OpenRaiser/Intern-Atlas huggingface dataset:
Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation
Venue: arXiv cs.LG 2025
Year: 2025

In recent years, deep learning techniques have made significant strides in molecular generation for specific targets, driving advancements in drug discovery. However, existing molecular generation methods present significant limitations: those operating at the atomic level often lack synthetic feasibility, drug-likeness, and interpretability, while fragment-based approaches frequently overlook comprehensive factors that influence protein-molecule interactions. To address these challenges, we propose a novel fragment-based molecular generation framework tailored for specific proteins. Our method begins by constructing a protein subpocket and molecular arm concept-based neural network, which systematically integrates interaction force information and geometric complementarity to sample molecular arms for specific protein subpockets. Subsequently, we introduce a diffusion model to generate molecular backbones that connect these arms, ensuring structural integrity and chemical diversity. Our approach significantly improves synthetic feasibility and binding affinity, with a 4% increase in drug-likeness and a 6% improvement in synthetic feasibility. Furthermore, by integrating explicit interaction data through a concept-based model, our framework enhances interpretability, offering valuable insights into the molecular design process.
Investigating the Effectiveness of a Socratic Chain-of-Thoughts Reasoning Method for Task Planning in Robotics, A Case Study
Venue: arXiv cs.RO 2025
Year: 2025

Large language models (LLMs) have demonstrated unprecedented capability in reasoning with natural language. Coupled with this development is the emergence of embodied AI in robotics. Despite showing promise for verbal and written reasoning tasks, it remains unknown whether LLMs are capable of navigating complex spatial tasks with physical actions in the real world. To this end, it is of interest to investigate applying LLMs to robotics in zero-shot learning scenarios, and in the absence of fine-tuning - a feat which could significantly improve human-robot interaction, alleviate compute cost, and eliminate low-level programming tasks associated with robot tasks. To explore this question, we apply GPT-4(Omni) with a simulated Tiago robot in Webots engine for an object search task. We evaluate the effectiveness of three reasoning strategies based on Chain-of-Thought (CoT) sub-task list generation with the Socratic method (SocraCoT) (in order of increasing rigor): (1) Non-CoT/Non-SocraCoT, (2) CoT only, and (3) SocraCoT. Performance was measured in terms of the proportion of tasks successfully completed and execution time (N = 20). Our preliminary results show that when combined with chain-of-thought reasoning, the Socratic method can be used for code generation for robotic tasks that require spatial awareness. In extension of this finding, we propose EVINCE-LoC; a modified EVINCE method that could further enhance performance in highly complex and or dynamic testing scenarios.
Dialogue Injection Attack: Jailbreaking LLMs through Context Manipulation
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) have demonstrated significant utility in a wide range of applications; however, their deployment is plagued by security vulnerabilities, notably jailbreak attacks. These attacks manipulate LLMs to generate harmful or unethical content by crafting adversarial prompts. While much of the current research on jailbreak attacks has focused on single-turn interactions, it has largely overlooked the impact of historical dialogues on model behavior. In this paper, we introduce a novel jailbreak paradigm, Dialogue Injection Attack (DIA), which leverages the dialogue history to enhance the success rates of such attacks. DIA operates in a black-box setting, requiring only access to the chat API or knowledge of the LLM's chat template. We propose two methods for constructing adversarial historical dialogues: one adapts gray-box prefilling attacks, and the other exploits deferred responses. Our experiments show that DIA achieves state-of-the-art attack success rates on recent LLMs, including Llama-3.1 and GPT-4o. Additionally, we demonstrate that DIA can bypass 5 different defense mechanisms, highlighting its robustness and effectiveness.
Attention Hijackers: Detect and Disentangle Attention Hijacking in LVLMs for Hallucination Mitigation
Venue: arXiv cs.CV 2025
Year: 2025

Despite their success, Large Vision-Language Models (LVLMs) remain vulnerable to hallucinations. While existing studies attribute the cause of hallucinations to insufficient visual attention to image tokens, our findings indicate that hallucinations also arise from interference from instruction tokens during decoding. Intuitively, certain instruction tokens continuously distort LVLMs' visual perception during decoding, hijacking their visual attention toward less discriminative visual regions. This distortion prevents them integrating broader contextual information from images, ultimately leading to hallucinations. We term this phenomenon 'Attention Hijacking', where disruptive instruction tokens act as 'Attention Hijackers'. To address this, we propose a novel, training-free strategy namely Attention HIjackers Detection and Disentanglement (AID), designed to isolate the influence of Hijackers, enabling LVLMs to rely on their context-aware intrinsic attention map. Specifically, AID consists of three components: First, Attention Hijackers Detection identifies Attention Hijackers by calculating instruction-driven visual salience. Next, Attention Disentanglement mechanism is proposed to mask the visual attention of these identified Hijackers, and thereby mitigate their disruptive influence on subsequent tokens. Finally, Re-Disentanglement recalculates the balance between instruction-driven and image-driven visual salience to avoid over-masking effects. Extensive experiments demonstrate that AID significantly reduces hallucination across various LVLMs on several benchmarks.
EnergyFormer: Energy Attention with Fourier Embedding for Hyperspectral Image Classification
Venue: arXiv cs.CV 2025
Year: 2025

Hyperspectral imaging (HSI) provides rich spectral-spatial information across hundreds of contiguous bands, enabling precise material discrimination in applications such as environmental monitoring, agriculture, and urban analysis. However, the high dimensionality and spectral variability of HSI data pose significant challenges for feature extraction and classification. This paper presents EnergyFormer, a transformer-based framework designed to address these challenges through three key innovations: (1) Multi-Head Energy Attention (MHEA), which optimizes an energy function to selectively enhance critical spectral-spatial features, improving feature discrimination; (2) Fourier Position Embedding (FoPE), which adaptively encodes spectral and spatial dependencies to reinforce long-range interactions; and (3) Enhanced Convolutional Block Attention Module (ECBAM), which selectively amplifies informative wavelength bands and spatial structures, enhancing representation learning. Extensive experiments on the WHU-Hi-HanChuan, Salinas, and Pavia University datasets demonstrate that EnergyFormer achieves exceptional overall accuracies of 99.28\%, 98.63\%, and 98.72\%, respectively, outperforming state-of-the-art CNN, transformer, and Mamba-based models. The source code will be made available at https://github.com/mahmad000.
Explainable Autoencoder Design for RSSI-Based Multi-User Beam Probing and Hybrid Precoding
Venue: arXiv cs.NI 2025
Year: 2025

This paper introduces a novel neural network (NN) structure referred to as an ``Auto-hybrid precoder'' (Auto-HP) and an unsupervised deep learning (DL) approach that jointly designs \ac{mmWave} probing beams and hybrid precoding matrix design for mmWave multi-user communication system with minimal training pilots. Our learning-based model capitalizes on prior channel observations to achieve two primary goals: designing a limited set of probing beams and predicting off-grid \ac{RF} beamforming vectors. The Auto-HP framework optimizes the probing beams in an unsupervised manner, concentrating the sensing power on the most promising spatial directions based on the surrounding environment. This is achieved through an innovative neural network architecture that respects \ac{RF} chain constraints and models received signal strength power measurements using complex-valued convolutional layers. Then, the autoencoder is trained to directly produce RF beamforming vectors for hybrid architectures, unconstrained by a predefined codebook, based on few projected received signal strength indicators (RSSIs). Finally, once the RF beamforming vectors for the multi-users are predicted, the baseband (BB) digital precoders are designed accounting for the multi-user interference. The Auto-HP neural network is trained end-to-end (E2E) in an unsupervised learning manner with a customized loss function that aims to maximizes the received signal strength. The adequacy of the Auto-HP NN's bottleneck layer dimension is evaluated from an information theory perspective, ensuring maximum data compression and reliable RF beam predictions.
OminiControl2: Efficient Conditioning for Diffusion Transformers
Venue: arXiv cs.CV 2025
Year: 2025

Fine-grained control of text-to-image diffusion transformer models (DiT) remains a critical challenge for practical deployment. While recent advances such as OminiControl and others have enabled a controllable generation of diverse control signals, these methods face significant computational inefficiency when handling long conditional inputs. We present OminiControl2, an efficient framework that achieves efficient image-conditional image generation. OminiControl2 introduces two key innovations: (1) a dynamic compression strategy that streamlines conditional inputs by preserving only the most semantically relevant tokens during generation, and (2) a conditional feature reuse mechanism that computes condition token features only once and reuses them across denoising steps. These architectural improvements preserve the original framework's parameter efficiency and multi-modal versatility while dramatically reducing computational costs. Our experiments demonstrate that OminiControl2 reduces conditional processing overhead by over 90% compared to its predecessor, achieving an overall 5.9$\times$ speedup in multi-conditional generation scenarios. This efficiency enables the practical implementation of complex, multi-modal control for high-quality image synthesis with DiT models.
Sorting permutations using a pop stack with a bypass
Venue: arXiv cs.DM 2025
Year: 2025

We introduce a new sorting device for permutations which makes use of a pop stack augmented with a bypass operation. This results in a sorting machine, which is more powerful than the usual Popstacksort algorithm and seems to have never been investigated previously. In the present paper, we give a characterization of sortable permutations in terms of forbidden patterns and reinterpret the resulting enumerating sequence using a class of restricted Motzkin paths. Moreover, we describe an algorithm to compute the set of all preimages of a given permutation, thanks to which we characterize permutations having a small number of preimages. Finally, we provide a full description of the preimages of principal classes of permutations, and we discuss the device consisting of two pop stacks in parallel, again with a bypass operation.
SegDesicNet: Lightweight Semantic Segmentation in Remote Sensing with Geo-Coordinate Embeddings for Domain Adaptation
Venue: arXiv cs.CV 2025
Year: 2025

Semantic segmentation is essential for analyzing highdefinition remote sensing images (HRSIs) because it allows the precise classification of objects and regions at the pixel level. However, remote sensing data present challenges owing to geographical location, weather, and environmental variations, making it difficult for semantic segmentation models to generalize across diverse scenarios. Existing methods are often limited to specific data domains and require expert annotators and specialized equipment for semantic labeling. In this study, we propose a novel unsupervised domain adaptation technique for remote sensing semantic segmentation by utilizing geographical coordinates that are readily accessible in remote sensing setups as metadata in a dataset. To bridge the domain gap, we propose a novel approach that considers the combination of an imageś location encoding trait and the spherical nature of Earthś surface. Our proposed SegDesicNet module regresses the GRID positional encoding of the geo coordinates projected over the unit sphere to obtain the domain loss. Our experimental results demonstrate that the proposed SegDesicNet outperforms state of the art domain adaptation methods in remote sensing image segmentation, achieving an improvement of approximately ~6% in the mean intersection over union (MIoU) with a ~ 27\% drop in parameter count on benchmarked subsets of the publicly available FLAIR #1 dataset. We also benchmarked our method performance on the custom split of the ISPRS Potsdam dataset. Our algorithm seeks to reduce the modeling disparity between artificial neural networks and human comprehension of the physical world, making the technology more human centric and scalable.
Preference-Based Alignment of Discrete Diffusion Models
Venue: arXiv cs.LG 2025
Year: 2025

Diffusion models have achieved state-of-the-art performance across multiple domains, with recent advancements extending their applicability to discrete data. However, aligning discrete diffusion models with task-specific preferences remains challenging, particularly in scenarios where explicit reward functions are unavailable. In this work, we introduce Discrete Diffusion DPO (D2-DPO), the first adaptation of Direct Preference Optimization (DPO) to discrete diffusion models formulated as continuous-time Markov chains. Our approach derives a novel loss function that directly fine-tunes the generative process using preference data while preserving fidelity to a reference distribution. We validate D2-DPO on a structured binary sequence generation task, demonstrating that the method effectively aligns model outputs with preferences while maintaining structural validity. Our results highlight that D2-DPO enables controlled fine-tuning without requiring explicit reward models, making it a practical alternative to reinforcement learning-based approaches. Future research will explore extending D2-DPO to more complex generative tasks, including language modeling and protein sequence generation, as well as investigating alternative noise schedules, such as uniform noising, to enhance flexibility across different applications.
Progressive Entity Resolution: A Design Space Exploration
Venue: arXiv cs.DB 2025
Year: 2025

Entity Resolution (ER) is typically implemented as a batch task that processes all available data before identifying duplicate records. However, applications with time or computational constraints, e.g., those running in the cloud, require a progressive approach that produces results in a pay-as-you-go fashion. Numerous algorithms have been proposed for Progressive ER in the literature. In this work, we propose a novel framework for Progressive Entity Resolution that organizes relevant techniques into four consecutive steps: (i) filtering, which reduces the search space to the most likely candidate matches, (ii) weighting, which associates every pair of candidate matches with a similarity score, (iii) scheduling, which prioritizes the execution of the candidate matches so that the real duplicates precede the non-matching pairs, and (iv) matching, which applies a complex, matching function to the pairs in the order defined by the previous step. We associate each step with existing and novel techniques, illustrating that our framework overall generates a superset of the main existing works in the field. We select the most representative combinations resulting from our framework and fine-tune them over 10 established datasets for Record Linkage and 8 for Deduplication, with our results indicating that our taxonomy yields a wide range of high performing progressive techniques both in terms of effectiveness and time efficiency.
Trinity: A Modular Humanoid Robot AI System
Venue: arXiv cs.RO 2025
Year: 2025

In recent years, research on humanoid robots has garnered increasing attention. With breakthroughs in various types of artificial intelligence algorithms, embodied intelligence, exemplified by humanoid robots, has been highly anticipated. The advancements in reinforcement learning (RL) algorithms have significantly improved the motion control and generalization capabilities of humanoid robots. Simultaneously, the groundbreaking progress in large language models (LLM) and visual language models (VLM) has brought more possibilities and imagination to humanoid robots. LLM enables humanoid robots to understand complex tasks from language instructions and perform long-term task planning, while VLM greatly enhances the robots' understanding and interaction with their environment. This paper introduces \textcolor{magenta}{Trinity}, a novel AI system for humanoid robots that integrates RL, LLM, and VLM. By combining these technologies, Trinity enables efficient control of humanoid robots in complex environments. This innovative approach not only enhances the capabilities but also opens new avenues for future research and applications of humanoid robotics.
LiPS: Large-Scale Humanoid Robot Reinforcement Learning with Parallel-Series Structures
Venue: arXiv cs.RO 2025
Year: 2025

In recent years, research on humanoid robots has garnered significant attention, particularly in reinforcement learning based control algorithms, which have achieved major breakthroughs. Compared to traditional model-based control algorithms, reinforcement learning based algorithms demonstrate substantial advantages in handling complex tasks. Leveraging the large-scale parallel computing capabilities of GPUs, contemporary humanoid robots can undergo extensive parallel training in simulated environments. A physical simulation platform capable of large-scale parallel training is crucial for the development of humanoid robots. As one of the most complex robot forms, humanoid robots typically possess intricate mechanical structures, encompassing numerous series and parallel mechanisms. However, many reinforcement learning based humanoid robot control algorithms currently employ open-loop topologies during training, deferring the conversion to series-parallel structures until the sim2real phase. This approach is primarily due to the limitations of physics engines, as current GPU-based physics engines often only support open-loop topologies or have limited capabilities in simulating multi-rigid-body closed-loop topologies. For enabling reinforcement learning-based humanoid robot control algorithms to train in large-scale parallel environments, we propose a novel training method LiPS. By incorporating multi-rigid-body dynamics modeling in the simulation environment, we significantly reduce the sim2real gap and the difficulty of converting to parallel structures during model deployment, thereby robustly supporting large-scale reinforcement learning for humanoid robots.
JurisTCU: A Brazilian Portuguese Information Retrieval Dataset with Query Relevance Judgments
Venue: arXiv cs.IR 2025
Year: 2025

This paper introduces JurisTCU, a Brazilian Portuguese dataset for legal information retrieval (LIR). The dataset is freely available and consists of 16,045 jurisprudential documents from the Brazilian Federal Court of Accounts, along with 150 queries annotated with relevance judgments. It addresses the scarcity of Portuguese-language LIR datasets with query relevance annotations. The queries are organized into three groups: real user keyword-based queries, synthetic keyword-based queries, and synthetic question-based queries. Relevance judgments were produced through a hybrid approach combining LLM-based scoring with expert domain validation. We used JurisTCU in 14 experiments using lexical search (document expansion methods) and semantic search (BERT-based and OpenAI embeddings). We show that the document expansion methods significantly improve the performance of standard BM25 search on this dataset, with improvements exceeding 45% in P@10, R@10, and nDCG@10 metrics when evaluating short keyword-based queries. Among the embedding models, the OpenAI models produced the best results, with improvements of approximately 70% in P@10, R@10, and nDCG@10 metrics for short keyword-based queries, suggesting that these dense embeddings capture semantic relationships in this domain, surpassing the reliance on lexical terms. Besides offering a dataset for the Portuguese-language IR research community, suitable for evaluating search systems, the results also contribute to enhancing a search system highly relevant to Brazilian citizens.
TokenSim: Enabling Hardware and Software Exploration for Large Language Model Inference Systems
Venue: arXiv cs.DC 2025
Year: 2025

The increasing demand for large language model (LLM) serving has necessitated significant advancements in the optimization and profiling of LLM inference systems. As these models become integral to a wide range of applications, the need for efficient and scalable serving solutions has grown exponentially. This work introduces TokenSim, a comprehensive hardware and software exploration system designed specifically for LLM inference. TokenSim is characterized by its support for extensible system optimizations including scheduling and memory management. We validate the results with systems running with realworld datasets, achieving an error rate of less than 1%. Furthermore, TokenSim facilitates various insightful explorations into the performance and optimization of LLM serving systems.
Bokeh Diffusion: Defocus Blur Control in Text-to-Image Diffusion Models
Venue: arXiv cs.GR 2025
Year: 2025

Recent advances in large-scale text-to-image models have revolutionized creative fields by generating visually captivating outputs from textual prompts; however, while traditional photography offers precise control over camera settings to shape visual aesthetics - such as depth-of-field via aperture - current diffusion models typically rely on prompt engineering to mimic such effects. This approach often results in crude approximations and inadvertently alters the scene content. In this work, we propose Bokeh Diffusion, a scene-consistent bokeh control framework that explicitly conditions a diffusion model on a physical defocus blur parameter. To overcome the scarcity of paired real-world images captured under different camera settings, we introduce a hybrid training pipeline that aligns in-the-wild images with synthetic blur augmentations, providing diverse scenes and subjects as well as supervision to learn the separation of image content from lens blur. Central to our framework is our grounded self-attention mechanism, trained on image pairs with different bokeh levels of the same scene, which enables blur strength to be adjusted in both directions while preserving the underlying scene. Extensive experiments demonstrate that our approach enables flexible, lens-like blur control, supports downstream applications such as real image editing via inversion, and generalizes effectively across both Stable Diffusion and FLUX architectures.