Ke Yu

Ke Yu, Shantanu Ghosh, Zhexiong Liu et al. · amazon-science, cmu

Creating a large-scale dataset of abnormality annotation on medical images is a labor-intensive and costly task. Leveraging weak supervision from readily available data such as radiology reports can compensate lack of large-scale data for anomaly detection methods. However, most of the current methods only use image-level pathological observations, failing to utilize the relevant anatomy mentions in reports. Furthermore, Natural Language Processing (NLP)-mined weak labels are noisy due to label sparsity and linguistic ambiguity. We propose an Anatomy-Guided chest X-ray Network (AGXNet) to address these issues of weak annotation. Our framework consists of a cascade of two networks, one responsible for identifying anatomical abnormalities and the second responsible for pathological observations. The critical component in our framework is an anatomy-guided attention module that aids the downstream observation network in focusing on the relevant anatomical regions generated by the anatomy network. We use Positive Unlabeled (PU) learning to account for the fact that lack of mention does not necessarily mean a negative label. Our quantitative and qualitative results on the MIMIC-CXR dataset demonstrate the effectiveness of AGXNet in disease and anatomical abnormality localization. Experiments on the NIH Chest X-ray dataset show that the learned feature representations are transferable and can achieve the state-of-the-art performances in disease classification and competitive disease localization results. Our code is available at https://github.com/batmanlab/AGXNet

Shantanu Ghosh, Ke Yu, Forough Arabshahi et al. · amazon-science, cmu

ML model design either starts with an interpretable model or a Blackbox and explains it post hoc. Blackbox models are flexible but difficult to explain, while interpretable models are inherently explainable. Yet, interpretable models require extensive ML knowledge and tend to be less flexible and underperforming than their Blackbox variants. This paper aims to blur the distinction between a post hoc explanation of a Blackbox and constructing interpretable models. Beginning with a Blackbox, we iteratively carve out a mixture of interpretable experts (MoIE) and a residual network. Each interpretable model specializes in a subset of samples and explains them using First Order Logic (FOL), providing basic reasoning on concepts from the Blackbox. We route the remaining samples through a flexible residual. We repeat the method on the residual network until all the interpretable models explain the desired proportion of data. Our extensive experiments show that our route, interpret, and repeat approach (1) identifies a diverse set of instance-specific concepts with high concept completeness via MoIE without compromising in performance, (2) identifies the relatively ``harder'' samples to explain via residuals, (3) outperforms the interpretable by-design models by significant margins during test-time interventions, and (4) fixes the shortcut learned by the original Blackbox. The code for MoIE is publicly available at: \url{https://github.com/batmanlab/ICML-2023-Route-interpret-repeat}

Shantanu Ghosh, Ke Yu, Forough Arabshahi et al. · amazon-science, cmu

We use concept-based interpretable models to mitigate shortcut learning. Existing methods lack interpretability. Beginning with a Blackbox, we iteratively carve out a mixture of interpretable experts (MoIE) and a residual network. Each expert explains a subset of data using First Order Logic (FOL). While explaining a sample, the FOL from biased BB-derived MoIE detects the shortcut effectively. Finetuning the BB with Metadata Normalization (MDN) eliminates the shortcut. The FOLs from the finetuned-BB-derived MoIE verify the elimination of the shortcut. Our experiments show that MoIE does not hurt the accuracy of the original BB and eliminates shortcuts effectively.

Erol Lale, Jan Eliáš, Ke Yu et al.

This article presents a comparison of various implementations of the Lattice Discrete Particle Model (LDPM) for the numerical simulation of concrete and other heterogeneous quasibrittle materials. The comparison involves the use of transient implicit and explicit solvers and steady-state (static) solvers and implementations for Central Processing Unit (CPU) as well as Graphics Processing Unit (GPU). The various implementations are compared on the basis of a set of benchmarks tests describing behaviors of increasing computational complexity. They include elastic vibrations, confined strain-hardening compressive response, tensile fracture, and unconfined strain-softening compressive response. Metrics of interest extracted from the simulations include macroscopic stress versus strain responses, computational times, number of iterations, and energy balance error. Pairwise comparison of final crack patterns is provided through the correlation coefficient and normalized root mean square error of the crack opening vectors. Moreover, for the most numerically challenging case of unconfined compression with sliding boundary conditions, the stability of the strain-softening response is tested by perturbing the solutions as well as changing the convergence criteria and time step size. Attached to this paper is the complete input data of the benchmark tests; this will allow researchers to run the examples and compare them with their own implementations. In addition, most of the reported implementations are publicly available in open source packages.

Xueting Hu, Ce Zhang, Yi Zhang et al. · cmu

Pre-trained Vision-Language Models (VLMs), such as CLIP, have shown enhanced performance across a range of tasks that involve the integration of visual and linguistic modalities. When CLIP is used for depth estimation tasks, the patches, divided from the input images, can be combined with a series of semantic descriptions of the depth information to obtain similarity results. The coarse estimation of depth is then achieved by weighting and summing the depth values, called depth bins, corresponding to the predefined semantic descriptions. The zero-shot approach circumvents the computational and time-intensive nature of traditional fully-supervised depth estimation methods. However, this method, utilizing fixed depth bins, may not effectively generalize as images from different scenes may exhibit distinct depth distributions. To address this challenge, we propose a few-shot-based method which learns to adapt the VLMs for monocular depth estimation to balance training costs and generalization capabilities. Specifically, it assigns different depth bins for different scenes, which can be selected by the model during inference. Additionally, we incorporate learnable prompts to preprocess the input text to convert the easily human-understood text into easily model-understood vectors and further enhance the performance. With only one image per scene for training, our extensive experiment results on the NYU V2 and KITTI dataset demonstrate that our method outperforms the previous state-of-the-art method by up to 10.6\% in terms of MARE.

Nihal Murali, Aahlad Puli, Ke Yu et al.

Deep Neural Networks (DNNs) are prone to learning spurious features that correlate with the label during training but are irrelevant to the learning problem. This hurts model generalization and poses problems when deploying them in safety-critical applications. This paper aims to better understand the effects of spurious features through the lens of the learning dynamics of the internal neurons during the training process. We make the following observations: (1) While previous works highlight the harmful effects of spurious features on the generalization ability of DNNs, we emphasize that not all spurious features are harmful. Spurious features can be "benign" or "harmful" depending on whether they are "harder" or "easier" to learn than the core features for a given model. This definition is model and dataset-dependent. (2) We build upon this premise and use instance difficulty methods (like Prediction Depth (Baldock et al., 2021)) to quantify "easiness" for a given model and to identify this behavior during the training phase. (3) We empirically show that the harmful spurious features can be detected by observing the learning dynamics of the DNN's early layers. In other words, easy features learned by the initial layers of a DNN early during the training can (potentially) hurt model generalization. We verify our claims on medical and vision datasets, both simulated and real, and justify the empirical success of our hypothesis by showing the theoretical connections between Prediction Depth and information-theoretic concepts like V-usable information (Ethayarajh et al., 2021). Lastly, our experiments show that monitoring only accuracy during training (as is common in machine learning pipelines) is insufficient to detect spurious features. We, therefore, highlight the need for monitoring early training dynamics using suitable instance difficulty metrics.

Ke Yu, Li Sun, Junxiang Chen et al.

Large-scale volumetric medical images with annotation are rare, costly, and time prohibitive to acquire. Self-supervised learning (SSL) offers a promising pre-training and feature extraction solution for many downstream tasks, as it only uses unlabeled data. Recently, SSL methods based on instance discrimination have gained popularity in the medical imaging domain. However, SSL pre-trained encoders may use many clues in the image to discriminate an instance that are not necessarily disease-related. Moreover, pathological patterns are often subtle and heterogeneous, requiring the ability of the desired method to represent anatomy-specific features that are sensitive to abnormal changes in different body parts. In this work, we present a novel SSL framework, named DrasCLR, for 3D medical imaging to overcome these challenges. We propose two domain-specific contrastive learning strategies: one aims to capture subtle disease patterns inside a local anatomical region, and the other aims to represent severe disease patterns that span larger regions. We formulate the encoder using conditional hyper-parameterized network, in which the parameters are dependant on the anatomical location, to extract anatomically sensitive features. Extensive experiments on large-scale computer tomography (CT) datasets of lung images show that our method improves the performance of many downstream prediction and segmentation tasks. The patient-level representation improves the performance of the patient survival prediction task. We show how our method can detect emphysema subtypes via dense prediction. We demonstrate that fine-tuning the pre-trained model can significantly reduce annotation efforts without sacrificing emphysema detection accuracy. Our ablation study highlights the importance of incorporating anatomical context into the SSL framework.

Li Sun, Ke Yu, Kayhan Batmanghelich

Although self-supervised learning enables us to bootstrap the training by exploiting unlabeled data, the generic self-supervised methods for natural images do not sufficiently incorporate the context. For medical images, a desirable method should be sensitive enough to detect deviation from normal-appearing tissue of each anatomical region; here, anatomy is the context. We introduce a novel approach with two levels of self-supervised representation learning objectives: one on the regional anatomical level and another on the patient-level. We use graph neural networks to incorporate the relationship between different anatomical regions. The structure of the graph is informed by anatomical correspondences between each patient and an anatomical atlas. In addition, the graph representation has the advantage of handling any arbitrarily sized image in full resolution. Experiments on large-scale Computer Tomography (CT) datasets of lung images show that our approach compares favorably to baseline methods that do not account for the context. We use the learned embedding for staging lung tissue abnormalities related to COVID-19.

Ke Yu, Shyam Visweswaran, Kayhan Batmanghelich

Learning accurate drug representations is essential for task such as computational drug repositioning. A drug hierarchy is a valuable source that encodes knowledge of relations among drugs in a tree-like structure where drugs that act on the same organs, treat the same disease, or bind to the same biological target are grouped together. However, its utility in learning drug representations has not yet been explored, and currently described drug representations cannot place novel molecules in a drug hierarchy. Here, we develop a semi-supervised drug embedding that incorporates two sources of information: (1) underlying chemical grammar that is inferred from chemical structures of drugs and drug-like molecules (unsupervised), and (2) hierarchical relations that are encoded in an expert-crafted hierarchy of approved drugs (supervised). We use the Variational Auto-Encoder (VAE) framework to encode the chemical structures of molecules and use the drug-drug similarity information obtained from the hierarchy to induce the clustering of drugs in hyperbolic space. The hyperbolic space is amenable for encoding hierarchical relations. Our qualitative results support that the learned drug embedding can induce the hierarchical relations among drugs. We demonstrate that the learned drug embedding can be used for drug repositioning.

Yi Zhang, Chun-Wun Cheng, Ke Yu et al.

In this paper, we consider the problem of prototype-based vision-language reasoning problem. We observe that existing methods encounter three major challenges: 1) escalating resource demands and prolonging training times, 2) contending with excessive learnable parameters, and 3) fine-tuning based only on a single modality. These challenges will hinder their capability to adapt Vision-Language Models (VLMs) to downstream tasks. Motivated by this critical observation, we propose a novel method called NODE-Adapter, which utilizes Neural Ordinary Differential Equations for better vision-language reasoning. To fully leverage both visual and textual modalities and estimate class prototypes more effectively and accurately, we divide our method into two stages: cross-modal prototype construction and cross-modal prototype optimization using neural ordinary differential equations. Specifically, we exploit VLM to encode hand-crafted prompts into textual features and few-shot support images into visual features. Then, we estimate the textual prototype and visual prototype by averaging the textual features and visual features, respectively, and adaptively combine the textual prototype and visual prototype to construct the cross-modal prototype. To alleviate the prototype bias, we then model the prototype optimization process as an initial value problem with Neural ODEs to estimate the continuous gradient flow. Our extensive experimental results, which cover few-shot classification, domain generalization, and visual reasoning on human-object interaction, demonstrate that the proposed method significantly outperforms existing state-of-the-art approaches.

Jiong Cai, Yong Jiang, Yue Zhang et al.

Discovering the intended items of user queries from a massive repository of items is one of the main goals of an e-commerce search system. Relevance prediction is essential to the search system since it helps improve performance. When online serving a relevance model, the model is required to perform fast and accurate inference. Currently, the widely used models such as Bi-encoder and Cross-encoder have their limitations in accuracy or inference speed respectively. In this work, we propose a novel model called the Entity-Based Relevance Model (EBRM). We identify the entities contained in an item and decompose the QI (query-item) relevance problem into multiple QE (query-entity) relevance problems; we then aggregate their results to form the QI prediction using a soft logic formulation. The decomposition allows us to use a Cross-encoder QE relevance module for high accuracy as well as cache QE predictions for fast online inference. Utilizing soft logic makes the prediction procedure interpretable and intervenable. We also show that pretraining the QE module with auto-generated QE data from user logs can further improve the overall performance. The proposed method is evaluated on labeled data from e-commerce websites. Empirical results show that it achieves promising improvements with computation efficiency.

Yi Zhang, Chun-Wun Cheng, Junyi He et al.

Recent research in Vision-Language Models (VLMs) has significantly advanced our capabilities in cross-modal reasoning. However, existing methods suffer from performance degradation with domain changes or require substantial computational resources for fine-tuning in new domains. To address this issue, we develop a new adaptation method for large vision-language models, called \textit{Training-free Dual Hyperbolic Adapters} (T-DHA). We characterize the vision-language relationship between semantic concepts, which typically has a hierarchical tree structure, in the hyperbolic space instead of the traditional Euclidean space. Hyperbolic spaces exhibit exponential volume growth with radius, unlike the polynomial growth in Euclidean space. We find that this unique property is particularly effective for embedding hierarchical data structures using the Poincaré ball model, achieving significantly improved representation and discrimination power. Coupled with negative learning, it provides more accurate and robust classifications with fewer feature dimensions. Our extensive experimental results on various datasets demonstrate that the T-DHA method significantly outperforms existing state-of-the-art methods in few-shot image recognition and domain generalization tasks.

Maxwell Reynolds, Chaitanya Srinivasan, Vijay Cherupally et al.

Discovery of sensitive and biologically grounded biomarkers is essential for early detection and monitoring of Alzheimer's disease (AD). Structural MRI is widely available but typically relies on hand-crafted features such as cortical thickness or volume. We ask whether self-supervised learning (SSL) can uncover more powerful biomarkers from the same data. Existing SSL methods underperform FreeSurfer-derived features in disease classification, conversion prediction, and amyloid status prediction. We introduce Residual Noise Contrastive Estimation (R-NCE), a new SSL framework that integrates auxiliary FreeSurfer features while maximizing additional augmentation-invariant information. R-NCE outperforms traditional features and existing SSL methods across multiple benchmarks, including AD conversion prediction. To assess biological relevance, we derive Brain Age Gap (BAG) measures and perform genome-wide association studies. R-NCE-BAG shows high heritability and associations with MAPT and IRAG1, with enrichment in astrocytes and oligodendrocytes, indicating sensitivity to neurodegenerative and cerebrovascular processes.

Eric Loreaux, Ke Yu, Jonas Kemp et al.

Machine learning systems show significant promise for forecasting patient adverse events via risk scores. However, these risk scores implicitly encode assumptions about future interventions that the patient is likely to receive, based on the intervention policy present in the training data. Without this important context, predictions from such systems are less interpretable for clinicians. We propose a joint model of intervention policy and adverse event risk as a means to explicitly communicate the model's assumptions about future interventions. We develop such an intervention policy model on MIMIC-III, a real world de-identified ICU dataset, and discuss some use cases that highlight the utility of this approach. We show how combining typical risk scores, such as the likelihood of mortality, with future intervention probability scores leads to more interpretable clinical predictions.

Ke Yu, Stephen Albro, Giulia DeSalvo et al.

Training high-quality instance segmentation models requires an abundance of labeled images with instance masks and classifications, which is often expensive to procure. Active learning addresses this challenge by striving for optimum performance with minimal labeling cost by selecting the most informative and representative images for labeling. Despite its potential, active learning has been less explored in instance segmentation compared to other tasks like image classification, which require less labeling. In this study, we propose a post-hoc active learning algorithm that integrates uncertainty-based sampling with diversity-based sampling. Our proposed algorithm is not only simple and easy to implement, but it also delivers superior performance on various datasets. Its practical application is demonstrated on a real-world overhead imagery dataset, where it increases the labeling efficiency fivefold.

Yi Zhang, Ke Yu, Siqi Wu et al.

In this paper, we propose Conceptual Codebook Learning (CoCoLe), a novel fine-tuning method for vision-language models (VLMs) to address the challenge of improving the generalization capability of VLMs while fine-tuning them on downstream tasks in a few-shot setting. We recognize that visual concepts, such as textures, shapes, and colors are naturally transferable across domains and play a crucial role in generalization tasks. Motivated by this interesting finding, we learn a conceptual codebook consisting of visual concepts as keys and conceptual prompts as values, which serves as a link between the image encoder's outputs and the text encoder's inputs. Specifically, for a given image, we leverage the codebook to identify the most relevant conceptual prompts associated with the class embeddings to perform the classification. Additionally, we incorporate a handcrafted concept cache as a regularization to alleviate the overfitting issues in low-shot scenarios. We observe that this conceptual codebook learning method is able to achieve enhanced alignment between visual and linguistic modalities. Extensive experimental results demonstrate that our CoCoLe method remarkably outperforms the existing state-of-the-art methods across various evaluation settings, including base-to-new generalization, cross-dataset evaluation, and domain generalization tasks. Detailed ablation studies further confirm the efficacy of each component in CoCoLe.

Hao Zhou, Suman Sourav, Binbin Chen et al.

Programmable Logic Controllers (PLCs) are critical components in Industrial Control Systems (ICSs). Their potential exposure to external world makes them susceptible to cyber-attacks. Existing detection methods against controller logic attacks use either specification-based or learnt models. However, specification-based models require experts' manual efforts or access to PLC's source code, while machine learning-based models often fall short of providing explanation for their decisions. We design SRLR -- a it Symbolic Regression based Logic Recovery} solution to identify the logic of a PLC based only on its inputs and outputs. The recovered logic is used to generate explainable rules for detecting controller logic attacks. SRLR enhances the latest deep symbolic regression methods using the following ICS-specific properties: (1) some important ICS control logic is best represented in frequency domain rather than time domain; (2) an ICS controller can operate in multiple modes, each using different logic, where mode switches usually do not happen frequently; (3) a robust controller usually filters out outlier inputs as ICS sensor data can be noisy; and (4) with the above factors captured, the degree of complexity of the formulas is reduced, making effective search possible. Thanks to these enhancements, SRLR consistently outperforms all existing methods in a variety of ICS settings that we evaluate. In terms of the recovery accuracy, SRLR's gain can be as high as 39% in some challenging environment. We also evaluate SRLR on a distribution grid containing hundreds of voltage regulators, demonstrating its stability in handling large-scale, complex systems with varied configurations.

Zhaoyi Li, Wenjie Mei, Ke Yu et al.

Learning models of dynamical systems with external inputs, which may be, for example, nonsmooth or piecewise, is crucial for studying complex phenomena and predicting future state evolution, which is essential for applications such as safety guarantees and decision-making. In this work, we introduce \emph{Input Concomitant Neural ODEs (ICODEs)}, which incorporate precise real-time input information into the learning process of the models, rather than treating the inputs as hidden parameters to be learned. The sufficient conditions to ensure the model's contraction property are provided to guarantee that system trajectories of the trained model converge to a fixed point, regardless of initial conditions across different training processes. We validate our method through experiments on several representative real dynamics: Single-link robot, DC-to-DC converter, motion dynamics of a rigid body, Rabinovich-Fabrikant equation, Glycolytic-glycogenolytic pathway model, and heat conduction equation. The experimental results demonstrate that our proposed ICODEs efficiently learn the ground truth systems, achieving superior prediction performance under both typical and atypical inputs. This work offers a valuable class of neural ODE models for understanding physical systems with explicit external input information, with potentially promising applications in fields such as physics and robotics. Our code is available online at https://github.com/EEE-ai59/ICODE.git.

Juntong Wu, Zijing Liu, He Cao et al.

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to accurately assess the model's performance in this domain. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data can be seen at https://github.com/IDEA-XL/RAPM.

Shantanu Ghosh, Ke Yu, Kayhan Batmanghelich

Building generalizable AI models is one of the primary challenges in the healthcare domain. While radiologists rely on generalizable descriptive rules of abnormality, Neural Network (NN) models suffer even with a slight shift in input distribution (e.g., scanner type). Fine-tuning a model to transfer knowledge from one domain to another requires a significant amount of labeled data in the target domain. In this paper, we develop an interpretable model that can be efficiently fine-tuned to an unseen target domain with minimal computational cost. We assume the interpretable component of NN to be approximately domain-invariant. However, interpretable models typically underperform compared to their Blackbox (BB) variants. We start with a BB in the source domain and distill it into a \emph{mixture} of shallow interpretable models using human-understandable concepts. As each interpretable model covers a subset of data, a mixture of interpretable models achieves comparable performance as BB. Further, we use the pseudo-labeling technique from semi-supervised learning (SSL) to learn the concept classifier in the target domain, followed by fine-tuning the interpretable models in the target domain. We evaluate our model using a real-life large-scale chest-X-ray (CXR) classification dataset. The code is available at: \url{https://github.com/batmanlab/MICCAI-2023-Route-interpret-repeat-CXRs}.

Joshua Robinson, Li Sun, Ke Yu et al.

The generalization of representations learned via contrastive learning depends crucially on what features of the data are extracted. However, we observe that the contrastive loss does not always sufficiently guide which features are extracted, a behavior that can negatively impact the performance on downstream tasks via "shortcuts", i.e., by inadvertently suppressing important predictive features. We find that feature extraction is influenced by the difficulty of the so-called instance discrimination task (i.e., the task of discriminating pairs of similar points from pairs of dissimilar ones). Although harder pairs improve the representation of some features, the improvement comes at the cost of suppressing previously well represented features. In response, we propose implicit feature modification (IFM), a method for altering positive and negative samples in order to guide contrastive models towards capturing a wider variety of predictive features. Empirically, we observe that IFM reduces feature suppression, and as a result improves performance on vision and medical imaging tasks. The code is available at: \url{https://github.com/joshr17/IFM}.

Xintao Wang, Kelvin C. K. Chan, Ke Yu et al.

Video restoration tasks, including super-resolution, deblurring, etc, are drawing increasing attention in the computer vision community. A challenging benchmark named REDS is released in the NTIRE19 Challenge. This new benchmark challenges existing methods from two aspects: (1) how to align multiple frames given large motions, and (2) how to effectively fuse different frames with diverse motion and blur. In this work, we propose a novel Video Restoration framework with Enhanced Deformable networks, termed EDVR, to address these challenges. First, to handle large motions, we devise a Pyramid, Cascading and Deformable (PCD) alignment module, in which frame alignment is done at the feature level using deformable convolutions in a coarse-to-fine manner. Second, we propose a Temporal and Spatial Attention (TSA) fusion module, in which attention is applied both temporally and spatially, so as to emphasize important features for subsequent restoration. Thanks to these modules, our EDVR wins the champions and outperforms the second place by a large margin in all four tracks in the NTIRE19 video restoration and enhancement challenges. EDVR also demonstrates superior performance to state-of-the-art published methods on video super-resolution and deblurring. The code is available at https://github.com/xinntao/EDVR.

Xintao Wang, Ke Yu, Shixiang Wu et al.

The Super-Resolution Generative Adversarial Network (SRGAN) is a seminal work that is capable of generating realistic textures during single image super-resolution. However, the hallucinated details are often accompanied with unpleasant artifacts. To further enhance the visual quality, we thoroughly study three key components of SRGAN - network architecture, adversarial loss and perceptual loss, and improve each of them to derive an Enhanced SRGAN (ESRGAN). In particular, we introduce the Residual-in-Residual Dense Block (RRDB) without batch normalization as the basic network building unit. Moreover, we borrow the idea from relativistic GAN to let the discriminator predict relative realness instead of the absolute value. Finally, we improve the perceptual loss by using the features before activation, which could provide stronger supervision for brightness consistency and texture recovery. Benefiting from these improvements, the proposed ESRGAN achieves consistently better visual quality with more realistic and natural textures than SRGAN and won the first place in the PIRM2018-SR Challenge. The code is available at https://github.com/xinntao/ESRGAN .

Fengming Zhang, Wenjie Du, Huan Zhang et al.

Time series imputation benefits from leveraging cross-feature correlations, yet existing attention-based methods re-discover feature relationships at each layer, lacking persistent anchors to maintain consistent representations. To address this, we propose HELIX, which assigns each feature a learnable feature identity, a persistent embedding that captures intrinsic semantic properties throughout the network. Unlike graph-based methods that rely on predefined topology and assume homogeneous spatial relationships, HELIX learns arbitrary feature dependencies end-to-end from temporal co-variation, naturally handling datasets where features mix spatial locations with semantic variables. Integrated with hybrid temporal-feature attention, HELIX achieves the state-of-the-art performance, surpassing all 16 baselines on 5 public datasets across 21 experimental settings in our evaluation. Furthermore, our mechanistic analysis reveals that HELIX aligns learned feature identities and dependencies with latent physical and semantic structure progressively across layers, demonstrating that it more effectively translates cross-feature structure into imputation accuracy.

Yi Zhang, Ce Zhang, Ke Yu et al. · cmu

Contrastive Language-Image Pretraining (CLIP) model has exhibited remarkable efficacy in establishing cross-modal connections between texts and images, yielding impressive performance across a broad spectrum of downstream applications through fine-tuning. However, for generalization tasks, the current fine-tuning methods for CLIP, such as CoOp and CoCoOp, demonstrate relatively low performance on some fine-grained datasets. We recognize the underlying reason is that these previous methods only projected global features into the prompt, neglecting the various visual concepts, such as colors, shapes, and sizes, which are naturally transferable across domains and play a crucial role in generalization tasks. To address this issue, in this work, we propose Concept-Guided Prompt Learning (CPL) for vision-language models. Specifically, we leverage the well-learned knowledge of CLIP to create a visual concept cache to enable concept-guided prompting. In order to refine the text features, we further develop a projector that transforms multi-level visual features into text features. We observe that this concept-guided prompt learning approach is able to achieve enhanced consistency between visual and linguistic modalities. Extensive experimental results demonstrate that our CPL method significantly improves generalization capabilities compared to the current state-of-the-art methods.

Wenjie Mei, Xiaorui Wang, Yanrong Lu et al.

Learning models for dynamical systems in continuous time is significant for understanding complex phenomena and making accurate predictions. This study presents a novel approach utilizing differential neural networks (DNNs) to model nonlinear systems, specifically permanent magnet synchronous motors (PMSMs), and to predict their current trajectories. The efficacy of our approach is validated through experiments conducted under various load disturbances and no-load conditions. The results demonstrate that our method effectively and accurately reconstructs the original systems, showcasing strong short-term and long-term prediction capabilities and robustness. This study provides valuable insights into learning the inherent dynamics of complex dynamical data and holds potential for further applications in fields such as weather forecasting, robotics, and collective behavior analysis.

Lu Gao, Ke Yu, Pan Lu

Pavement deterioration modeling is important in providing information regarding the future state of the road network and in determining the needs of preventive maintenance or rehabilitation treatments. This research incorporated spatial dependence of road network into pavement deterioration modeling through a graph neural network (GNN). The key motivation of using a GNN for pavement performance modeling is the ability to easily and directly exploit the rich structural information in the network. This paper explored if considering spatial structure of the road network will improve the prediction performance of the deterioration models. The data used in this research comprises a large pavement condition data set with more than a half million observations taken from the Pavement Management Information System (PMIS) maintained by the Texas Department of Transportation. The promising comparison results indicates that pavement deterioration prediction models perform better when spatial relationship is considered.

Jun Liu, Ke Yu, Keliang Chen et al.

With the rapid advancement of artificial intelligence, the proliferation of autonomous agents has introduced new challenges in interoperability, scalability, and coordination. The Internet of Agents (IoA) aims to interconnect heterogeneous agents through standardized communication protocols, enabling seamless collaboration and intelligent task execution. However, existing agent communication protocols such as MCP, A2A, and ANP remain fragmented and scenario-specific. To address this gap, we propose Agent Collaboration Protocols (ACPs), a comprehensive protocol suite for the IoA. ACPs include registration, discovery, interaction, and tooling protocols to support trustable access, capability orchestration, and workflow construction. We present the architecture, key technologies, and application workflows of ACPs, and demonstrate its effectiveness in a collaborative restaurant booking scenario. ACPs lay the foundation for building a secure, open, and scalable agent internet infrastructure.

Ying Cui, Dongzhe Zheng, Ke Yu et al.

Clear cell renal cell carcinoma (ccRCC) exhibits extensive intratumoral heterogeneity on multiple biological scales, contributing to variable clinical outcomes and limiting the effectiveness of conventional TNM staging, which highlights the urgent need for multiscale integrative analytic frameworks. The lipid-deficient de-clear cell differentiated (DCCD) ccRCC subtype, defined by multi-omics analyses, is associated with adverse outcomes even in early-stage disease. Here, we establish a hierarchical cross-scale framework for the preoperative identification of DCCD-ccRCC. At the highest layer, cross-modal mapping transferred molecular signatures to histological and CT phenotypes, establishing a molecular-to-pathology-to-radiology supervisory bridge. Within this framework, each modality-specific model is designed to mirror the inherent hierarchical structure of tumor biology. PathoDCCD captured multi-scale microscopic features, from cellular morphology and tissue architecture to meso-regional organization. RadioDCCD integrated complementary macroscopic information by combining whole-tumor and its habitat-subregions radiomics with a 2D maximal-section heterogeneity metric. These nested models enabled integrated molecular subtype prediction and clinical risk stratification. Across five cohorts totaling 1,659 patients, PathoDCCD reliably recapitulated molecular subtypes, while RadioDCCD provided reliable preoperative prediction. The consistent predictions identified patients with the poorest clinical outcomes. This cross-scale paradigm unifies molecular biology, computational pathology, and quantitative radiology into a biologically grounded strategy for preoperative noninvasive molecular phenotyping of ccRCC.

Xinrui Li, Qilin Fan, Tianfu Wang et al.

Federated graph learning (FGL) enables multiple clients to collaboratively train powerful graph neural networks without sharing their private, decentralized graph data. Inherited from generic federated learning, FGL is critically challenged by statistical heterogeneity, where non-IID data distributions across clients can severely impair model performance. A particularly destructive form of this is class imbalance, which causes the global model to become biased towards majority classes and fail at identifying rare but critical events. This issue is exacerbated in FGL, as nodes from a minority class are often surrounded by biased neighborhood information, hindering the learning of expressive embeddings. To grapple with this challenge, we propose GraphFedMIG, a novel FGL framework that reframes the problem as a federated generative data augmentation task. GraphFedMIG employs a hierarchical generative adversarial network where each client trains a local generator to synthesize high-fidelity feature representations. To provide tailored supervision, clients are grouped into clusters, each sharing a dedicated discriminator. Crucially, the framework designs a mutual information-guided mechanism to steer the evolution of these client generators. By calculating each client's unique informational value, this mechanism corrects the local generator parameters, ensuring that subsequent rounds of mutual information-guided generation are focused on producing high-value, minority-class features. We conduct extensive experiments on four real-world datasets, and the results demonstrate the superiority of the proposed GraphFedMIG compared with other baselines.

Ke Yu, Zexian Li, Yue Peng et al.

Image Signal Processor (ISP) is a crucial component in digital cameras that transforms sensor signals into images for us to perceive and understand. Existing ISP designs always adopt a fixed architecture, e.g., several sequential modules connected in a rigid order. Such a fixed ISP architecture may be suboptimal for real-world applications, where camera sensors, scenes and tasks are diverse. In this study, we propose a novel Reconfigurable ISP (ReconfigISP) whose architecture and parameters can be automatically tailored to specific data and tasks. In particular, we implement several ISP modules, and enable backpropagation for each module by training a differentiable proxy, hence allowing us to leverage the popular differentiable neural architecture search and effectively search for the optimal ISP architecture. A proxy tuning mechanism is adopted to maintain the accuracy of proxy networks in all cases. Extensive experiments conducted on image restoration and object detection, with different sensors, light conditions and efficiency constraints, validate the effectiveness of ReconfigISP. Only hundreds of parameters need tuning for every task.

Li Sun, Ke Yu, Kayhan Batmanghelich

Supervised learning method requires a large volume of annotated datasets. Collecting such datasets is time-consuming and expensive. Until now, very few annotated COVID-19 imaging datasets are available. Although self-supervised learning enables us to bootstrap the training by exploiting unlabeled data, the generic self-supervised methods for natural images do not sufficiently incorporate the context. For medical images, a desirable method should be sensitive enough to detect deviation from normal-appearing tissue of each anatomical region; here, anatomy is the context. We introduce a novel approach with two levels of self-supervised representation learning objectives: one on the regional anatomical level and another on the patient-level. We use graph neural networks to incorporate the relationship between different anatomical regions. The structure of the graph is informed by anatomical correspondences between each patient and an anatomical atlas. In addition, the graph representation has the advantage of handling any arbitrarily sized image in full resolution. Experiments on large-scale Computer Tomography (CT) datasets of lung images show that our approach compares favorably to baseline methods that do not account for the context. We use the learnt embedding to quantify the clinical progression of COVID-19 and show that our method generalizes well to COVID-19 patients from different hospitals. Qualitative results suggest that our model can identify clinically relevant regions in the images.

Kelvin C. K. Chan, Xintao Wang, Ke Yu et al.

Video super-resolution (VSR) approaches tend to have more components than the image counterparts as they need to exploit the additional temporal dimension. Complex designs are not uncommon. In this study, we wish to untangle the knots and reconsider some most essential components for VSR guided by four basic functionalities, i.e., Propagation, Alignment, Aggregation, and Upsampling. By reusing some existing components added with minimal redesigns, we show a succinct pipeline, BasicVSR, that achieves appealing improvements in terms of speed and restoration quality in comparison to many state-of-the-art algorithms. We conduct systematic analysis to explain how such gain can be obtained and discuss the pitfalls. We further show the extensibility of BasicVSR by presenting an information-refill mechanism and a coupled propagation scheme to facilitate information aggregation. The BasicVSR and its extension, IconVSR, can serve as strong baselines for future VSR approaches.

Kelvin C. K. Chan, Xintao Wang, Ke Yu et al.

Deformable convolution, originally proposed for the adaptation to geometric variations of objects, has recently shown compelling performance in aligning multiple frames and is increasingly adopted for video super-resolution. Despite its remarkable performance, its underlying mechanism for alignment remains unclear. In this study, we carefully investigate the relation between deformable alignment and the classic flow-based alignment. We show that deformable convolution can be decomposed into a combination of spatial warping and convolution. This decomposition reveals the commonality of deformable alignment and flow-based alignment in formulation, but with a key difference in their offset diversity. We further demonstrate through experiments that the increased diversity in deformable alignment yields better-aligned features, and hence significantly improves the quality of video super-resolution output. Based on our observations, we propose an offset-fidelity loss that guides the offset learning with optical flow. Experiments show that our loss successfully avoids the overflow of offsets and alleviates the instability problem of deformable alignment. Aside from the contributions to deformable alignment, our formulation inspires a more flexible approach to introduce offset diversity to flow-based alignment, improving its performance.

Li Sun, Junxiang Chen, Yanwu Xu et al.

Generative Adversarial Networks (GAN) have many potential medical imaging applications, including data augmentation, domain adaptation, and model explanation. Due to the limited memory of Graphical Processing Units (GPUs), most current 3D GAN models are trained on low-resolution medical images, these models either cannot scale to high-resolution or are prone to patchy artifacts. In this work, we propose a novel end-to-end GAN architecture that can generate high-resolution 3D images. We achieve this goal by using different configurations between training and inference. During training, we adopt a hierarchical structure that simultaneously generates a low-resolution version of the image and a randomly selected sub-volume of the high-resolution image. The hierarchical design has two advantages: First, the memory demand for training on high-resolution images is amortized among sub-volumes. Furthermore, anchoring the high-resolution sub-volumes to a single low-resolution image ensures anatomical consistency between sub-volumes. During inference, our model can directly generate full high-resolution images. We also incorporate an encoder with a similar hierarchical structure into the model to extract features from the images. Experiments on 3D thorax CT and brain MRI demonstrate that our approach outperforms state of the art in image generation. We also demonstrate clinical applications of the proposed model in data augmentation and clinical-relevant feature extraction.

Ke Yu, Shyam Visweswaran, Kayhan Batmanghelich

Learning accurate drug representation is essential for tasks such as computational drug repositioning and prediction of drug side-effects. A drug hierarchy is a valuable source that encodes human knowledge of drug relations in a tree-like structure where drugs that act on the same organs, treat the same disease, or bind to the same biological target are grouped together. However, its utility in learning drug representations has not yet been explored, and currently described drug representations cannot place novel molecules in a drug hierarchy. Here, we develop a semi-supervised drug embedding that incorporates two sources of information: (1) underlying chemical grammar that is inferred from molecular structures of drugs and drug-like molecules (unsupervised), and (2) hierarchical relations that are encoded in an expert-crafted hierarchy of approved drugs (supervised). We use the Variational Auto-Encoder (VAE) framework to encode the chemical structures of molecules and use the knowledge-based drug-drug similarity to induce the clustering of drugs in hyperbolic space. The hyperbolic space is amenable for encoding hierarchical concepts. Both quantitative and qualitative results support that the learned drug embedding can accurately reproduce the chemical structure and induce the hierarchical relations among drugs. Furthermore, our approach can infer the pharmacological properties of novel molecules by retrieving similar drugs from the embedding space. We demonstrate that the learned drug embedding can be used to find new uses for existing drugs and to discover side-effects. We show that it significantly outperforms baselines in both tasks.

Ke Yu, Xintao Wang, Chao Dong et al.

Very deep Convolutional Neural Networks (CNNs) have greatly improved the performance on various image restoration tasks. However, this comes at a price of increasing computational burden, hence limiting their practical usages. We observe that some corrupted image regions are inherently easier to restore than others since the distortion and content vary within an image. To leverage this, we propose Path-Restore, a multi-path CNN with a pathfinder that can dynamically select an appropriate route for each image region. We train the pathfinder using reinforcement learning with a difficulty-regulated reward. This reward is related to the performance, complexity and "the difficulty of restoring a region". A policy mask is further investigated to jointly process all the image regions. We conduct experiments on denoising and mixed restoration tasks. The results show that our method achieves comparable or superior performance to existing approaches with less computational cost. In particular, Path-Restore is effective for real-world denoising, where the noise distribution varies across different regions on a single image. Compared to the state-of-the-art RIDNet, our method achieves comparable performance and runs 2.7x faster on the realistic Darmstadt Noise Dataset.

Xintao Wang, Ke Yu, Chao Dong et al.

Deep convolutional neural network has demonstrated its capability of learning a deterministic mapping for the desired imagery effect. However, the large variety of user flavors motivates the possibility of continuous transition among different output effects. Unlike existing methods that require a specific design to achieve one particular transition (e.g., style transfer), we propose a simple yet universal approach to attain a smooth control of diverse imagery effects in many low-level vision tasks, including image restoration, image-to-image translation, and style transfer. Specifically, our method, namely Deep Network Interpolation (DNI), applies linear interpolation in the parameter space of two or more correlated networks. A smooth control of imagery effects can be achieved by tweaking the interpolation coefficients. In addition to DNI and its broad applications, we also investigate the mechanism of network interpolation from the perspective of learned filters.

Yubin Deng, Ke Yu, Dahua Lin et al.

Deep reinforcement learning has obtained significant breakthroughs in recent years. Most methods in deep-RL achieve good results via the maximization of the reward signal provided by the environment, typically in the form of discounted cumulative returns. Such reward signals represent the immediate feedback of a particular action performed by an agent. However, tasks with sparse reward signals are still challenging to on-policy methods. In this paper, we introduce an effective characterization of past reward statistics (which can be seen as long-term feedback signals) to supplement this immediate reward feedback. In particular, value functions are learned with multi-critics supervision, enabling complex value functions to be more easily approximated in on-policy learning, even when the reward signals are sparse. We also introduce a novel exploration mechanism called "hot-wiring" that can give a boost to seemingly trapped agents. We demonstrate the effectiveness of our advantage actor multi-critic (A2MC) method across the discrete domains in Atari games as well as continuous domains in the MuJoCo environments. A video demo is provided at https://youtu.be/zBmpf3Yz8tc.

Ke Yu, Chao Dong, Liang Lin et al.

We investigate a novel approach for image restoration by reinforcement learning. Unlike existing studies that mostly train a single large network for a specialized task, we prepare a toolbox consisting of small-scale convolutional networks of different complexities and specialized in different tasks. Our method, RL-Restore, then learns a policy to select appropriate tools from the toolbox to progressively restore the quality of a corrupted image. We formulate a step-wise reward function proportional to how well the image is restored at each step to learn the action policy. We also devise a joint learning scheme to train the agent and tools for better performance in handling uncertainty. In comparison to conventional human-designed networks, RL-Restore is capable of restoring images corrupted with complex and unknown distortions in a more parameter-efficient manner using the dynamically formed toolchain.

Xintao Wang, Ke Yu, Chao Dong et al.

Despite that convolutional neural networks (CNN) have recently demonstrated high-quality reconstruction for single-image super-resolution (SR), recovering natural and realistic texture remains a challenging problem. In this paper, we show that it is possible to recover textures faithful to semantic classes. In particular, we only need to modulate features of a few intermediate layers in a single network conditioned on semantic segmentation probability maps. This is made possible through a novel Spatial Feature Transform (SFT) layer that generates affine transformation parameters for spatial-wise feature modulation. SFT layers can be trained end-to-end together with the SR network using the same loss function. During testing, it accepts an input image of arbitrary size and generates a high-resolution image with just a single forward pass conditioned on the categorical priors. Our final results show that an SR network equipped with SFT can generate more realistic and visually pleasing textures in comparison to state-of-the-art SRGAN and EnhanceNet.

Ke Yu, Chao Dong, Chen Change Loy et al.

Lossy compression introduces complex compression artifacts, particularly blocking artifacts, ringing effects and blurring. Existing algorithms either focus on removing blocking artifacts and produce blurred output, or restore sharpened images that are accompanied with ringing effects. Inspired by the success of deep convolutional networks (DCN) on superresolution, we formulate a compact and efficient network for seamless attenuation of different compression artifacts. To meet the speed requirement of real-world applications, we further accelerate the proposed baseline model by layer decomposition and joint use of large-stride convolutional and deconvolutional layers. This also leads to a more general CNN framework that has a close relationship with the conventional Multi-Layer Perceptron (MLP). Finally, the modified network achieves a speed up of 7.5 times with almost no performance loss compared to the baseline model. We also demonstrate that a deeper model can be effectively trained with features learned in a shallow network. Following a similar "easy to hard" idea, we systematically investigate three practical transfer settings and show the effectiveness of transfer learning in low-level vision problems. Our method shows superior performance than the state-of-the-art methods both on benchmark datasets and a real-world use case.