pwc-archive/papers-with-abstracts huggingface dataset:
SimGen: A Diffusion-Based Framework for Simultaneous Surgical Image and Segmentation Mask Generation
Authors: Aditya Bhat, Rupak Bose, Chinedu Innocent Nwoye, Nicolas Padoy
Date: 2025-01-15 00:00:00
Tasks: Segmentation

Acquiring and annotating surgical data is often resource-intensive, ethical constraining, and requiring significant expert involvement. While generative AI models like text-to-image can alleviate data scarcity, incorporating spatial annotations, such as segmentation masks, is crucial for precision-driven surgical applications, simulation, and education. This study introduces both a novel task and method, SimGen, for Simultaneous Image and Mask Generation. SimGen is a diffusion model based on the DDPM framework and Residual U-Net, designed to jointly generate high-fidelity surgical images and their corresponding segmentation masks. The model leverages cross-correlation priors to capture dependencies between continuous image and discrete mask distributions. Additionally, a Canonical Fibonacci Lattice (CFL) is employed to enhance class separability and uniformity in the RGB space of the masks. SimGen delivers high-fidelity images and accurate segmentation masks, outperforming baselines across six public datasets assessed on image and semantic inception distance metrics. Ablation study shows that the CFL improves mask quality and spatial separation. Downstream experiments suggest generated image-mask pairs are usable if regulations limit human data release for research. This work offers a cost-effective solution for generating paired surgical images and complex labels, advancing surgical AI development by reducing the need for expensive manual annotations.
Vision Foundation Models for Computed Tomography
Authors: Suraj Pai, Ibrahim Hadzic, Dennis Bontempi, Keno Bressem, Benjamin H. Kann, Andriy Fedorov, Raymond H. Mak, Hugo J. W. L. Aerts
Date: 2025-01-15 00:00:00
Tasks: Computed Tomography (CT), Contrastive Learning, Image Retrieval, Medical Image Retrieval, Tumor Segmentation

Foundation models (FMs) have shown transformative potential in radiology by performing diverse, complex tasks across imaging modalities. Here, we developed CT-FM, a large-scale 3D image-based pre-trained model designed explicitly for various radiological tasks. CT-FM was pre-trained using 148,000 computed tomography (CT) scans from the Imaging Data Commons through label-agnostic contrastive learning. We evaluated CT-FM across four categories of tasks, namely, whole-body and tumor segmentation, head CT triage, medical image retrieval, and semantic understanding, showing superior performance against state-of-the-art models. Beyond quantitative success, CT-FM demonstrated the ability to cluster regions anatomically and identify similar anatomical and structural concepts across scans. Furthermore, it remained robust across test-retest settings and indicated reasonable salient regions attached to its embeddings. This study demonstrates the value of large-scale medical imaging foundation models and by open-sourcing the model weights, code, and data, aims to support more adaptable, reliable, and interpretable AI solutions in radiology.
RepVideo: Rethinking Cross-Layer Representation for Video Generation
Authors: Chenyang Si, Weichen Fan, Zhengyao Lv, Ziqi Huang, Yu Qiao, Ziwei Liu
Date: 2025-01-15 00:00:00
Tasks: Video Generation

Video generation has achieved remarkable progress with the introduction of diffusion models, which have significantly improved the quality of generated videos. However, recent research has primarily focused on scaling up model training, while offering limited insights into the direct impact of representations on the video generation process. In this paper, we initially investigate the characteristics of features in intermediate layers, finding substantial variations in attention maps across different layers. These variations lead to unstable semantic representations and contribute to cumulative differences between features, which ultimately reduce the similarity between adjacent frames and negatively affect temporal coherence. To address this, we propose RepVideo, an enhanced representation framework for text-to-video diffusion models. By accumulating features from neighboring layers to form enriched representations, this approach captures more stable semantic information. These enhanced representations are then used as inputs to the attention mechanism, thereby improving semantic expressiveness while ensuring feature consistency across adjacent frames. Extensive experiments demonstrate that our RepVideo not only significantly enhances the ability to generate accurate spatial appearances, such as capturing complex spatial relationships between multiple objects, but also improves temporal consistency in video generation.
CityLoc: 6DoF Pose Distributional Localization for Text Descriptions in Large-Scale Scenes with Gaussian Representation
Authors: Qi Ma, Runyi Yang, Bin Ren, Nicu Sebe, Ender Konukoglu, Luc van Gool, Danda Pani Paudel
Date: 2025-01-15 00:00:00
Tasks: Language Modeling, Language Modelling, Visual Reasoning

Localizing textual descriptions within large-scale 3D scenes presents inherent ambiguities, such as identifying all traffic lights in a city. Addressing this, we introduce a method to generate distributions of camera poses conditioned on textual descriptions, facilitating robust reasoning for broadly defined concepts. Our approach employs a diffusion-based architecture to refine noisy 6DoF camera poses towards plausible locations, with conditional signals derived from pre-trained text encoders. Integration with the pretrained Vision-Language Model, CLIP, establishes a strong linkage between text descriptions and pose distributions. Enhancement of localization accuracy is achieved by rendering candidate poses using 3D Gaussian splatting, which corrects misaligned samples through visual reasoning. We validate our method's superiority by comparing it against standard distribution estimation methods across five large-scale datasets, demonstrating consistent outperformance. Code, datasets and more information will be publicly available at our project page.
Towards Fast, Specialized Machine Learning Force Fields: Distilling Foundation Models via Energy Hessians
Authors: Ishan Amin, Sanjeev Raja, Aditi Krishnapriyan
Date: 2025-01-15 00:00:00
Tasks: Computational chemistry, Knowledge Distillation

The foundation model (FM) paradigm is transforming Machine Learning Force Fields (MLFFs), leveraging general-purpose representations and scalable training to perform a variety of computational chemistry tasks. Although MLFF FMs have begun to close the accuracy gap relative to first-principles methods, there is still a strong need for faster inference speed. Additionally, while research is increasingly focused on general-purpose models which transfer across chemical space, practitioners typically only study a small subset of systems at a given time. This underscores the need for fast, specialized MLFFs relevant to specific downstream applications, which preserve test-time physical soundness while maintaining train-time scalability. In this work, we introduce a method for transferring general-purpose representations from MLFF foundation models to smaller, faster MLFFs specialized to specific regions of chemical space. We formulate our approach as a knowledge distillation procedure, where the smaller "student" MLFF is trained to match the Hessians of the energy predictions of the "teacher" foundation model. Our specialized MLFFs can be up to 20 $\times$ faster than the original foundation model, while retaining, and in some cases exceeding, its performance and that of undistilled models. We also show that distilling from a teacher model with a direct force parameterization into a student model trained with conservative forces (i.e., computed as derivatives of the potential energy) successfully leverages the representations from the large-scale teacher for improved accuracy, while maintaining energy conservation during test-time molecular dynamics simulations. More broadly, our work suggests a new paradigm for MLFF development, in which foundation models are released along with smaller, specialized simulation "engines" for common chemical subsets.
Improving Stability Estimates in Adversarial Explainable AI through Alternate Search Methods
Authors: Christopher Burger, Charles Walter
Date: 2025-01-15 00:00:00

Advances in the effectiveness of machine learning models have come at the cost of enormous complexity resulting in a poor understanding of how they function. Local surrogate methods have been used to approximate the workings of these complex models, but recent work has revealed their vulnerability to adversarial attacks where the explanation produced is appreciably different while the meaning and structure of the complex model's output remains similar. This prior work has focused on the existence of these weaknesses but not on their magnitude. Here we explore using an alternate search method with the goal of finding minimum viable perturbations, the fewest perturbations necessary to achieve a fixed similarity value between the original and altered text's explanation. Intuitively, a method that requires fewer perturbations to expose a given level of instability is inferior to one which requires more. This nuance allows for superior comparisons of the stability of explainability methods.
CrystalGRW: Generative Modeling of Crystal Structures with Targeted Properties via Geodesic Random Walks
Authors: Krit Tangsongcharoen, Teerachote Pakornchote, Chayanon Atthapak, Natthaphon Choomphon-anomakhun, Annop Ektarawong, Björn Alling, Christopher Sutton, Thiti Bovornratanaraks, Thiparat Chotibut
Date: 2025-01-15 00:00:00
Tasks: Graph Neural Network

Determining whether a candidate crystalline material is thermodynamically stable depends on identifying its true ground-state structure, a central challenge in computational materials science. We introduce CrystalGRW, a diffusion-based generative model on Riemannian manifolds that proposes novel crystal configurations and can predict stable phases validated by density functional theory. The crystal properties, such as fractional coordinates, atomic types, and lattice matrices, are represented on suitable Riemannian manifolds, ensuring that new predictions generated through the diffusion process preserve the periodicity of crystal structures. We incorporate an equivariant graph neural network to also account for rotational and translational symmetries during the generation process. CrystalGRW demonstrates the ability to generate realistic crystal structures that are close to their ground states with accuracy comparable to existing models, while also enabling conditional control, such as specifying a desired crystallographic point group. These features help accelerate materials discovery and inverse design by offering stable, symmetry-consistent crystal candidates for experimental validation.
Neural Risk-sensitive Satisficing in Contextual Bandits
Authors: Shogo Ito, Tatsuji Takahashi, Yu Kono
Date: 2025-01-15 00:00:00
Tasks: Multi-Armed Bandits, Recommendation Systems

The contextual bandit problem, which is a type of reinforcement learning tasks, provides an effective framework for solving challenges in recommendation systems, such as satisfying real-time requirements, enabling personalization, addressing cold-start problems. However, contextual bandit algorithms face challenges since they need to handle large state-action spaces sequentially. These challenges include the high costs for learning and balancing exploration and exploitation, as well as large variations in performance that depend on the domain of application. To address these challenges, Tsuboya et~al. proposed the Regional Linear Risk-sensitive Satisficing (RegLinRS) algorithm. RegLinRS switches between exploration and exploitation based on how well the agent has achieved the target. However, the reward expectations in RegLinRS are linearly approximated based on features, which limits its applicability when the relationship between features and reward expectations is non-linear. To handle more complex environments, we proposed Neural Risk-sensitive Satisficing (NeuralRS), which incorporates neural networks into RegLinRS, and demonstrated its utility.
Molecular Graph Contrastive Learning with Line Graph
Authors: Xueyuan Chen, Shangzhe Li, Ruomei Liu, Bowen Shi, Jiaheng Liu, Junran Wu, Ke Xu
Date: 2025-01-15 00:00:00
Tasks: Attribute, Contrastive Learning, Drug Design, Molecular Property Prediction, Property Prediction

Trapped by the label scarcity in molecular property prediction and drug design, graph contrastive learning (GCL) came forward. Leading contrastive learning works show two kinds of view generators, that is, random or learnable data corruption and domain knowledge incorporation. While effective, the two ways also lead to molecular semantics altering and limited generalization capability, respectively. To this end, we relate the \textbf{L}in\textbf{E} graph with \textbf{MO}lecular graph co\textbf{N}trastive learning and propose a novel method termed \textit{LEMON}. Specifically, by contrasting the given graph with the corresponding line graph, the graph encoder can freely encode the molecular semantics without omission. Furthermore, we present a new patch with edge attribute fusion and two local contrastive losses enhance information transmission and tackle hard negative samples. Compared with state-of-the-art (SOTA) methods for view generation, superior performance on molecular property prediction suggests the effectiveness of our proposed framework.
Normalize Then Propagate: Efficient Homophilous Regularization for Few-shot Semi-Supervised Node Classification
Authors: Baoming Zhang, Mingcai Chen, Jianqing Song, Shuangjie Li, Jie Zhang, Chongjun Wang
Date: 2025-01-15 00:00:00
Tasks: Node Classification

Graph Neural Networks (GNNs) have demonstrated remarkable ability in semi-supervised node classification. However, most existing GNNs rely heavily on a large amount of labeled data for training, which is labor-intensive and requires extensive domain knowledge. In this paper, we first analyze the restrictions of GNNs generalization from the perspective of supervision signals in the context of few-shot semi-supervised node classification. To address these challenges, we propose a novel algorithm named NormProp, which utilizes the homophily assumption of unlabeled nodes to generate additional supervision signals, thereby enhancing the generalization against label scarcity. The key idea is to efficiently capture both the class information and the consistency of aggregation during message passing, via decoupling the direction and Euclidean norm of node representations. Moreover, we conduct a theoretical analysis to determine the upper bound of Euclidean norm, and then propose homophilous regularization to constraint the consistency of unlabeled nodes. Extensive experiments demonstrate that NormProp achieve state-of-the-art performance under low-label rate scenarios with low computational complexity.
DNMDR: Dynamic Networks and Multi-view Drug Representations for Safe Medication Recommendation
Authors: Guanlin Liu, Xiaomei Yu, Zihao Liu, Xue Li, Xingxu Fan, Xiangwei Zheng
Date: 2025-01-15 00:00:00
Tasks: Representation Learning

Medication Recommendation (MR) is a promising research topic which booms diverse applications in the healthcare and clinical domains. However, existing methods mainly rely on sequential modeling and static graphs for representation learning, which ignore the dynamic correlations in diverse medical events of a patient's temporal visits, leading to insufficient global structural exploration on nodes. Additionally, mitigating drug-drug interactions (DDIs) is another issue determining the utility of the MR systems. To address the challenges mentioned above, this paper proposes a novel MR method with the integration of dynamic networks and multi-view drug representations (DNMDR). Specifically, weighted snapshot sequences for dynamic heterogeneous networks are constructed based on discrete visits in temporal EHRs, and all the dynamic networks are jointly trained to gain both structural correlations in diverse medical events and temporal dependency in historical health conditions, for achieving comprehensive patient representations with both semantic features and structural relationships. Moreover, combining the drug co-occurrences and adverse drug-drug interactions (DDIs) in internal view of drug molecule structure and interactive view of drug pairs, the safe drug representations are available to obtain high-quality medication combination recommendation. Finally, extensive experiments on real world datasets are conducted for performance evaluation, and the experimental results demonstrate that the proposed DNMDR method outperforms the state-of-the-art baseline models with a large margin on various metrics such as PRAUC, Jaccard, DDI rates and so on.
Adaptive Sampled Softmax with Inverted Multi-Index: Methods, Theory and Applications
Authors: Jin Chen, Jin Zhang, Xu Huang, Yi Yang, Defu Lian, Enhong Chen
Date: 2025-01-15 00:00:00
Tasks: Multi-class Classification

The softmax function is a cornerstone of multi-class classification, integral to a wide range of machine learning applications, from large-scale retrieval and ranking models to advanced large language models. However, its computational cost grows linearly with the number of classes, which becomes prohibitively expensive in scenarios with millions or even billions of classes. The sampled softmax, which relies on self-normalized importance sampling, has emerged as a powerful alternative, significantly reducing computational complexity. Yet, its estimator remains unbiased only when the sampling distribution matches the true softmax distribution. To improve both approximation accuracy and sampling efficiency, we propose the MIDX Sampler, a novel adaptive sampling strategy based on an inverted multi-index approach. Concretely, we decompose the softmax probability into several multinomial probabilities, each associated with a specific set of codewords and the last associated with the residual score of queries, thus reducing time complexity to the number of codewords instead of the number of classes. To further boost efficiency, we replace the query-specific residual probability with a simple uniform distribution, simplifying the computation while retaining high performance. Our method is backed by rigorous theoretical analysis, addressing key concerns such as sampling bias, gradient bias, convergence rates, and generalization error bounds. The results demonstrate that a smaller divergence from the ideal softmax distribution leads to faster convergence and improved generalization. Extensive experiments on large-scale language models, sequential recommenders, and extreme multi-class classification tasks confirm that the MIDX-Sampler delivers superior effectiveness and efficiency compared to existing approaches.
MIAFEx: An Attention-based Feature Extraction Method for Medical Image Classification
Authors: Oscar Ramos-Soto, Jorge Ramos-Frutos, Ezequiel Perez-Zarate, Diego Oliva, Sandra E. Balderas-Mata
Date: 2025-01-15 00:00:00
Tasks: Classification, image-classification, Image Classification, Medical Image Classification

Feature extraction techniques are crucial in medical image classification; however, classical feature extractors in addition to traditional machine learning classifiers often exhibit significant limitations in providing sufficient discriminative information for complex image sets. While Convolutional Neural Networks (CNNs) and Vision Transformer (ViT) have shown promise in feature extraction, they are prone to overfitting due to the inherent characteristics of medical imaging data, including small sample sizes or high intra-class variance. In this work, the Medical Image Attention-based Feature Extractor (MIAFEx) is proposed, a novel method that employs a learnable refinement mechanism to enhance the classification token within the Transformer encoder architecture. This mechanism adjusts the token based on learned weights, improving the extraction of salient features and enhancing the model's adaptability to the challenges presented by medical imaging data. The MIAFEx output features quality is compared against classical feature extractors using traditional and hybrid classifiers. Also, the performance of these features is compared against modern CNN and ViT models in classification tasks, demonstrating its superiority in accuracy and robustness across multiple complex classification medical imaging datasets. This advantage is particularly pronounced in scenarios with limited training data, where traditional and modern models often struggle to generalize effectively. The source code of this proposal can be found at https://github.com/Oscar-RamosS/Medical-Image-Attention-based-Feature-Extractor-MIAFEx
A Theory of Optimistically Universal Online Learnability for General Concept Classes
Authors: Steve Hanneke, Hongao Wang
Date: 2025-01-15 00:00:00
Tasks: Philosophy

We provide a full characterization of the concept classes that are optimistically universally online learnable with $\{0, 1\}$ labels. The notion of optimistically universal online learning was defined in [Hanneke, 2021] in order to understand learnability under minimal assumptions. In this paper, following the philosophy behind that work, we investigate two questions, namely, for every concept class: (1) What are the minimal assumptions on the data process admitting online learnability? (2) Is there a learning algorithm which succeeds under every data process satisfying the minimal assumptions? Such an algorithm is said to be optimistically universal for the given concept class. We resolve both of these questions for all concept classes, and moreover, as part of our solution, we design general learning algorithms for each case. Finally, we extend these algorithms and results to the agnostic case, showing an equivalence between the minimal assumptions on the data process for learnability in the agnostic and realizable cases, for every concept class, as well as the equivalence of optimistically universal learnability.
OMEGA: A Low-Latency GNN Serving System for Large Graphs
Authors: Geon-Woo Kim, Donghyun Kim, Jeongyoon Moon, Henry Liu, Tarannum Khan, Anand Iyer, Daehyeok Kim, Aditya Akella
Date: 2025-01-15 00:00:00

Graph Neural Networks (GNNs) have been widely adopted for their ability to compute expressive node representations in graph datasets. However, serving GNNs on large graphs is challenging due to the high communication, computation, and memory overheads of constructing and executing computation graphs, which represent information flow across large neighborhoods. Existing approximation techniques in training can mitigate the overheads but, in serving, still lead to high latency and/or accuracy loss. To this end, we propose OMEGA, a system that enables low-latency GNN serving for large graphs with minimal accuracy loss through two key ideas. First, OMEGA employs selective recomputation of precomputed embeddings, which allows for reusing precomputed computation subgraphs while selectively recomputing a small fraction to minimize accuracy loss. Second, we develop computation graph parallelism, which reduces communication overhead by parallelizing the creation and execution of computation graphs across machines. Our evaluation with large graph datasets and GNN models shows that OMEGA significantly outperforms state-of-the-art techniques.