OpenRaiser/Intern-Atlas huggingface dataset:
Optimizing Tree-structure Indexes for CXL-based Heterogeneous Memory with SINLK
Venue: arXiv cs.OS 2025
Year: 2025

On heterogeneous memory (HM) where fast memory (i.e., CPU-attached DRAM) and slow memory (e.g., remote NUMA memory, RDMA-connected memory, Persistent Memory (PM)) coexist, optimizing the placement of tree-structure indexes (e.g., B+tree) is crucial to achieving high performance while enjoying memory expansion. Nowadays, CXL-based heterogeneous memory (CXL-HM) is emerging due to its high efficiency and memory semantics. Prior tree-structure index placement schemes for HM cannot effectively boost performance on CXL-HM, as they fail to adapt to the changes in hardware characteristics and semantics. Additionally, existing CXL-HM page-level data placement schemes are not efficient for tree-structure indexes due to the granularity mismatch between the tree nodes and the page. In this paper, we argue for a CXL native, tree-structure aware data placement scheme to optimize tree-structure indexes on CXL-HM. Our key insight is that the placement of tree-structure indexes on CXL-HM should match the tree's inherent characteristics with CXL-HM features. We present SINLK, a tree-structure aware, node-grained data placement scheme for tree-structure indexes on CXL-HM. With SINLK, developers can easily adapt existing tree-structure indexes to CXL-HM. We have integrated the B+tree and radix tree with SINLK to demonstrate its effectiveness. Evaluations show that SINLK improves throughput by up to 71% and reduces P99 latency by up to 81% compared with state-of-the-art data placement schemes (e.g., MEMTIS) and HM-optimized tree-structure indexes in YCSB and real-world workloads.
PRACtical: Subarray-Level Counter Update and Bank-Level Recovery Isolation for Efficient PRAC Rowhammer Mitigation
Venue: arXiv cs.AR 2025
Year: 2025

As DRAM density increases, Rowhammer becomes more severe due to heightened charge leakage, reducing the number of activations needed to induce bit flips. The DDR5 standard addresses this threat with in-DRAM per-row activation counters (PRAC) and the Alert Back-Off (ABO) signal to trigger mitigation. However, PRAC adds performance overhead by incrementing counters during the precharge phase, and recovery refreshes stalls the entire memory channel, even if only one bank is under attack. We propose PRACtical, a performance-optimized approach to PRAC+ABO that maintains the same security guarantees. First, we reduce counter update latency by introducing a centralized increment circuit, enabling overlap between counter updates and subsequent row activations in other subarrays. Second, we enhance the $RFM_{ab}$ mitigation by enabling bank-level granularity: instead of stalling the entire channel, only affected banks are paused. This is achieved through a DRAM-resident register that identifies attacked banks. PRACtical improves performance by 8% on average (up to 20%) over the state-of-the-art, reduces energy by 19%, and limits performance degradation from aggressive performance attacks to less than 6%, all while preserving Rowhammer protection.
DR.EHR: Dense Retrieval for Electronic Health Record with Knowledge Injection and Synthetic Data
Venue: arXiv cs.IR 2025
Year: 2025

Electronic Health Records (EHRs) are pivotal in clinical practices, yet their retrieval remains a challenge mainly due to semantic gap issues. Recent advancements in dense retrieval offer promising solutions but existing models, both general-domain and biomedical-domain, fall short due to insufficient medical knowledge or mismatched training corpora. This paper introduces \texttt{DR.EHR}, a series of dense retrieval models specifically tailored for EHR retrieval. We propose a two-stage training pipeline utilizing MIMIC-IV discharge summaries to address the need for extensive medical knowledge and large-scale training data. The first stage involves medical entity extraction and knowledge injection from a biomedical knowledge graph, while the second stage employs large language models to generate diverse training data. We train two variants of \texttt{DR.EHR}, with 110M and 7B parameters, respectively. Evaluated on the CliniQ benchmark, our models significantly outperforms all existing dense retrievers, achieving state-of-the-art results. Detailed analyses confirm our models' superiority across various match and query types, particularly in challenging semantic matches like implication and abbreviation. Ablation studies validate the effectiveness of each pipeline component, and supplementary experiments on EHR QA datasets demonstrate the models' generalizability on natural language questions, including complex ones with multiple entities. This work significantly advances EHR retrieval, offering a robust solution for clinical applications.
TRPrompt: Bootstrapping Query-Aware Prompt Optimization from Textual Rewards
Venue: arXiv cs.CL 2025
Year: 2025

Prompt optimization improves the reasoning abilities of large language models (LLMs) without requiring parameter updates to the target model. Following heuristic-based "Think step by step" approaches, the field has evolved in two main directions: while one group of methods uses textual feedback to elicit improved prompts from general-purpose LLMs in a training-free way, a concurrent line of research relies on numerical rewards to train a special prompt model, tailored for providing optimal prompts to the target model. In this paper, we introduce the Textual Reward Prompt framework (TRPrompt), which unifies these approaches by directly incorporating textual feedback into training of the prompt model. Our framework does not require prior dataset collection and is being iteratively improved with the feedback on the generated prompts. When coupled with the capacity of an LLM to internalize the notion of what a "good" prompt is, the high-resolution signal provided by the textual rewards allows us to train a prompt model yielding state-of-the-art query-specific prompts for the problems from the challenging math datasets GSMHard and MATH.
3D Software Synthesis Guided by Constraint-Expressive Intermediate Representation
Venue: arXiv cs.CV 2025
Year: 2025

Graphical user interface (UI) software has undergone a fundamental transformation from traditional two-dimensional (2D) desktop/web/mobile interfaces to spatial three-dimensional (3D) environments. While existing work has made remarkable success in automated 2D software generation, such as HTML/CSS and mobile app interface code synthesis, the generation of 3D software still remains under-explored. Current methods for 3D software generation usually generate the 3D environments as a whole and cannot modify or control specific elements in the software. Furthermore, these methods struggle to handle the complex spatial and semantic constraints inherent in the real world. To address the challenges, we present Scenethesis, a novel requirement-sensitive 3D software synthesis approach that maintains formal traceability between user specifications and generated 3D software. Scenethesis is built upon ScenethesisLang, a domain-specific language that serves as a granular constraint-aware intermediate representation (IR) to bridge natural language requirements and executable 3D software. It serves both as a comprehensive scene description language enabling fine-grained modification of 3D software elements and as a formal constraint-expressive specification language capable of expressing complex spatial constraints. By decomposing 3D software synthesis into stages operating on ScenethesisLang, Scenethesis enables independent verification, targeted modification, and systematic constraint satisfaction. Our evaluation demonstrates that Scenethesis accurately captures over 80% of user requirements and satisfies more than 90% of hard constraints while handling over 100 constraints simultaneously. Furthermore, Scenethesis achieves a 42.8% improvement in BLIP-2 visual evaluation scores compared to the state-of-the-art method.
Layer-Aware Representation Filtering: Purifying Finetuning Data to Preserve LLM Safety Alignment
Venue: arXiv cs.CR 2025
Year: 2025

With rapid advancement and increasing accessibility of LLMs, fine-tuning aligned models has become a critical step for adapting them to real-world applications, which makes the safety of this fine-tuning process more important than ever. However, recent studies have highlighted a critical challenge: even when fine-tuning with seemingly benign downstream datasets, the safety of aligned LLMs can be compromised, making them more susceptible to malicious instructions. In this paper, we show that fine-tuning datasets often contain samples with safety-degrading features that are not easily identifiable on the surface. These samples can significantly degrade the safety alignment of LLMs during fine-tuning. To address this issue, we propose LARF, a Layer-Aware Representation Filtering method. This method identifies safety-sensitive layers within the LLM and leverages their representations to detect which data samples in the post-training dataset contain safety-degrading features. Experimental results demonstrate that LARF can effectively identify benign data with safety-degrading features. After removing such data, the safety alignment degradation caused by fine-tuning is mitigated. Please see our code at https://github.com/LLLeoLi/LARF.
Features extraction for image identification using computer vision
Venue: arXiv cs.CV 2025
Year: 2025

This study examines various feature extraction techniques in computer vision, the primary focus of which is on Vision Transformers (ViTs) and other approaches such as Generative Adversarial Networks (GANs), deep feature models, traditional approaches (SIFT, SURF, ORB), and non-contrastive and contrastive feature models. Emphasizing ViTs, the report summarizes their architecture, including patch embedding, positional encoding, and multi-head self-attention mechanisms with which they overperform conventional convolutional neural networks (CNNs). Experimental results determine the merits and limitations of both methods and their utilitarian applications in advancing computer vision.
Part Segmentation of Human Meshes via Multi-View Human Parsing
Venue: arXiv cs.CV 2025
Year: 2025

Recent advances in point cloud deep learning have led to models that achieve high per-part labeling accuracy on large-scale point clouds, using only the raw geometry of unordered point sets. In parallel, the field of human parsing focuses on predicting body part and clothing/accessory labels from images. This work aims to bridge these two domains by enabling per-vertex semantic segmentation of large-scale human meshes. To achieve this, a pseudo-ground truth labeling pipeline is developed for the Thuman2.1 dataset: meshes are first aligned to a canonical pose, segmented from multiple viewpoints, and the resulting point-level labels are then backprojected onto the original mesh to produce per-point pseudo ground truth annotations. Subsequently, a novel, memory-efficient sampling strategy is introduced, a windowed iterative farthest point sampling (FPS) with space-filling curve-based serialization to effectively downsample the point clouds. This is followed by a purely geometric segmentation using PointTransformer, enabling semantic parsing of human meshes without relying on texture information. Experimental results confirm the effectiveness and accuracy of the proposed approach. Project code and pre-processed data is available at https://github.com/JamesMcCullochDickens/Human3DParsing/tree/master.
Fuzzy Theory in Computer Vision: A Review
Venue: arXiv cs.CV 2025
Year: 2025

Computer vision applications are omnipresent nowadays. The current paper explores the use of fuzzy logic in computer vision, stressing its role in handling uncertainty, noise, and imprecision in image data. Fuzzy logic is able to model gradual transitions and human-like reasoning and provides a promising approach to computer vision. Fuzzy approaches offer a way to improve object recognition, image segmentation, and feature extraction by providing more adaptable and interpretable solutions compared to traditional methods. We discuss key fuzzy techniques, including fuzzy clustering, fuzzy inference systems, type-2 fuzzy sets, and fuzzy rule-based decision-making. The paper also discusses various applications, including medical imaging, autonomous systems, and industrial inspection. Additionally, we explore the integration of fuzzy logic with deep learning models such as convolutional neural networks (CNNs) to enhance performance in complex vision tasks. Finally, we examine emerging trends such as hybrid fuzzy-deep learning models and explainable AI.
Eyes Will Shut: A Vision-Based Next GPS Location Prediction Model by Reinforcement Learning from Visual Map Feed Back
Venue: arXiv cs.CV 2025
Year: 2025

Next Location Prediction is a fundamental task in the study of human mobility, with wide-ranging applications in transportation planning, urban governance, and epidemic forecasting. In practice, when humans attempt to predict the next location in a trajectory, they often visualize the trajectory on a map and reason based on road connectivity and movement trends. However, the vast majority of existing next-location prediction models do not reason over maps \textbf{in the way that humans do}. Fortunately, the recent development of Vision-Language Models (VLMs) has demonstrated strong capabilities in visual perception and even visual reasoning. This opens up a new possibility: by rendering both the road network and trajectory onto an image and leveraging the reasoning abilities of VLMs, we can enable models to perform trajectory inference in a human-like manner. To explore this idea, we first propose a method called Vision-Guided Location Search (VGLS), which evaluates whether a general-purpose VLM is capable of trajectory-based reasoning without modifying any of its internal parameters. Based on insights from the VGLS results, we further propose our main approach: VLMLocPredictor, which is composed of two stages: In the first stage, we design two Supervised Fine-Tuning (SFT) tasks that help the VLM understand road network and trajectory structures and acquire basic reasoning ability on such visual inputs. In the second stage, we introduce Reinforcement Learning from Visual Map Feedback, enabling the model to self-improve its next-location prediction ability through interaction with the environment. Experiments conducted on datasets from four different cities show that our method achieves state-of-the-art (SOTA) performance and exhibits superior cross-city generalization compared to other LLM-based approaches.
Simulating Evolvability as a Learning Algorithm: Empirical Investigations on Distribution Sensitivity, Robustness, and Constraint Tradeoffs
Venue: arXiv cs.CC 2025
Year: 2025

The theory of evolvability, introduced by Valiant (2009), formalizes evolution as a constrained learning algorithm operating without labeled examples or structural knowledge. While theoretical work has established the evolvability of specific function classes under idealized conditions, the framework remains largely untested empirically. In this paper, we implement a genetic algorithm that faithfully simulates Valiant's model and conduct extensive experiments across six Boolean function classes: monotone conjunctions, monotone disjunctions, parity, majority, general conjunctions, and general disjunctions. Our study examines evolvability under uniform and non-uniform distributions, investigates the effects of fixed initial hypotheses and the removal of neutral mutations, and highlights how these constraints alter convergence behavior. We validate known results (e.g., evolvability of monotone conjunctions, non-evolvability of parity) and offer the first empirical evidence on the evolvability of majority and general Boolean classes. Our findings reveal sharp performance drops at intermediate dimensions and expose the essential role of neutral mutations in escaping fitness plateaus. We also demonstrate that evolvability can depend strongly on the input distribution. These insights clarify practical limits of evolutionary search and suggest new directions for theoretical work, including potential refinements to evolvability definitions and bounds. Our implementation provides a rigorous, extensible framework for empirical analysis and serves as a testbed for future explorations of learning through evolution.
Innovator: Scientific Continued Pretraining with Fine-grained MoE Upcycling
Venue: arXiv cs.LG 2025
Year: 2025

A large language model (LLM) with knowledge in both scientific and general tasks is the foundation of science general intelligence. However, directly continued pretraining an LLM using science data usually leads to catastrophic forgetting, which indicates severe degradation in general ability. In this report, we present Innovator, which solves this problem by upcycling a pre-trained dense LLM into a fine-grained Mixtures-of-Experts model during continued pretraining, where different experts are expected to learn science knowledge in different disciplines, and a shared expert is utilized for general tasks. Innovator introduces a four-stage upcycle training paradigm: (1) Scientific Expert Induction on discipline-specific data, (2) Fine-grained Expert Splitting via FFN dimension decomposition, (3) Science-Aware Routing warmup, and (4) Generalist-Scientist Integration training on hybrid datasets. Such a paradigm enables knowledge in the general domain, and different scientific disciplines can be decoupled, avoiding the negative influence among knowledge in different domains. With 53.3B total parameters and 13.3B activated, Innovator extends Qwen2.5-7B using a shared general expert and 64 specialized scientific experts with 8 activated. Trained on 300B tokens with tri-level quality-controlled data, Innovator achieves 25% average improvement across 30 scientific tasks with a win rate as 70%, while retaining 99% performance in general tasks. Furthermore, Innovator-Reason, which is post-trained from Innovator for reasoning boosting, exhibits excellent reasoning performance in solving complex scientific problems with improvements over 30%.
HeartUnloadNet: A Weakly-Supervised Cycle-Consistent Graph Network for Predicting Unloaded Cardiac Geometry from Diastolic States
Venue: arXiv cs.CV 2025
Year: 2025

The unloaded cardiac geometry (i.e., the state of the heart devoid of luminal pressure) serves as a valuable zero-stress and zero-strain reference and is critical for personalized biomechanical modeling of cardiac function, to understand both healthy and diseased physiology and to predict the effects of cardiac interventions. However, estimating the unloaded geometry from clinical images remains a challenging task. Traditional approaches rely on inverse finite element (FE) solvers that require iterative optimization and are computationally expensive. In this work, we introduce HeartUnloadNet, a deep learning framework that predicts the unloaded left ventricular (LV) shape directly from the end diastolic (ED) mesh while explicitly incorporating biophysical priors. The network accepts a mesh of arbitrary size along with physiological parameters such as ED pressure, myocardial stiffness scale, and fiber helix orientation, and outputs the corresponding unloaded mesh. It adopts a graph attention architecture and employs a cycle-consistency strategy to enable bidirectional (loading and unloading) prediction, allowing for partial self-supervision that improves accuracy and reduces the need for large training datasets. Trained and tested on 20,700 FE simulations across diverse LV geometries and physiological conditions, HeartUnloadNet achieves sub-millimeter accuracy, with an average DSC of 0.986 and HD of 0.083 cm, while reducing inference time to just 0.02 seconds per case, over 10^5 times faster and significantly more accurate than traditional inverse FE solvers. Ablation studies confirm the effectiveness of the architecture. Notably, the cycle-consistent design enables the model to maintain a DSC of 97% even with as few as 200 training samples. This work thus presents a scalable and accurate surrogate for inverse FE solvers, supporting real-time clinical applications in the future.
The Right to be Forgotten in Pruning: Unveil Machine Unlearning on Sparse Models
Venue: arXiv cs.LG 2025
Year: 2025

Machine unlearning aims to efficiently eliminate the memory about deleted data from trained models and address the right to be forgotten. Despite the success of existing unlearning algorithms, unlearning in sparse models has not yet been well studied. In this paper, we empirically find that the deleted data has an impact on the pruned topology in a sparse model. Motivated by the observation and the right to be forgotten, we define a new terminology ``un-pruning" to eliminate the impact of deleted data on model pruning. Then we propose an un-pruning algorithm to approximate the pruned topology driven by retained data. We remark that any existing unlearning algorithm can be integrated with the proposed un-pruning workflow and the error of un-pruning is upper-bounded in theory. Also, our un-pruning algorithm can be applied to both structured sparse models and unstructured sparse models. In the experiment, we further find that Membership Inference Attack (MIA) accuracy is unreliable for assessing whether a model has forgotten deleted data, as a small change in the amount of deleted data can produce arbitrary MIA results. Accordingly, we devise new performance metrics for sparse models to evaluate the success of un-pruning. Lastly, we conduct extensive experiments to verify the efficacy of un-pruning with various pruning methods and unlearning algorithms. Our code is released at https://github.com/NKUShaw/SparseModels .
PPipe: Efficient Video Analytics Serving on Heterogeneous GPU Clusters via Pool-Based Pipeline Parallelism
Venue: arXiv cs.DC 2025
Year: 2025

With the rapid innovation of GPUs, heterogeneous GPU clusters in both public clouds and on-premise data centers have become increasingly commonplace. In this paper, we demonstrate how pipeline parallelism, a technique wellstudied for throughput-oriented deep learning model training, can be used effectively for serving latency-bound model inference, e.g., in video analytics systems, on heterogeneous GPU clusters. Our work exploits the synergy between diversity in model layers and diversity in GPU architectures, which results in comparable inference latency for many layers when running on low-class and high-class GPUs. We explore how such overlooked capability of low-class GPUs can be exploited using pipeline parallelism and present a novel inference serving system, PPipe, that employs pool-based pipeline parallelism via an MILP-based control plane and a data plane that performs resource reservation-based adaptive batching. Evaluation results on diverse workloads (18 CNN models) show that PPipe achieves 41.1% - 65.5% higher utilization of low-class GPUs while maintaining high utilization of high-class GPUs, leading to 32.2% - 75.1% higher serving throughput compared to various baselines.