OpenRaiser/Intern-Atlas huggingface dataset:
Benchmarking drug-drug interaction prediction methods: a perspective of distribution changes
Venue: arXiv cs.LG 2025
Year: 2025

Motivation: Emerging drug-drug interaction (DDI) prediction is crucial for new drugs but is hindered by distribution changes between known and new drugs in real-world scenarios. Current evaluation often neglects these changes, relying on unrealistic i.i.d. split due to the absence of drug approval data. Results: We propose DDI-Ben, a benchmarking framework for emerging DDI prediction under distribution changes. DDI-Ben introduces a distribution change simulation framework that leverages distribution changes between drug sets as a surrogate for real-world distribution changes of DDIs, and is compatible with various drug split strategies. Through extensive benchmarking on ten representative methods, we show that most existing approaches suffer substantial performance degradation under distribution changes. Our analysis further indicates that large language model (LLM) based methods and the integration of drug-related textual information offer promising robustness against such degradation. To support future research, we release the benchmark datasets with simulated distribution changes. Overall, DDI-Ben highlights the importance of explicitly addressing distribution changes and provides a foundation for developing more resilient methods for emerging DDI prediction. Availability and implementation: Our code and data are available at https://github.com/LARS-research/DDI-Bench.
SAMG: Offline-to-Online Reinforcement Learning via State-Action-Conditional Offline Model Guidance
Venue: arXiv cs.LG 2025
Year: 2025

Offline-to-online (O2O) reinforcement learning (RL) pre-trains models on offline data and refines policies through online fine-tuning. However, existing O2O RL algorithms typically require maintaining the tedious offline datasets to mitigate the effects of out-of-distribution (OOD) data, which significantly limits their efficiency in exploiting online samples. To address this deficiency, we introduce a new paradigm for O2O RL called State-Action-Conditional Offline \Model Guidance (SAMG). It freezes the pre-trained offline critic to provide compact offline understanding for each state-action sample, thus eliminating the need for retraining on offline data. The frozen offline critic is incorporated with the online target critic weighted by a state-action-adaptive coefficient. This coefficient aims to capture the offline degree of samples at the state-action level, and is updated adaptively during training. In practice, SAMG could be easily integrated with Q-function-based algorithms. Theoretical analysis shows good optimality and lower estimation error. Empirically, SAMG outperforms state-of-the-art O2O RL algorithms on the D4RL benchmark.
Towards Better Open-Ended Text Generation: A Multicriteria Evaluation Framework
Venue: arXiv cs.CL 2025
Year: 2025

Open-ended text generation has become a prominent task in natural language processing due to the rise of powerful (large) language models. However, evaluating the quality of these models and the employed decoding strategies remains challenging due to trade-offs among widely used metrics such as coherence, diversity, and perplexity. This paper addresses the specific problem of multicriteria evaluation for open-ended text generation, proposing novel methods for both relative and absolute rankings of decoding methods. Specifically, we employ benchmarking approaches based on partial orderings and present a new summary metric to balance existing automatic indicators, providing a more holistic evaluation of text generation quality. Our experiments demonstrate that the proposed approaches offer a robust way to compare decoding strategies and serve as valuable tools to guide model selection for open-ended text generation tasks. We suggest future directions for improving evaluation methodologies in text generation and make our code, datasets, and models publicly available.
Unleashing LLM Reasoning Capability via Scalable Question Synthesis from Scratch
Venue: arXiv cs.CL 2025
Year: 2025

Improving the mathematical reasoning capabilities of Large Language Models (LLMs) is critical for advancing artificial intelligence. However, access to extensive, diverse, and high-quality reasoning datasets remains a significant challenge, particularly for the open-source community. In this paper, we propose ScaleQuest, a novel, scalable, and cost-effective data synthesis method that enables the generation of large-scale mathematical reasoning datasets using lightweight 7B-scale models. ScaleQuest introduces a two-stage question-tuning process comprising Question Fine-Tuning (QFT) and Question Preference Optimization (QPO) to unlock the question generation capabilities of problem-solving models. By generating diverse questions from scratch -- without relying on powerful proprietary models or seed data -- we produce a dataset of 1 million problem-solution pairs. Our experiments demonstrate that models trained on our data outperform existing open-source datasets in both in-domain and out-of-domain evaluations. Furthermore, our approach shows continued performance improvement as the volume of training data increases, highlighting its potential for ongoing data scaling. The extensive improvements observed in code reasoning tasks demonstrate the generalization capabilities of our proposed method. Our work provides the open-source community with a practical solution to enhance the mathematical reasoning abilities of LLMs.
WARP-LCA: Efficient Convolutional Sparse Coding with Locally Competitive Algorithm
Venue: arXiv cs.CV 2025
Year: 2025

The locally competitive algorithm (LCA) can solve sparse coding problems across a wide range of use cases. Recently, convolution-based LCA approaches have been shown to be highly effective for enhancing robustness for image recognition tasks in vision pipelines. To additionally maximize representational sparsity, LCA with hard-thresholding can be applied. While this combination often yields very good solutions satisfying an $\ell_0$ sparsity criterion, it comes with significant drawbacks for practical application: (i) LCA is very inefficient, typically requiring hundreds of optimization cycles for convergence; (ii) the use of hard-thresholding results in a non-convex loss function, which might lead to suboptimal minima. To address these issues, we propose the Locally Competitive Algorithm with State Warm-up via Predictive Priming (WARP-LCA), which leverages a predictor network to provide a suitable initial guess of the LCA state based on the current input. Our approach significantly improves both convergence speed and the quality of solutions, while maintaining and even enhancing the overall strengths of LCA. We demonstrate that WARP-LCA converges faster by orders of magnitude and reaches better minima compared to conventional LCA. Moreover, the learned representations are more sparse and exhibit superior properties in terms of reconstruction and denoising quality as well as robustness when applied in deep recognition pipelines. Furthermore, we apply WARP-LCA to image denoising tasks, showcasing its robustness and practical effectiveness. Our findings confirm that the naive use of LCA with hard-thresholding results in suboptimal minima, whereas initializing LCA with a predictive guess results in better outcomes. This research advances the field of biologically inspired deep learning by providing a novel approach to convolutional sparse coding.
Distill Visual Chart Reasoning Ability from LLMs to MLLMs
Venue: arXiv cs.CL 2025
Year: 2025

Solving complex chart Q&A tasks requires advanced visual reasoning abilities in multimodal large language models (MLLMs), including recognizing key information from visual inputs and conducting reasoning over it. While fine-tuning MLLMs for reasoning is critical, collecting and annotating charts and questions is expensive, hard to scale, and often results in low-quality annotations. To address this, we propose Code-as-Intermediary Translation (CIT), a cost-effective, efficient and scalable data synthesis method for distilling visual reasoning abilities from LLMs to MLLMs. The code serves as an intermediary that translates visual chart representations into textual representations, enabling language models to understand cross-modal information and generate reasoning chains accordingly. In this way, we can employ text-based synthesizing techniques to expand chart-plotting code and generate high-quality Q&A pairs for training models. This produces ReachQA, a dataset containing 3k reasoning-intensive charts and 20k Q&A pairs to enhance both recognition and reasoning abilities of MLLMs. Experiments show that models fine-tuned with ReachQA not only perform well on chart-related tasks but also show performance gains on general reasoning benchmarks. The code and dataset are publicly available at https://github.com/hewei2001/ReachQA.
Multi-Scale Diffusion: Enhancing Spatial Layout in High-Resolution Panoramic Image Generation
Venue: arXiv cs.CV 2025
Year: 2025

Diffusion models have recently gained recognition for generating diverse and high-quality content, especially in image synthesis. These models excel not only in creating fixed-size images but also in producing panoramic images. However, existing methods often struggle with spatial layout consistency when producing high-resolution panoramas due to the lack of guidance on the global image layout. This paper introduces the Multi-Scale Diffusion (MSD), an optimized framework that extends the panoramic image generation framework to multiple resolution levels. Our method leverages gradient descent techniques to incorporate structural information from low-resolution images into high-resolution outputs. Through comprehensive qualitative and quantitative evaluations against prior work, we demonstrate that our approach significantly improves the coherence of high-resolution panorama generation.
MazeNet: An Accurate, Fast, and Scalable Deep Learning Solution for Steiner Minimum Trees
Venue: arXiv cs.LG 2025
Year: 2025

The Obstacle Avoiding Rectilinear Steiner Minimum Tree (OARSMT) problem, which seeks the shortest interconnection of a given number of terminals in a rectilinear plane while avoiding obstacles, is a critical task in integrated circuit design, network optimization, and robot path planning. Since OARSMT is NP-hard, exact algorithms scale poorly with the number of terminals, leading practical solvers to sacrifice accuracy for large problems. We propose MazeNet, a deep learning-based method that learns to solve the OARSMT from data. MazeNet reframes OARSMT as a maze-solving task that can be addressed with a recurrent convolutional neural network (RCNN). A key hallmark of MazeNet is its scalability: we only need to train the RCNN blocks on mazes with a small number of terminals; larger mazes can be solved by replicating the same pre-trained blocks to create a larger network. Across a wide range of experiments, MazeNet achieves perfect OARSMT-solving accuracy, significantly reduces runtime compared to classical exact algorithms, and can handle more terminals than state-of-the-art approximate algorithms.
CapsoNet: A CNN-Transformer Ensemble for Multi-Class Abnormality Detection in Video Capsule Endoscopy
Venue: arXiv cs.CV 2025
Year: 2025

We present CapsoNet, a deep learning framework developed for the Capsule Vision 2024 Challenge, designed to perform multi-class abnormality classification in video capsule endoscopy (VCE) frames. CapsoNet leverages an ensemble of convolutional neural networks (CNNs) and transformer-based architectures to capture both local and global visual features. The model was trained and evaluated on a dataset of over 50,000 annotated frames spanning ten abnormality classes, sourced from three public and one private dataset. To address the challenge of class imbalance, we employed focal loss, weighted random sampling, and extensive data augmentation strategies. All models were fully fine-tuned to maximize performance within the ensemble. CapsoNet achieved a balanced accuracy of 86.34 percent and a mean AUC-ROC of 0.9908 on the official validation set, securing Team Seq2Cure 5th place in the competition. Our implementation is available at http://github.com/arnavs04/capsule-vision-2024
Diff-Instruct++: Training One-step Text-to-image Generator Model to Align with Human Preferences
Venue: arXiv cs.CV 2025
Year: 2025

One-step text-to-image generator models offer advantages such as swift inference efficiency, flexible architectures, and state-of-the-art generation performance. In this paper, we study the problem of aligning one-step generator models with human preferences for the first time. Inspired by the success of reinforcement learning using human feedback (RLHF), we formulate the alignment problem as maximizing expected human reward functions while adding an Integral Kullback-Leibler divergence term to prevent the generator from diverging. By overcoming technical challenges, we introduce Diff-Instruct++ (DI++), the first, fast-converging and image data-free human preference alignment method for one-step text-to-image generators. We also introduce novel theoretical insights, showing that using CFG for diffusion distillation is secretly doing RLHF with DI++. Such an interesting finding brings understanding and potential contributions to future research involving CFG. In the experiment sections, we align both UNet-based and DiT-based one-step generators using DI++, which use the Stable Diffusion 1.5 and the PixelArt-$α$ as the reference diffusion processes. The resulting DiT-based one-step text-to-image model achieves a strong Aesthetic Score of 6.19 and an Image Reward of 1.24 on the COCO validation prompt dataset. It also achieves a leading Human preference Score (HPSv2.0) of 28.48, outperforming other open-sourced models such as Stable Diffusion XL, DMD2, SD-Turbo, as well as PixelArt-$α$. Both theoretical contributions and empirical evidence indicate that DI++ is a strong human-preference alignment approach for one-step text-to-image models. The homepage of the paper is https://github.com/pkulwj1994/diff_instruct_pp.
LLMs for Extremely Low-Resource Finno-Ugric Languages
Venue: arXiv cs.CL 2025
Year: 2025

The advancement of large language models (LLMs) has predominantly focused on high-resource languages, leaving low-resource languages, such as those in the Finno-Ugric family, significantly underrepresented. This paper addresses this gap by focusing on Võro, Livonian, and Komi. We cover almost the entire cycle of LLM creation, from data collection to instruction tuning and evaluation. Our contributions include developing multilingual base and instruction-tuned models; creating evaluation benchmarks, including the smugri-MT-bench multi-turn conversational benchmark; and conducting human evaluation. We intend for this work to promote linguistic diversity, ensuring that lesser-resourced languages can benefit from advancements in NLP.
Pay Attention and Move Better: Harnessing Attention for Interactive Motion Generation and Training-free Editing
Venue: arXiv cs.CV 2025
Year: 2025

This research delves into the problem of interactive editing of human motion generation. Previous motion diffusion models lack explicit modeling of the word-level text-motion correspondence and good explainability, hence restricting their fine-grained editing ability. To address this issue, we propose an attention-based motion diffusion model, namely MotionCLR, with CLeaR modeling of attention mechanisms. Technically, MotionCLR models the in-modality and cross-modality interactions with self-attention and cross-attention, respectively. More specifically, the self-attention mechanism aims to measure the sequential similarity between frames and impacts the order of motion features. By contrast, the cross-attention mechanism works to find the fine-grained word-sequence correspondence and activate the corresponding timesteps in the motion sequence. Based on these key properties, we develop a versatile set of simple yet effective motion editing methods via manipulating attention maps, such as motion (de-)emphasizing, in-place motion replacement, and example-based motion generation, etc. For further verification of the explainability of the attention mechanism, we additionally explore the potential of action-counting and grounded motion generation ability via attention maps. Our experimental results show that our method enjoys good generation and editing ability with good explainability.
Quantifying the Value of Revert Protection
Venue: arXiv cs.GT 2025
Year: 2025

Revert protection is a feature provided by some blockchain platforms that prevents users from incurring fees for failed transactions. We study the economic implications and benefits of revert protection in the context of priority gas auctions and maximal extractable value. We develop a model in which searchers bid for a top-of-block arbitrage opportunity under varying degrees of revert protection. This model applies to a broad range of settings, including bundle auctions on L1s and priority ordering sequencing rules on L2s. We quantify, in closed form, how revert protection improves equilibrium auction revenue, market efficiency, and blockspace efficiency.
New Fault Domains for Conformance Testing of Finite State Machines
Venue: arXiv cs.FL 2025
Year: 2025

A fault domain reflects a tester's assumptions about faults that may occur in an implementation and that need to be detected during testing. A fault domain that has been widely studied in the literature on black-box conformance testing is the class of finite state machines (FSMs) with at most $m$ states. Numerous strategies for generating test suites have been proposed that guarantee fault coverage for this class. These so-called $m$-complete test suites grow exponentially in $m-n$, where $n$ is the number of states of the specification, so one can only run them for small values of $m-n$. But the assumption that $m-n$ is small is not realistic in practice. In his seminal paper from 1964, Hennie raised the challenge to design checking experiments in which the number of states may increase appreciably. In order to solve this long-standing open problem, we propose (much larger) fault domains that capture the assumption that all states in an implementation can be reached by first performing a sequence from some set $A$ (typically a state cover for the specification), followed by $k$ arbitrary inputs, for some small $k$. The number of states of FSMs in these fault domains grows exponentially in $k$. We present a sufficient condition for $k$-$A$-completeness of test suites with respect to these fault domains. Our condition implies $k$-$A$-completeness of two prominent $m$-complete test suite generation strategies, the Wp and HSI methods. Thus these strategies are complete for much larger fault domains than those for which they were originally designed, and thereby solve Hennie's challenge. We show that three other prominent $m$-complete methods (H, SPY and SPYH) do not always generate $k$-$A$-complete test suites.
Faithful Reeb Graph Reconstruction of a Tectonic Subduction Zone from Earthquake Hypocenters
Venue: arXiv cs.CG 2025
Year: 2025

An important problem in topological data analysis (TDA)$\unicode{x2014}$of both theoretical and practical interest$\unicode{x2014}$is to reconstruct the topology and geometry of an underlying (usually unknown) metric graph from possibly noisy data sampled around it. Reeb graphs have recently been successfully employed in abstract metric graph reconstruction under Gromov$\unicode{x2013}$Hausdorff noise: the sample is assumed to be metrically close to the ground truth. However, such a strong global density guarantee is often unavailable, making the existing Reeb graph-based methods unusable. A very different yet more relevant paradigm focuses on the reconstruction of metric graphs$\unicode{x2014}$embedded in the Euclidean space$\unicode{x2014}$from Euclidean samples that are only Hausdorff-close. We relax the density assumption to give provable geometric reconstruction schemes, even when the sample is metrically close only locally, but still provide provable guarantees for the successful geometric reconstruction of Euclidean graphs under the Hausdorff noise model. We apply our graph reconstruction techniques to reconstruct earthquake plate tectonic boundaries from the global earthquake catalog. The SLAB2.0 model is a comprehensive spatial summary of all known subduction zone slabs on Earth. We reconstruct parts of the SLAB2.0 model from possibly noisy earthquake hypocenter data.
Introducing MAPO: Momentum-Aided Gradient Descent Prompt Optimization
Venue: arXiv cs.CL 2025
Year: 2025

Momentum-Aided Prompt Optimization (MAPO) enhances the efficiency and efficacy of prompt optimization for Large Language Models (LLMs). Building on ProTeGi, MAPO uses positive natural language "gradients" and a momentum-based extension to refine prompts effectively. By tracking gradient history, MAPO avoids local minima and oscillations. It also utilizes beam search and an Upper Confidence Bound (UCB) algorithm for balanced candidate expansion and selection. Benchmark testing shows that MAPO achieves faster convergence time with fewer API calls and higher F1 scores than ProTeGi, proving it as a robust and scalable solution for automated prompt engineering in LLMs.
ChunkRAG: Novel LLM-Chunk Filtering Method for RAG Systems
Venue: arXiv cs.CL 2025
Year: 2025

Retrieval-Augmented Generation (RAG) systems using large language models (LLMs) often generate inaccurate responses due to the retrieval of irrelevant or loosely related information. Existing methods, which operate at the document level, fail to effectively filter out such content. We propose LLM-driven chunk filtering, ChunkRAG, a framework that enhances RAG systems by evaluating and filtering retrieved information at the chunk level. Our approach employs semantic chunking to divide documents into coherent sections and utilizes LLM-based relevance scoring to assess each chunk's alignment with the user's query. By filtering out less pertinent chunks before the generation phase, we significantly reduce hallucinations and improve factual accuracy. Experiments show that our method outperforms existing RAG models, achieving higher accuracy on tasks requiring precise information retrieval. This advancement enhances the reliability of RAG systems, making them particularly beneficial for applications like fact-checking and multi-hop reasoning.
Hypergraph Neural Networks Reveal Spatial Domains from Single-cell Transcriptomics Data
Venue: arXiv cs.LG 2025
Year: 2025

The task of spatial clustering of transcriptomics data is of paramount importance. It enables the classification of tissue samples into diverse subpopulations of cells, which, in turn, facilitates the analysis of the biological functions of clusters, tissue reconstruction, and cell-cell interactions. Many approaches leverage gene expressions, spatial locations, and histological images to detect spatial domains; however, Graph Neural Networks (GNNs) as state of the art models suffer from a limitation in the assumption of pairwise connections between nodes. In the case of domain detection in spatial transcriptomics, some cells are found to be not directly related. Still, they are grouped as the same domain, which shows the incapability of GNNs for capturing implicit connections among the cells. While graph edges connect only two nodes, hyperedges connect an arbitrary number of nodes along their edges, which lets Hypergraph Neural Networks (HGNNs) capture and utilize richer and more complex structural information than traditional GNNs. We use autoencoders to address the limitation of not having the actual labels, which are well-suited for unsupervised learning. Our model has demonstrated exceptional performance, achieving the highest iLISI score of 1.843 compared to other methods. This score indicates the greatest diversity of cell types identified by our method. Furthermore, our model outperforms other methods in downstream clustering, achieving the highest ARI values of 0.51 and Leiden score of 0.60.