that automatically adjusts reuse thresholds based on scene complexity estimated directly from the input prompt. By incorporating prompt-derived semantic cues, PCA enables more adaptive and informed reuse decisions than conventional caching methods. We also revisit the assumptions behind TeaCache and identify a key limitation: it suffers from poor input-output relationship modeling due to an oversimplified prior. To overcome this, we decouple the noisy input, enhance the contribution of meaningful textual information, and improve the model's predictive accuracy through multivariate polynomial feature expansion. To further reduce computational cost, we replace the static CFGCache with DynCFGCache, a dynamic mechanism that selectively reuses classifier-free guidance (CFG) outputs based on estimated output variations. This allows for more flexible reuse without compromising output quality. Extensive experiments demonstrate that our approach achieves significant acceleration-for example, 2.79x speedup on the Wan2.1 model-while maintaining high visual fidelity across a range of scenes.
Checklist Engineering Empowers Multilingual LLM Judges
Venue: arXiv cs.CL 2025
Year: 2025

Automated text evaluation has long been a central issue in Natural Language Processing (NLP). Recently, the field has shifted toward using Large Language Models (LLMs) as evaluators-a trend known as the LLM-as-a-Judge paradigm. While promising and easily adaptable across tasks, this approach has seen limited exploration in multilingual contexts. Existing multilingual studies often rely on proprietary models or require extensive training data for fine-tuning, raising concerns about cost, time, and efficiency. In this paper, we propose Checklist Engineering based LLM-as-a-Judge (CE-Judge), a training-free framework that uses checklist intuition for multilingual evaluation with an open-source model. Experiments across multiple languages and three benchmark datasets, under both pointwise and pairwise settings, show that our method generally surpasses the baselines and performs on par with the GPT-4o model.
Towards Solving More Challenging IMO Problems via Decoupled Reasoning and Proving
Venue: arXiv cs.LO 2025
Year: 2025

Automated Theorem Proving (ATP) in formal languages is a foundational challenge for AI. While Large Language Models (LLMs) have driven remarkable progress, a significant gap remains between their powerful informal reasoning capabilities and their weak formal proving performance. Recent studies show that the informal accuracy exceeds 80% while formal success remains below 8% on benchmarks like PutnamBench. We argue this gap persists because current state-of-the-art provers, by tightly coupling reasoning and proving, are trained with paradigms that inadvertently punish deep reasoning in favor of shallow, tactic-based strategies. To bridge this fundamental gap, we propose a novel framework that decouples high-level reasoning from low-level proof generation. Our approach utilizes two distinct, specialized models: a powerful, general-purpose Reasoner to generate diverse, strategic subgoal lemmas, and an efficient Prover to rigorously verify them. This modular design liberates the model's full reasoning potential and bypasses the pitfalls of end-to-end training. We evaluate our method on a challenging set of post-2000 IMO problems, a problem set on which no prior open-source prover has reported success. Our decoupled framework successfully solves 5 of these problems, demonstrating a significant step towards automated reasoning on exceptionally difficult mathematical challenges. To foster future research, we release our full dataset of generated and verified lemmas for a wide range of IMO problems, available at https://tencent-imo.github.io/ .
GreenHyperSpectra: A multi-source hyperspectral dataset for global vegetation trait prediction
Venue: arXiv cs.CV 2025
Year: 2025

Plant traits such as leaf carbon content and leaf mass are essential variables in the study of biodiversity and climate change. However, conventional field sampling cannot feasibly cover trait variation at ecologically meaningful spatial scales. Machine learning represents a valuable solution for plant trait prediction across ecosystems, leveraging hyperspectral data from remote sensing. Nevertheless, trait prediction from hyperspectral data is challenged by label scarcity and substantial domain shifts (\eg across sensors, ecological distributions), requiring robust cross-domain methods. Here, we present GreenHyperSpectra, a pretraining dataset encompassing real-world cross-sensor and cross-ecosystem samples designed to benchmark trait prediction with semi- and self-supervised methods. We adopt an evaluation framework encompassing in-distribution and out-of-distribution scenarios. We successfully leverage GreenHyperSpectra to pretrain label-efficient multi-output regression models that outperform the state-of-the-art supervised baseline. Our empirical analyses demonstrate substantial improvements in learning spectral representations for trait prediction, establishing a comprehensive methodological framework to catalyze research at the intersection of representation learning and plant functional traits assessment. All code and data are available at: https://github.com/echerif18/HyspectraSSL.
Scalable Gaussian Processes: Advances in Iterative Methods and Pathwise Conditioning
Venue: arXiv cs.LG 2025
Year: 2025

Gaussian processes are a powerful framework for uncertainty-aware function approximation and sequential decision-making. Unfortunately, their classical formulation does not scale gracefully to large amounts of data and modern hardware for massively-parallel computation, prompting many researchers to develop techniques which improve their scalability. This dissertation focuses on the powerful combination of iterative methods and pathwise conditioning to develop methodological contributions which facilitate the use of Gaussian processes in modern large-scale settings. By combining these two techniques synergistically, expensive computations are expressed as solutions to systems of linear equations and obtained by leveraging iterative linear system solvers. This drastically reduces memory requirements, facilitating application to significantly larger amounts of data, and introduces matrix multiplication as the main computational operation, which is ideal for modern hardware.