SUMMARY: The examination of high-risk cells and regions in tissue samples from spatially resolved transcriptomics platforms offers meaningful insights into specific disease processes. For existing methods, while cell types or clusters can be identified and associated with disease attributes, individual cells are unable to be associated in the same manner. METHOD: Diagnostic Evidence Gauge of Single-Cells and Spatial Transcriptomics (DEGAS) solves the above problem by employing latent representations of gene expression data and domain adaptation to transfer disease attributes from patients to individual cells from single-cell RNA sequencing datasets. In this research, we present and evaluate DEGAS's versatility in adapting to data arising from various single-cell spatially resolved transcriptomics (scSRT) platforms. DEGAS successfully identified high-risk cells and regions in liver hepatocellular carcinoma and skin cutaneous melanoma, which were validated through known markers. Additionally, DEGAS was applied to our newly generated Type II Diabetes Xenium dataset, revealing high-risk cells within the tissue samples. AVAILABILITY AND IMPLEMENTATION: The DEGAS software can be accessed at https://github.com/tsteelejohnson91/DEGAS. For the updated smoothing functions and associated codes, visit https://github.com/dchatter04/DEGAS-Spatial-Smoothing, which is archived at https://doi.org/10.5281/zenodo.18510221. Sources for the datasets reviewed are detailed in their respective sections. A description of some datasets, along with extra tables and figures, is provided in the Supplementary Materials file. Our newly generated Xenium data for Type II Diabetes can be found at https://doi.org/10.7303/syn68699752.

Accurate segmentation of Optical Coherence Tomography (OCT) images is crucial for diagnosing and monitoring retinal diseases. However, the labor-intensive nature of pixel-level annotation limits the scalability of supervised learning for large datasets. Weakly Supervised Semantic Segmentation (WSSS) offers a promising alternative by using weaker forms of supervision, such as image-level labels, to reduce the annotation burden. Despite its advantages, weak supervision inherently carries limited information. We propose a novel WSSS framework with only image-level labels for OCT lesion segmentation that integrates structural and text-driven guidance to produce high-quality, pixel-level pseudo labels. The framework employs two visual processing modules: one that processes the original OCT images and another that operates on layer segmentations augmented with anomalous signals, enabling the model to associate lesions with their corresponding anatomical layers. Complementing these visual cues, we leverage large-scale pretrained models to provide two forms of textual guidance: label-derived descriptions that encode local semantics, and domain-agnostic synthetic descriptions that, although expressed in natural image terms, capture spatial and relational semantics useful for generating globally consistent representations. By fusing these visual and textual features in a multi-modal framework, our method aligns semantic meaning with structural relevance, thereby improving lesion localization and segmentation performance. Experiments on three OCT datasets demonstrate state-of-the-art results, highlighting its potential to advance diagnostic accuracy and efficiency in medical imaging.

Brightfield Multiplex Immunohistochemistry (mIHC) provides simultaneous labeling of multiple protein biomarkers in the same tissue section. It enables the exploration of spatial relationships between the inflammatory microenvironment and tumor cells, and to uncover how tumor cell morphology relates to cancer biomarker expression. Color deconvolution is required to analyze and quantify the different cell phenotype populations present as indicated by the biomarkers. However, this becomes a challenging task as the number of multiplexed stains increase. In this work, we present self-supervised and semi-supervised approaches to mIHC color deconvolution. Our proposed methods are based on deep convolutional autoencoders and learn using innovative reconstruction losses inspired by physics. We show how we can integrate weak annotations and the abundant unlabeled data available to train a model to reliably unmix the multiplexed stains and generate stain segmentation maps. We demonstrate the effectiveness of our proposed methods through experiments on mIHC dataset of 7-plexed IHC images.

Recent advances in Spatial Transcriptomics (ST) pair histology images with spatially resolved gene expression profiles, enabling predictions of gene expression across different tissue locations based on image patches. This opens up new possibilities for enhancing whole slide image (WSI) prediction tasks with localized gene expression. However, existing methods fail to fully leverage the interactions between different tissue locations, which are crucial for accurate joint prediction. To address this, we introduce MERGE (Multi-faceted hiErarchical gRaph for Gene Expressions), which combines a multi-faceted hierarchical graph construction strategy with graph neural networks (GNN) to improve gene expression predictions from WSIs. By clustering tissue image patches based on both spatial and morphological features, and incorporating intra- and inter-cluster edges, our approach fosters interactions between distant tissue locations during GNN learning. As an additional contribution, we evaluate different data smoothing techniques that are necessary to mitigate artifacts in ST data, often caused by technical imperfections. We advocate for adopting gene-aware smoothing methods that are more biologically justified. Experimental results on gene expression prediction show that our GNN method outperforms state-of-the-art techniques across multiple metrics.

Accurately modeling multi-class cell topology is crucial in digital pathology, as it provides critical insights into tissue structure and pathology. The synthetic generation of cell topology enables realistic simulations of complex tissue environments, enhances downstream tasks by augmenting training data, aligns more closely with pathologists' domain knowledge, and offers new opportunities for controlling and generalizing the tumor microenvironment. In this paper, we propose a novel approach that integrates topological constraints into a diffusion model to improve the generation of realistic, contextually accurate cell topologies. Our method refines the simulation of cell distributions and interactions, increasing the precision and interpretability of results in downstream tasks such as cell detection and classification. To assess the topological fidelity of generated layouts, we introduce a new metric, Topological Fréchet Distance (TopoFD), which overcomes the limitations of traditional metrics like FID in evaluating topological structure. Experimental results demonstrate the effectiveness of our approach in generating multi-class cell layouts that capture intricate topological relationships. Code is available at https://github.com/Melon-Xu/TopoCellGen.

Diffusion models excel at creating visually impressive images but often struggle to generate images with a specified topology. The Betti number, which represents the number of structures in an image, is a fundamental measure in topology. Yet, diffusion models fail to satisfy even this basic constraint. This limitation restricts their utility in applications requiring exact control, like robotics and environmental modeling. To address this, we propose TopoDiffusionNet (TDN), a novel approach that enforces diffusion models to maintain the desired topology. We leverage tools from topological data analysis, particularly persistent homology, to extract the topological structures within an image. We then design a topology-based objective function to guide the denoising process, preserving intended structures while suppressing noisy ones. Our experiments across four datasets demonstrate significant improvements in topological accuracy. TDN is the first to integrate topology with diffusion models, opening new avenues of research in this area.

The emergence of Vision-Language Models (VLMs) represents a significant advancement in integrating computer vision with Large Language Models (LLMs) to generate detailed text descriptions from visual inputs. Despite their growing importance, the security of VLMs, particularly against backdoor attacks, is under explored. Moreover, prior works often assume attackers have access to the original training data, which is often unrealistic. In this paper, we address a more practical and challenging scenario where attackers must rely solely on Out-Of-Distribution (OOD) data. We introduce VLOOD (Backdoor Vision-Language Models using Out-of-Distribution Data), a novel approach with two key contributions: (1) demonstrating backdoor attacks on VLMs in complex image-to-text tasks while minimizing degradation of the original semantics under poisoned inputs, and (2) proposing innovative techniques for backdoor injection without requiring any access to the original training data. Our evaluation on image captioning and visual question answering (VQA) tasks confirms the effectiveness of VLOOD, revealing a critical security vulnerability in VLMs and laying the foundation for future research on securing multimodal models against sophisticated threats.

Deep learning has achieved significant success by training on balanced datasets. However, real-world data often exhibit long-tailed distributions. Empirical studies have revealed that long-tailed data skew data representations, where head classes dominate the feature space. Many methods have been proposed to empirically rectify the skewed representations. However, a clear understanding of the underlying cause and extent of this skew remains lacking. In this study, we provide a comprehensive theoretical analysis to elucidate how long-tailed data affect feature distributions, deriving the conditions under which centers of tail classes shrink together or even collapse into a single point. This results in overlapping feature distributions of tail classes, making features in the overlapping regions inseparable. Moreover, we demonstrate that merely empirically correcting the skewed representations of the training data is insufficient to separate the overlapping features due to distribution shifts between the training and real data. To address these challenges, we propose a novel long-tailed representation learning method, FeatRecon. It reconstructs the feature space in order to arrange features from different classes into symmetricial and linearly separable regions. This, in turn, enhances the model’s robustness to long-tailed data. We validate the effectiveness of our method through extensive experiments on the CIFAR-10-LT, CIFAR-100-LT, ImageNet-LT, and iNaturalist 2018 datasets.

In semi-supervised segmentation, capturing meaningful semantic structures from unlabeled data is essential. This is particularly challenging in histopathology image analysis, where objects are densely distributed. To address this issue, we propose a semi-supervised segmentation framework designed to robustly identify and preserve relevant topological features. Our method leverages multiple perturbed predictions obtained through stochastic dropouts and temporal training snapshots, enforcing topological consistency across these varied outputs. This consistency mechanism helps distinguish biologically meaningful structures from transient and noisy artifacts. A key challenge in this process is to accurately match the corresponding topological features across the predictions in the absence of ground truth. To overcome this, we introduce a novel matching strategy that integrates spatial overlap with global structural alignment, minimizing discrepancies among predictions. Extensive experiments demonstrate that our approach effectively reduces topological errors, resulting in more robust and accurate segmentations essential for reliable downstream analysis. Code is available at https://github.com/Melon-Xu/MATCH.

Self-supervised learning plays an important role in current state-of-the-art semi-supervised learning (SSL) methods. These methods learn inter-class heterogeneity among data and generate pseudo-labels based on class level representations. However, they often neglect intra-class heterogeneity, resulting in the under-exploitation of finer-grained semantic relationships within classes. To address this limitation, we introduce PivotAlign, a novel SSL approach that aims to 1) learn hierarchical representations to detect both interclass and intra-class semantic relationships, and 2) refine pseudo-labels based on learned representations with a class-debiasing strategy. Specifically, we first learn a set of pivots as sub-prototypes of classes. We then train representations so that features align with the assigned pivot and are hierarchically grouped based on both inter-class and intra-class heterogeneity. This allows us to capture both inter-class and intra-class semantic relationships among data and leverage them to better assign and refine pseudo-labels. Additionally, since SSL methods are prone to bias toward classes that are easier to learn, we further re-balance class predictions to alleviate this class bias. We demonstrate the effectiveness of PivotAlign on various SSL benchmarks, where PivotAlign achieves state-of-the-art performances. The source code will be released upon publication of the work.

Representation learning on graphs is a fundamental problem that can be crucial in various tasks. Graph neural networks, the dominant approach for graph representation learning, are limited in their representation power. Therefore, it can be beneficial to explicitly extract and incorporate high-order topological and geometric information into these models. In this paper, we propose a principled approach to extract the rich connectivity information of graphs based on the theory of persistent homology. Our method utilizes the topological features to enhance the representation learning of graph neural networks and achieve state-of-the-art performance on various node classification and link prediction benchmarks. We also explore the option of end-to-end learning of the topological features, i.e., treating topological computation as a differentiable operator during learning. Our theoretical analysis and empirical study provide insights and potential guidelines for employing topological features in graph learning tasks.

Introducing interpretability and reasoning into Multiple Instance Learning (MIL) methods for Whole Slide Image (WSI) analysis is challenging, given the complexity of gigapixel slides. Traditionally, MIL interpretability is limited to identifying salient regions deemed pertinent for downstream tasks, offering little insight to the end-user (pathologist) regarding the rationale behind these selections. To address this, we propose Self-Interpretable MIL (SI-MIL), a method intrinsically designed for interpretability from the very outset. SI-MIL employs a deep MIL framework to guide an interpretable branch grounded on handcrafted pathological features, facilitating linear predictions. Beyond identifying salient regions, SI-MIL uniquely provides feature-level interpretations rooted in pathological insights for WSIs. Notably, SI-MIL, with its linear prediction constraints, challenges the prevalent myth of an inevitable trade-off between model interpretability and performance, demonstrating competitive results compared to state-of-the-art methods on WSI-level prediction tasks across three cancer types. In addition, we thoroughly benchmark the local-and global-interpretability of SI-MIL in terms of statistical analysis, a domain expert study, and desiderata of interpretability, namely, user-friendliness and faithfulness.

Due to the increasing computational demand of Deep Neural Networks (DNNs), companies and organizations have begun to outsource the training process. However, the externally trained DNNs can potentially be backdoor attacked. It is crucial to defend against such attacks, i.e., to postprocess a suspicious model so that its backdoor behavior is mitigated while its normal prediction power on clean inputs remain uncompromised. To remove the abnormal backdoor behavior, existing methods mostly rely on additional labeled clean samples. However, such requirement may be unrealistic as the training data are often unavailable to end users. In this paper, we investigate the possibility of circumventing such barrier. We propose a novel defense method that does not require training labels. Through a carefully designed layer-wise weight reinitialization and knowledge distillation, our method can effectively cleanse backdoor behaviors of a suspicious network with negligible compromise in its normal behavior. In experiments, we show that our method, trained without labels, is on-par with state-of-the-art defense methods trained using labels. We also observe promising defense results even on out-of-distribution data. This makes our method very practical. Code is available at: https://github.com/luluppang/BCU.

In digital pathology, the spatial context of cells is important for cell classification, cancer diagnosis and prognosis. To model such complex cell context, however, is challenging. Cells form different mixtures, lineages, clusters and holes. To model such structural patterns in a learnable fashion, we introduce several mathematical tools from spatial statistics and topological data analysis. We incorporate such structural descriptors into a deep generative model as both conditional inputs and a differentiable loss. This way, we are able to generate high quality multi-class cell layouts for the first time. We show that the topology-rich cell layouts can be used for data augmentation and improve the performance of downstream tasks such as cell classification.

In medical vision, different imaging modalities provide complementary information. However, in practice, not all modalities may be available during inference or even training. Previous approaches, e.g., knowledge distillation or image synthesis, often assume the availability of full modalities for all subjects during training; this is unrealistic and impractical due to the variability in data collection across sites. We propose a novel approach to learn enhanced modality-agnostic representations by employing a meta-learning strategy in training, even when only limited full modality samples are available. Meta-learning enhances partial modality representations to full modality representations by meta-training on partial modality data and meta-testing on limited full modality samples. Additionally, we co-supervise this feature enrichment by introducing an auxiliary adversarial learning branch. More specifically, a missing modality detector is used as a discriminator to mimic the full modality setting. Our segmentation framework significantly outperforms state-of-the-art brain tumor segmentation techniques in missing modality scenarios.

Semi-supervised crowd counting is an important yet challenging task. A popular approach is to iteratively generate pseudo-labels for unlabeled data and add them to the training set. The key is to use uncertainty to select reliable pseudo-labels. In this paper, we propose a novel method to calibrate model uncertainty for crowd counting. Our method takes a supervised uncertainty estimation strategy to train the model through a surrogate function. This ensures the uncertainty is well controlled through-out the training. We propose a matching-based patch-wise surrogate function to better approximate uncertainty for crowd counting tasks. The proposed method pays a sufficient amount of attention to details, while maintaining a proper granularity. Altogether our method is able to generate reliable uncertainty estimation, high quality pseudolabels, and achieve state-of-the-art performance in semi-supervised crowd counting.

Segmentation of curvilinear structures such as vasculature and road networks is challenging due to relatively weak signals and complex geometry/topology. To facilitate and accelerate large scale annotation, one has to adopt semi-automatic approaches such as proofreading by experts. In this work, we focus on uncertainty estimation for such tasks, so that highly uncertain, and thus error-prone structures can be identified for human annotators to verify. Unlike most existing works, which provide pixel-wise uncertainty maps, we stipulate it is crucial to estimate uncertainty in the units of topological structures, e.g., small pieces of connections and branches. To achieve this, we leverage tools from topological data analysis, specifically discrete Morse theory (DMT), to first capture the structures, and then reason about their uncertainties. To model the uncertainty, we (1) propose a joint prediction model that estimates the uncertainty of a structure while taking the neighboring structures into consideration (inter-structural uncertainty); (2) propose a novel Probabilistic DMT to model the inherent uncertainty within each structure (intra-structural uncertainty) by sampling its representations via a perturb-and-walk scheme. On various 2D and 3D datasets, our method produces better structure-wise uncertainty maps compared to existing works. Code available at: https://github.com/Saumya-Gupta-26/struct-uncertainty

The adversarial risk of a machine learning model has been widely studied. Most previous works assume that the data lies in the whole ambient space. We propose to take a new angle and take the manifold assumption into consideration. Assuming data lies in a manifold, we investigate two new types of adversarial risk, the normal adversarial risk due to perturbation along normal direction, and the in-manifold adversarial risk due to perturbation within the manifold. We prove that the classic adversarial risk can be bounded from both sides using the normal and in-manifold adversarial risks. We also show with a surprisingly pessimistic case that the standard adversarial risk can be nonzero even when both normal and in-manifold risks are zero. We finalize the paper with empirical studies supporting our theoretical results. Our results suggest the possibility of improving the robustness of a classifier by only focusing on the normal adversarial risk.

Persistent homology is perhaps the most popular and useful tool offered by topological data analysis, with point-cloud data being the most common setup. Its older cousin, the Euler characteristic curve (ECC) is less expressive, but far easier to compute. It is particularly suitable for analyzing imaging data, and is commonly used in fields ranging from astrophysics to biomedical image analysis. These fields are embracing GPU computations to handle increasingly large datasets. We therefore propose an optimized GPU implementation of ECC computation for 2D and 3D grayscale images. The goal of this paper is twofold. First, we offer a practical tool, illustrating its performance with thorough experimentation, but also explain its inherent shortcomings. Second, this simple algorithm serves as a perfect backdrop for highlighting basic GPU programming techniques that make our implementation so efficient, and some common pitfalls we avoided. This is intended as a step towards a wider usage of GPU programming in computational geometry and topology software. We find this is particularly important as geometric and topological tools are used in conjunction with modern, GPU-accelerated machine learning frameworks.

Clinical outcome or severity prediction from medical images has largely focused on learning representations from single-timepoint or snapshot scans. It has been shown that disease progression can be better characterized by temporal imaging. We therefore hypothesized that outcome predictions can be improved by utilizing the disease progression informationfrom sequential images. We present a deep learning approach that leverages temporal progression information to improve clinical outcome predictions from single-timepoint images. In our method, a self-attention based Temporal Convolutional Network (TCN) is used to learn a representation that is most reflective of the disease trajectory. Meanwhile, a Vision Transformer is pretrained in a self-supervised fashion to extract features from single-timepoint images. The key contribution is to design a recalibration module that employs maximum mean discrepancy loss (MMD) to align distributions of the above two contextual representations. We train our system to predict clinical outcomes and severity grades from single-timepoint images. Experiments on chest and osteoarthritis radiography datasets demonstrate that our approach outperforms other state-of-the-art techniques.

In recent years, algebraic topology and its modern development, the theory of persistent homology, has shown great potential in graph representation learning. In this paper, based on the mathematics of algebraic topology, we propose a novel solution for inductive relation prediction, an important learning task for knowledge graph completion. To predict the relation between two entities, one can use the existence of rules, namely a sequence of relations. Previous works view rules as paths and primarily focus on the searching of paths between entities. The space of rules is huge, and one has to sacrifice either efficiency or accuracy. In this paper, we consider rules as cycles and show that the space of cycles has a unique structure based on the mathematics of algebraic topology. By exploring the linear structure of the cycle space, we can improve the searching efficiency of rules. We propose to collect cycle bases that span the space of cycles. We build a novel GNN framework on the collected cycles to learn the representations of cycles, and to predict the existence/non-existence of a relation. Our method achieves state-of-the-art performance on benchmarks.

Trojan attacks raise serious security concerns.In this paper, we investigate the underlying mechanism of Trojaned BERT models.We observe the attention focus drifting behavior of Trojaned models, i.e., when encountering an poisoned input, the trigger token hijacks the attention focus regardless of the context.We provide a thorough qualitative and quantitative analysis of this phenomenon, revealing insights into the Trojan mechanism.Based on the observation, we propose an attention-based Trojan detector to distinguish Trojaned models from clean ones.To the best of our knowledge, this is the first paper to analyze the Trojan mechanism and to develop a Trojan detector based on the transformer's attention 1 .

Topological features based on persistent homology capture high-order structural information so as to augment graph neural network methods. However, computing extended persistent homology summaries remains slow for large and dense graphs and can be a serious bottleneck for the learning pipeline. Inspired by recent success in neural algorithmic reasoning, we propose a novel graph neural network to estimate extended persistence diagrams (EPDs) on graphs efficiently. Our model is built on algorithmic insights, and benefits from better supervision and closer alignment with the EPD computation algorithm. We validate our method with convincing empirical results on approximating EPDs and downstream graph representation learning tasks. Our method is also efficient; on large and dense graphs, we accelerate the computation by nearly 100 times.

Stochastic Gradient Descent (SGD) based methods have been widely used for training large-scale machine learning models that also generalize well in practice. Several explanations have been offered for this generalization performance, a prominent one being algorithmic stability Hardt et al [2016]. However, there are no known examples of smooth loss functions for which the analysis can be shown to be tight. Furthermore, apart from properties of the loss function, data distribution has also been shown to be an important factor in generalization performance. This raises the question: is the stability analysis of Hardt et al [2016] tight for smooth functions, and if not, for what kind of loss functions and data distributions can the stability analysis be improved? In this paper we first settle open questions regarding tightness of bounds in the data-independent setting: we show that for general datasets, the existing analysis for convex and strongly-convex loss functions is tight, but it can be improved for non-convex loss functions. Next, we give novel and improved data-dependent bounds: we show stability upper bounds for a large class of convex regularized loss functions, with negligible regularization parameters, and improve existing data-dependent bounds in the non-convex setting. We hope that our results will initiate further efforts to better understand the data-dependent setting under non-convex loss functions, leading to an improved understanding of the generalization abilities of deep networks.

We address the problem of crowd localization, i.e., the prediction of dots corresponding to people in a crowded scene. Due to various challenges, a localization method is prone to spatial semantic errors, i.e., predicting multiple dots within a same person or collapsing multiple dots in a cluttered region. We propose a topological approach targeting these semantic errors. We introduce a topological constraint that teaches the model to reason about the spatial arrangement of dots. To enforce this constraint, we define a persistence loss based on the theory of persistent homology. The loss compares the topographic landscape of the likelihood map and the topology of the ground truth. Topological reasoning improves the quality of the localization algorithm especially near cluttered regions. On multiple public benchmarks, our method outperforms previous localization methods. Additionally, we demonstrate the potential of our method in improving the performance in the crowd counting task.

In digital pathology, both detection and classification of cells are important for automatic diagnostic and prognostic tasks. Classifying cells into subtypes, such as tumor cells, lymphocytes or stromal cells is particularly challenging. Existing methods focus on morphological appearance of individual cells, whereas in practice pathologists often infer cell classes through their spatial context. In this paper, we propose a novel method for both detection and classification that explicitly incorporates spatial contextual information. We use the spatial statistical function to describe local density in both a multi-class and a multi-scale manner. Through representation learning and deep clustering techniques, we learn advanced cell representation with both appearance and spatial context. On various benchmarks, our method achieves better performance than state-of-the-arts, especially on the classification task. We also create a new dataset for multi-class cell detection and classification in breast cancer and we make both our code and data publicly available.

Link prediction is an important learning task for graph-structured data. In this paper, we propose a novel topological approach to characterize interactions between two nodes. Our topological feature, based on the extended persistent homology, encodes rich structural information regarding the multi-hop paths connecting nodes. Based on this feature, we propose a graph neural network method that outperforms state-of-the-arts on different benchmarks. As another contribution, we propose a novel algorithm to more efficiently compute the extended persistence diagrams for graphs. This algorithm can be generally applied to accelerate many other topological methods for graph learning tasks.

Deep neural networks are known to have security issues. One particular threat is the Trojan attack. It occurs when the attackers stealthily manipulate the model's behavior through Trojaned training samples, which can later be exploited. Guided by basic neuroscientific principles, we discover subtle -- yet critical -- structural deviation characterizing Trojaned models. In our analysis we use topological tools. They allow us to model high-order dependencies in the networks, robustly compare different networks, and localize structural abnormalities. One interesting observation is that Trojaned models develop short-cuts from shallow to deep layers. Inspired by these observations, we devise a strategy for robust detection of Trojaned models. Compared to standard baselines it displays better performance on multiple benchmarks.

Autism spectrum disorder (ASD) is accompanied with impaired social-emotional functioning, such as emotional regulation and recognition, communication, and related behavior. Study of the alternations of the brain networks in ASD may not only help us in understanding this disorder but also inform us the mechanisms of affective computing in the brain. Although morphological features have been used in the diagnosis of a variety of neurological and psychiatric disorders, these features did not show significant discriminative value in identifying patients with ASD, possibly due to the omission of the information related to the changes in structural similarities among cortical regions. In this study, structural images from 66 high-functioning adults with ASD and 66 matched typically-developing controls (TDC) were used to test the hypothesis of cortico-cortical relationships are abnormal in ASD. Seven morphological features of each of the 360 brain regions were extracted and elastic network was used to quantify the similarities between each target region and all other regions. The similarities were then used to construct multi-feature-based networks (MFN), which were then submitted to a support vector machine classifier to classify the individuals of the two groups. Results showed that the classifier with features of MFN significantly improved the accuracy of discriminating patients with ASD from TDCs (78.63 percent) compared to using morphological features only (<; 65 percent). The combination of MFN features with morphological features and other high-level MFN properties did not further enhance the classification performance. Our findings demonstrate that the variations in cortico-cortical similarities are important in the etiology of ASD and can be used as biomarkers in the diagnostic process.

Regularization plays an important role in generalization of deep learning. In this paper, we study the generalization power of an unbiased regularizor for training algorithms in deep learning. We focus on training methods called Locally Regularized Stochastic Gradient Descent (LRSGD). An LRSGD leverages a proximal type penalty in gradient descent steps to regularize SGD in training. We show that by carefully choosing relevant parameters, LRSGD generalizes better than SGD. Our thorough theoretical analysis is supported by experimental evidence. It advances our theoretical understanding of deep learning and provides new perspectives on designing training algorithms. The code is available at https://github.com/huiqu18/LRSGD.

Local structural information can increase the adaptability of graph convolutional networks to large graphs with heterogeneous topology. Existing methods only use relatively simplistic topological information, such as node degrees.We present a novel approach leveraging advanced topological information, i.e., persistent homology, which measures the information flow efficiency at different parts of the graph. To fully exploit such structural information in real world graphs, we propose a new network architecture which learns to use persistent homology information to reweight messages passed between graph nodes during convolution. For node classification tasks, our network outperforms existing ones on a broad spectrum of graph benchmarks.

In this paper, we propose a data privacy-preserving and communication efficient distributed GAN learning framework named Distributed Asynchronized Discriminator GAN (AsynDGAN). Our proposed framework aims to train a central generator learns from distributed discriminator, and use the generated synthetic image solely to train the segmentation model. We validate the proposed framework on the application of health entities learning problem which is known to be privacy sensitive. Our experiments show that our approach: 1) could learn the real image’s distribution from multiple datasets without sharing the patient’s raw data. 2) is more efficient and requires lower bandwidth than other distributed deep learning methods. 3) achieves higher performance compared to the model trained by one real dataset, and almost the same performance compared to the model trained by all real datasets. 4) has provable guarantees that the generator could learn the distributed distribution in an all important fashion thus is unbiased.We release our AsynDGAN source code at: https://github.com/tommy-qichang/AsynDGAN

To collect large scale annotated data, it is inevitable to introduce label noise, i.e., incorrect class labels. To be robust against label noise, many successful methods rely on the noisy classifiers (i.e., models trained on the noisy training data) to determine whether a label is trustworthy. However, it remains unknown why this heuristic works well in practice. In this paper, we provide the first theoretical explanation for these methods. We prove that the prediction of a noisy classifier can indeed be a good indicator of whether the label of a training data is clean. Based on the theoretical result, we propose a novel algorithm that corrects the labels based on the noisy classifier prediction. The corrected labels are consistent with the true Bayesian optimal classifier with high probability. We incorporate our label correction algorithm into the training of deep neural networks and train models that achieve superior testing performance on multiple public datasets.

Noisy labels can impair the performance of deep neural networks. To tackle this problem, in this paper, we propose a new method for filtering label noise. Unlike most existing methods relying on the posterior probability of a noisy classifier, we focus on the much richer spatial behavior of data in the latent representational space. By leveraging the high-order topological information of data, we are able to collect most of the clean data and train a high-quality model. Theoretically we prove that this topological approach is guaranteed to collect the clean data with high probability. Empirical results show that our method outperforms the state-of-the-arts and is robust to a broad spectrum of noise types and levels.

Instance segmentation, which seeks to obtain both class and instance labels for each pixel in the input image, is a challenging task in computer vision. State-of- the-art algorithms often employ a search-based strategy, which first divides the output image with a regular grid and generate proposals at each grid cell, then the proposals are classified and boundaries refined. In this paper, we propose a novel algorithm that directly utilizes a fully convolutional network (FCN) to predict instance labels. Specifically, we propose a variational relaxation of instance segmentation as minimizing an optimization functional for a piecewise-constant segmentation problem, which can be used to train an FCN end-to-end. It extends the classical Mumford-Shah variational segmentation algorithm to be able to handle the permutation-invariant ground truth in instance segmentation. Experiments on PASCAL VOC 2012 and the MSCOCO 2017 dataset show that the proposed approach efficiently tackles the instance segmentation task.

We present a new permutation-invariant network for 3D point cloud processing. Our network is composed of a recurrent set encoder and a convolutional feature aggregator. Given an unordered point set, the encoder firstly partitions its ambient space into parallel beams. Points within each beam are then modeled as a sequence and encoded into subregional geometric features by a shared recurrent neural network (RNN). The spatial layout of the beams is regular, and this allows the beam features to be further fed into an efficient 2D convolutional neural network (CNN) for hierarchical feature aggregation. Our network is effective at spatial feature learning, and competes favorably with the state-of-the-arts (SOTAs) on a number of benchmarks. Meanwhile, it is significantly more efficient compared to the SOTAs.

Regularization plays a crucial role in supervised learning. Most existing methods enforce a global regularization in a structure agnostic manner. In this paper, we initiate a new direction and propose to enforce the structural simplicity of the classification boundary by regularizing over its topological complexity. In particular, our measurement of topological complexity incorporates the importance of topological features (e.g., connected components, handles, and so on) in a meaningful manner, and provides a direct control over spurious topological structures. We incorporate the new measurement as a topological penalty in training classifiers. We also propose an efficient algorithm to compute the gradient of such penalty. Our method provides a novel way to topologically simplify the global structure of the model, without having to sacrifice too much of the flexibility of the model. We demonstrate the effectiveness of our new topological regularizer on a range of synthetic and real-world datasets.

In modern production platforms, large scale online learning models are applied to data of very high dimension. To save computational resource, it is important to have an efficient algorithm to select the most significant features from an enormous feature pool. In this paper, we propose a novel neural-network-suitable feature selection algorithm, which selects important features from the input layer during training. Instead of directly regularizing the training loss, we inject group-sparsity regularization into the (stochastic) training algorithm. In particular, we introduce a group sparsity norm into the proximally regularized stochastical gradient descent algorithm. To fully evaluate the practical performance, we apply our method to Facebook News Feed dataset, and achieve favorable performance compared with state-of-the-arts using traditional regularizers.

Deep learning architectures are usually proposed with millions of parameters, resulting in a memory issue when training deep neural networks with stochastic gradient descent type methods using large batch sizes. However, training with small batch sizes tends to produce low quality solution due to the large variance of stochastic gradients. In this paper, we tackle this problem by proposing a new framework for training deep neural network with small batches/noisy gradient. During optimization, our method iteratively applies a proximal type regularizer to make loss function strongly convex. Such regularizer stablizes the gradient, leading to better training performance. We prove that our algorithm achieves comparable convergence rate as vanilla SGD even with small batch size. Our framework is simple to implement and can be potentially combined with many existing optimization algorithms. Empirical results show that our method outperforms SGD and Adam when batch size is small. Our implementation is available at https://github.com/huiqu18/TRAlgorithm.

Cardiac trabeculae are fine rod-like muscles whose ends are attached to the inner walls of ventricles. Accurate extraction of trabeculae is important yet challenging, due to the background noise and limited resolution of cardiac images. Existing works proposed to handle this task by modeling the trabeculae as topological handles for better extraction. Computing optimal representation of these handles is essential yet very expensive. In this work, we formulate the problem as a heuristic search problem, and propose novel heuristic functions based on advanced topological techniques. We show in experiments that the proposed heuristic functions improve the computation in both time and memory.

Segmentation algorithms are prone to make topological errors on fine-scale struc- tures, e.g., broken connections. We propose a novel method that learns to segment with correct topology. In particular, we design a continuous-valued loss function that enforces a segmentation to have the same topology as the ground truth, i.e.,having the same Betti number. The proposed topology-preserving loss function is differentiable and can be incorporated into end-to-end training of a deep neural network. Our method achieves much better performance on the Betti number error, which directly accounts for the topological correctness. It also performs superior on other topology-relevant metrics, e.g., the Adjusted Rand Index and the Variation of Information, without sacrificing per-pixel accuracy. We illustrate the effectiveness of the proposed method on a broad spectrum of natural and biomedical datasets.

Exploiting intrinsic structures in sparse signals underpins the recent progress in compressive sensing (CS). The key for exploiting such structures is to achieve two desirable properties: generality (i.e., the ability to fit a wide range of signals with diverse structures) and adaptability (i.e., being adaptive to a specific signal). Most existing approaches, however, often only achieve one of these two properties. In this study, we propose a novel adaptive Markov random field sparsity prior for CS, which not only is able to capture a broad range of sparsity structures, but also can adapt to each sparse signal through refining the parameters of the sparsity prior with respect to the compressed measurements. To maximize the adaptability, we also propose a new sparse signal estimation where the sparse signals, support, noise and signal parameter estimation are unified into a variational optimization problem, which can be effectively solved with an alternative minimization scheme. Extensive experiments on three real-world datasets demonstrate the effectiveness of the proposed method in recovery accuracy, noise tolerance, and runtime.

In this video, we present a research project on cardiac trabeculae segmentation. Trabeculae are fine muscle columns within human ventricles whose both ends are attached to the wall. Extracting these structures are very challenging even with state-of-the-art image segmentation techniques. We observed that these structures form natural topological handles. Based on such observation, we developed a topological approach, which employs advanced computational topology methods and achieve high quality segmentation results.

Clustering data with both continuous and discrete attributes is a challenging task. Existing methods lack a principled probabilistic formulation. In this paper, we propose a clustering method based on a tree-structured graphical model to describe the generation process of mixed-type data. Our tree-structured model factorized into a product of pairwise interactions, and thus localizes the interaction between feature variables of different types. To provide a robust clustering method based on the tree-model, we adopt a topographical view and compute peaks of the density function and their attractive basins for clustering. Furthermore, we leverage the theory from topology data analysis to adaptively merge trivial peaks into large ones in order to achieve meaningful clusterings. Our method outperforms state-of-the-art methods on mixed-type data.

Analysis of categorical data is a challenging task. In this paper, we propose to compute topographical features of high-dimensional categorical data. We propose an efficient algorithm to extract modes of the underlying distribution and their attractive basins. These topographical features provide a geometric view of the data and can be applied to visualization and clustering of real world challenging datasets. Experiments show that our principled method outperforms state-of-the-art clustering methods while also admits an embarrassingly parallel property.

We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data.

In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ>0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0,1), the running time is O(C(1-δ)ΓR(n)log n), where C(1-δ)Γ is the number of homology classes with persistence at least (1-δ)Γ, n is the total number of simplices, and R(n) is the complexity of computing the rank of an n x n matrix with O(n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O(C(1-δ)Γn2.376) algorithm, a O(C(1-δ)Γn2.28) Las-Vegas algorithm, or a O(C(1-δ)Γn2+ε) Monte-Carlo algorithm for an arbitrary ε>0.

We introduce TopoCut: a new way to integrate knowledge about topological properties (TPs) into random field image segmentation model. Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.

Interpreting an image as a function on a compact subset of the Euclidean plane, we get its scale-space by diffusion, spreading the image over the entire plane. This generates a 1-parameter family of functions alternatively defined as convolutions with a progressively wider Gaussian kernel. We prove that the corresponding 1-parameter family of persistence diagrams have norms that go rapidly to zero as time goes to infinity. This result rationalizes experimental observations about scale-space. We hope this will lead to targeted improvements of related computer vision methods.

Abstract The unintentional scattering of light between neighboring surfaces in complex projection environments increases the brightness and decreases the contrast, disrupting the appearance of the desired imagery. To achieve satisfactory projection results, the inverse problem of global illumination must be solved to cancel this secondary scattering. In this paper, we propose a global illumination cancellation method that minimizes the perceptual difference between the desired imagery and the actual total illumination in the resulting physical environment. Using Gauss‐Newton and active set methods, we design a fast solver for the bound constrained nonlinear least squares problem raised by the perceptual error metrics. Our solver is further accelerated with a CUDA implementation and multi‐resolution method to achieve 1–2 fps for problems with approximately 3000 variables. We demonstrate the global illumination cancellation algorithm with our multi‐projector system. Results show that our method preserves the color fidelity of the desired imagery significantly better than previous methods.

We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We focus on the volume measure, that is, the 1-norm of a cycle. Two main results are presented. First, we prove the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). A side effect is the inapproximability of the problem of computing the nonbounding cycle with the smallest volume, and computing cycles representing a homology basis with the minimal total volume. We also discuss other geometric measures (diameter and radius) and show their disadvantages in homology localization. Our work is restricted to homology over the ℤ2 field.

We develop a method for measuring homology classes. This involves three problems. First, we define the size of a homology class, using ideas from relative homology. Second, we define an optimal basis of a homology group to be the basis whose elements' size have the minimal sum. We provide a greedy algorithm to compute the optimal basis and measure classes in it. The algorithm runs in $O(\beta^4 n^3 log^2 n)$ time, where $n$ is the size of the simplicial complex and $\beta$ is the Betti number of the homology group. Third, we discuss different ways of localizing homology classes and prove some hardness results.