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A wide range of graph embedding objectives decompose into two components: one that attracts the embeddings of nodes that are perceived as similar, and another that repels embeddings of nodes that are perceived as dissimilar. Because real-world graphs are sparse and the number of dissimilar pairs grows quadratically with the number of nodes, Skip-Gram Negative Sampling (SGNS) has emerged as a popular and efficient repulsion approach. SGNS repels each node from a sample of dissimilar nodes, as opposed to all dissimilar nodes. In this work, we show that node-wise repulsion is, in aggregate, an approximate re-centering of the node embedding dimensions. Such dimension operations are much more scalable than node operations. The dimension approach, in addition to being more efficient, yields a simpler geometric interpretation of the repulsion. Our result extends findings from the self-supervised learning literature to the skip-gram model, establishing a connection between skip-gram node contrast and dimension regularization. We show that in the limit of large graphs, under mild regularity conditions, the original node repulsion objective converges to optimization with dimension regularization. We use this observation to propose an algorithm augmentation framework that speeds up any existing algorithm, supervised or unsupervised, using SGNS. The framework prioritizes node attraction and replaces SGNS with dimension regularization. We instantiate this generic framework for LINE and node2vec and show that the augmented algorithms preserve downstream performance while dramatically increasing efficiency.

The quantum backtracking algorithm proposed by Ashley Montanaro raised considerable interest, as it provides a quantum speed-up for a large class of classical optimization algorithms. It does not suffer from Barren-Plateaus and transfers well into the fault-tolerant era, as it requires only a limited number of arbitrary angle gates. Despite its potential, the algorithm has seen limited implementation efforts, presumably due to its abstract formulation. In this work, we provide a detailed instruction on implementing the quantum step operator for arbitrary backtracking instances. For a single controlled diffuser of a binary backtracking tree with depth n, our implementation requires only $6n+14$ CX gates. We detail the process of constructing accept and reject oracles for Sudoku problems using our interface to quantum backtracking. The presented code is written using Qrisp, a high-level quantum programming language, making it executable on most current physical backends and simulators. Subsequently, we perform several simulator based experiments and demonstrate solving 4x4 Sudoku instances with up to 9 empty fields. This is, to the best of our knowledge, the first instance of a compilable implementation of this generality, marking a significant and exciting step forward in quantum software engineering.

Autonomous robotic ultrasound System (RUSS) has been extensively studied. However, fully automated ultrasound image acquisition is still challenging, partly due to the lack of study in combining two phases of path planning: guiding the ultrasound probe to the scan target and covering the scan surface or volume. This paper presents a system of Automated Path Planning for RUSS (APP-RUSS). Our focus is on the first phase of automation, which emphasizes directing the ultrasound probe's path toward the target over extended distances. Specifically, our APP-RUSS system consists of a RealSense D405 RGB-D camera that is employed for visual guidance of the UR5e robotic arm and a cubic Bezier curve path planning model that is customized for delivering the probe to the recognized target. APP-RUSS can contribute to understanding the integration of the two phases of path planning in robotic ultrasound imaging, paving the way for its clinical adoption.

Robotic crop phenotyping has emerged as a key technology to assess crops' morphological and physiological traits at scale. These phenotypical measurements are essential for developing new crop varieties with the aim of increasing productivity and dealing with environmental challenges such as climate change. However, developing and deploying crop phenotyping robots face many challenges such as complex and variable crop shapes that complicate robotic object detection, dynamic and unstructured environments that baffle robotic control, and real-time computing and managing big data that challenge robotic hardware/software. This work specifically tackles the first challenge by proposing a novel Digital-Twin(DT)MARS-CycleGAN model for image augmentation to improve our Modular Agricultural Robotic System (MARS)'s crop object detection from complex and variable backgrounds. Our core idea is that in addition to the cycle consistency losses in the CycleGAN model, we designed and enforced a new DT-MARS loss in the deep learning model to penalize the inconsistency between real crop images captured by MARS and synthesized images sensed by DT MARS. Therefore, the generated synthesized crop images closely mimic real images in terms of realism, and they are employed to fine-tune object detectors such as YOLOv8. Extensive experiments demonstrated that our new DT/MARS-CycleGAN framework significantly boosts our MARS' crop object/row detector's performance, contributing to the field of robotic crop phenotyping.

We study the fairness of dimensionality reduction methods for recommendations. We focus on the established method of principal component analysis (PCA), which identifies latent components and produces a low-rank approximation via the leading components while discarding the trailing components. Prior works have defined notions of "fair PCA"; however, these definitions do not answer the following question: what makes PCA unfair? We identify two underlying mechanisms of PCA that induce unfairness at the item level. The first negatively impacts less popular items, due to the fact that less popular items rely on trailing latent components to recover their values. The second negatively impacts the highly popular items, since the leading PCA components specialize in individual popular items instead of capturing similarities between items. To address these issues, we develop a polynomial-time algorithm, Item-Weighted PCA, a modification of PCA that uses item-specific weights in the objective. On a stylized class of matrices, we prove that Item-Weighted PCA using a specific set of weights minimizes a popularity-normalized error metric. Our evaluations on real-world datasets show that Item-Weighted PCA not only improves overall recommendation quality by up to $0.1$ item-level AUC-ROC but also improves on both popular and less popular items.

Materials property prediction models are usually evaluated using random splitting of datasets into training and test datasets, which not only leads to over-estimated performance due to inherent redundancy, typically existent in material datasets, but also deviate away from the common practice of materials scientists: they are usually interested in predicting properties for a known subset of related out-of-distribution (OOD) materials rather than a universally distributed samples. Feeding such target material formulas/structures to the machine learning models should improve the prediction performance while most current machine learning (ML) models neglect this information. Here we propose to use domain adaptation (DA) to enhance current ML models for property prediction and evaluate their performance improvements in a set of five realistic application scenarios. Our systematic benchmark studies show that there exist DA models that can significantly improve the OOD test set prediction performance while standard ML models and most of the other DAs cannot improve or even deteriorate the performance. Our benchmark datasets and DA code can be freely accessed at https://github.com/Little-Cheryl/MatDA.

With the popularity of deep neural networks (DNNs), model interpretability is becoming a critical concern. Many approaches have been developed to tackle the problem through post-hoc analysis, such as explaining how predictions are made or understanding the meaning of neurons in middle layers. Nevertheless, these methods can only discover the patterns or rules that naturally exist in models. In this work, rather than relying on post-hoc schemes, we proactively instill knowledge to alter the representation of human-understandable concepts in hidden layers. Specifically, we use a hierarchical tree of semantic concepts to store the knowledge, which is leveraged to regularize the representations of image data instances while training deep models. The axes of the latent space are aligned with the semantic concepts, where the hierarchical relations between concepts are also preserved. Experiments on real-world image datasets show that our method improves model interpretability, showing better disentanglement of semantic concepts, without negatively affecting model classification performance.

Group fairness is a popular approach to prevent unfavorable treatment of individuals based on sensitive attributes such as race, gender, and disability. However, the reliance of group fairness on access to discrete group information raises several limitations and concerns, especially with regard to privacy, intersectionality, and unforeseen biases. In this work, we propose a "group-free" measure of fairness that does not rely on sensitive attributes and, instead, is based on homophily in social networks, i.e., the common property that individuals sharing similar attributes are more likely to be connected. Our measure is group-free as it avoids recovering any form of group memberships and uses only pairwise similarities between individuals to define inequality in outcomes relative to the homophily structure in the network. We theoretically justify our measure by showing it is commensurate with the notion of additive decomposability in the economic inequality literature and also bound the impact of non-sensitive confounding attributes. Furthermore, we apply our measure to develop fair algorithms for classification, maximizing information access, and recommender systems. Our experimental results show that the proposed approach can reduce inequality among protected classes without knowledge of sensitive attribute labels. We conclude with a discussion of the limitations of our approach when applied in real-world settings.

We present Multiscale Multiview Vision Transformers (MMViT), which introduces multiscale feature maps and multiview encodings to transformer models. Our model encodes different views of the input signal and builds several channel-resolution feature stages to process the multiple views of the input at different resolutions in parallel. At each scale stage, we use a cross-attention block to fuse information across different views. This enables the MMViT model to acquire complex high-dimensional representations of the input at different resolutions. The proposed model can serve as a backbone model in multiple domains. We demonstrate the effectiveness of MMViT on audio and image classification tasks, achieving state-of-the-art results.

Purpose: In some proton therapy facilities, patient alignment relies on two 2D orthogonal kV images, taken at fixed, oblique angles, as no 3D on-the-bed imaging is available. The visibility of the tumor in kV images is limited since the patient's 3D anatomy is projected onto a 2D plane, especially when the tumor is behind high-density structures such as bones. This can lead to large patient setup errors. A solution is to reconstruct the 3D CT image from the kV images obtained at the treatment isocenter in the treatment position. Methods: An asymmetric autoencoder-like network built with vision-transformer blocks was developed. The data was collected from 1 head and neck patient: 2 orthogonal kV images (1024x1024 voxels), 1 3D CT with padding (512x512x512) acquired from the in-room CT-on-rails before kVs were taken and 2 digitally-reconstructed-radiograph (DRR) images (512x512) based on the CT. We resampled kV images every 8 voxels and DRR and CT every 4 voxels, thus formed a dataset consisting of 262,144 samples, in which the images have a dimension of 128 for each direction. In training, both kV and DRR images were utilized, and the encoder was encouraged to learn the jointed feature map from both kV and DRR images. In testing, only independent kV images were used. The full-size synthetic CT (sCT) was achieved by concatenating the sCTs generated by the model according to their spatial information. The image quality of the synthetic CT (sCT) was evaluated using mean absolute error (MAE) and per-voxel-absolute-CT-number-difference volume histogram (CDVH). Results: The model achieved a speed of 2.1s and a MAE of <40HU. The CDVH showed that <5% of the voxels had a per-voxel-absolute-CT-number-difference larger than 185 HU. Conclusion: A patient-specific vision-transformer-based network was developed and shown to be accurate and efficient to reconstruct 3D CT images from kV images., Comment: 9 figures

Designing more efficient, reliable, and explainable neural network architectures is critical to studies that are based on artificial intelligence (AI) techniques. Previous studies, by post-hoc analysis, have found that the best-performing ANNs surprisingly resemble biological neural networks (BNN), which indicates that ANNs and BNNs may share some common principles to achieve optimal performance in either machine learning or cognitive/behavior tasks. Inspired by this phenomenon, we proactively instill organizational principles of BNNs to guide the redesign of ANNs. We leverage the Core-Periphery (CP) organization, which is widely found in human brain networks, to guide the information communication mechanism in the self-attention of vision transformer (ViT) and name this novel framework as CP-ViT. In CP-ViT, the attention operation between nodes is defined by a sparse graph with a Core-Periphery structure (CP graph), where the core nodes are redesigned and reorganized to play an integrative role and serve as a center for other periphery nodes to exchange information. We evaluated the proposed CP-ViT on multiple public datasets, including medical image datasets (INbreast) and natural image datasets. Interestingly, by incorporating the BNN-derived principle (CP structure) into the redesign of ViT, our CP-ViT outperforms other state-of-the-art ANNs. In general, our work advances the state of the art in three aspects: 1) This work provides novel insights for brain-inspired AI: we can utilize the principles found in BNNs to guide and improve our ANN architecture design; 2) We show that there exist sweet spots of CP graphs that lead to CP-ViTs with significantly improved performance; and 3) The core nodes in CP-ViT correspond to task-related meaningful and important image patches, which can significantly enhance the interpretability of the trained deep model., Comment: Core-periphery, functional brain networks, ViT

Linking computational natural language processing (NLP) models and neural responses to language in the human brain on the one hand facilitates the effort towards disentangling the neural representations underpinning language perception, on the other hand provides neurolinguistics evidence to evaluate and improve NLP models. Mappings of an NLP model's representations of and the brain activities evoked by linguistic input are typically deployed to reveal this symbiosis. However, two critical problems limit its advancement: 1) The model's representations (artificial neurons, ANs) rely on layer-level embeddings and thus lack fine-granularity; 2) The brain activities (biological neurons, BNs) are limited to neural recordings of isolated cortical unit (i.e., voxel/region) and thus lack integrations and interactions among brain functions. To address those problems, in this study, we 1) define ANs with fine-granularity in transformer-based NLP models (BERT in this study) and measure their temporal activations to input text sequences; 2) define BNs as functional brain networks (FBNs) extracted from functional magnetic resonance imaging (fMRI) data to capture functional interactions in the brain; 3) couple ANs and BNs by maximizing the synchronization of their temporal activations. Our experimental results demonstrate 1) The activations of ANs and BNs are significantly synchronized; 2) the ANs carry meaningful linguistic/semantic information and anchor to their BN signatures; 3) the anchored BNs are interpretable in a neurolinguistic context. Overall, our study introduces a novel, general, and effective framework to link transformer-based NLP models and neural activities in response to language and may provide novel insights for future studies such as brain-inspired evaluation and development of NLP models.

Normalizing flows model probability distributions through an expressive tractable density. They transform a simple base distribution, such as a Gaussian, through a sequence of invertible functions, which are referred to as layers. These layers typically use neural networks to become very expressive. Flows are ubiquitous in machine learning and have been applied to image generation, text modeling, variational inference, approximating Boltzmann distributions, and many other problems. Here, we present normflows, a Python package for normalizing flows. It allows to build normalizing flow models from a suite of base distributions, flow layers, and neural networks. The package is implemented in the popular deep learning framework PyTorch, which simplifies the integration of flows in larger machine learning models or pipelines. It supports most of the common normalizing flow architectures, such as Real NVP, Glow, Masked Autoregressive Flows, Neural Spline Flows, Residual Flows, and many more. The package can be easily installed via pip and the code is publicly available on GitHub.

The issue of bias (i.e., systematic unfairness) in machine learning models has recently attracted the attention of both researchers and practitioners. For the graph mining community in particular, an important goal toward algorithmic fairness is to detect and mitigate bias incorporated into graph embeddings since they are commonly used in human-centered applications, e.g., social-media recommendations. However, simple analytical methods for detecting bias typically involve aggregate statistics which do not reveal the sources of unfairness. Instead, visual methods can provide a holistic fairness characterization of graph embeddings and help uncover the causes of observed bias. In this work, we present BiaScope, an interactive visualization tool that supports end-to-end visual unfairness diagnosis for graph embeddings. The tool is the product of a design study in collaboration with domain experts. It allows the user to (i) visually compare two embeddings with respect to fairness, (ii) locate nodes or graph communities that are unfairly embedded, and (iii) understand the source of bias by interactively linking the relevant embedding subspace with the corresponding graph topology. Experts' feedback confirms that our tool is effective at detecting and diagnosing unfairness. Thus, we envision our tool both as a companion for researchers in designing their algorithms as well as a guide for practitioners who use off-the-shelf graph embeddings., Comment: Accepted to VDS at IEEE VIS 2022

Artificial neural networks (ANNs), originally inspired by biological neural networks (BNNs), have achieved remarkable successes in many tasks such as visual representation learning. However, whether there exists semantic correlations/connections between the visual representations in ANNs and those in BNNs remains largely unexplored due to both the lack of an effective tool to link and couple two different domains, and the lack of a general and effective framework of representing the visual semantics in BNNs such as human functional brain networks (FBNs). To answer this question, we propose a novel computational framework, Synchronized Activations (Sync-ACT), to couple the visual representation spaces and semantics between ANNs and BNNs in human brain based on naturalistic functional magnetic resonance imaging (nfMRI) data. With this approach, we are able to semantically annotate the neurons in ANNs with biologically meaningful description derived from human brain imaging for the first time. We evaluated the Sync-ACT framework on two publicly available movie-watching nfMRI datasets. The experiments demonstrate a) the significant correlation and similarity of the semantics between the visual representations in FBNs and those in a variety of convolutional neural networks (CNNs) models; b) the close relationship between CNN's visual representation similarity to BNNs and its performance in image classification tasks. Overall, our study introduces a general and effective paradigm to couple the ANNs and BNNs and provides novel insights for future studies such as brain-inspired artificial intelligence.

Shortcut learning is common but harmful to deep learning models, leading to degenerated feature representations and consequently jeopardizing the model's generalizability and interpretability. However, shortcut learning in the widely used Vision Transformer framework is largely unknown. Meanwhile, introducing domain-specific knowledge is a major approach to rectifying the shortcuts, which are predominated by background related factors. For example, in the medical imaging field, eye-gaze data from radiologists is an effective human visual prior knowledge that has the great potential to guide the deep learning models to focus on meaningful foreground regions of interest. However, obtaining eye-gaze data is time-consuming, labor-intensive and sometimes even not practical. In this work, we propose a novel and effective saliency-guided vision transformer (SGT) model to rectify shortcut learning in ViT with the absence of eye-gaze data. Specifically, a computational visual saliency model is adopted to predict saliency maps for input image samples. Then, the saliency maps are used to distil the most informative image patches. In the proposed SGT, the self-attention among image patches focus only on the distilled informative ones. Considering this distill operation may lead to global information lost, we further introduce, in the last encoder layer, a residual connection that captures the self-attention across all the image patches. The experiment results on four independent public datasets show that our SGT framework can effectively learn and leverage human prior knowledge without eye gaze data and achieves much better performance than baselines. Meanwhile, it successfully rectifies the harmful shortcut learning and significantly improves the interpretability of the ViT model, demonstrating the promise of transferring human prior knowledge derived visual saliency in rectifying shortcut learning, Comment: NeurIPS2022 Under Review

Learning harmful shortcuts such as spurious correlations and biases prevents deep neural networks from learning the meaningful and useful representations, thus jeopardizing the generalizability and interpretability of the learned representation. The situation becomes even more serious in medical imaging, where the clinical data (e.g., MR images with pathology) are limited and scarce while the reliability, generalizability and transparency of the learned model are highly required. To address this problem, we propose to infuse human experts' intelligence and domain knowledge into the training of deep neural networks. The core idea is that we infuse the visual attention information from expert radiologists to proactively guide the deep model to focus on regions with potential pathology and avoid being trapped in learning harmful shortcuts. To do so, we propose a novel eye-gaze-guided vision transformer (EG-ViT) for diagnosis with limited medical image data. We mask the input image patches that are out of the radiologists' interest and add an additional residual connection in the last encoder layer of EG-ViT to maintain the correlations of all patches. The experiments on two public datasets of INbreast and SIIM-ACR demonstrate our EG-ViT model can effectively learn/transfer experts' domain knowledge and achieve much better performance than baselines. Meanwhile, it successfully rectifies the harmful shortcut learning and significantly improves the EG-ViT model's interpretability. In general, EG-ViT takes the advantages of both human expert's prior knowledge and the power of deep neural networks. This work opens new avenues for advancing current artificial intelligence paradigms by infusing human intelligence.

Are the embeddings of a graph's degenerate core stable? What happens to the embeddings of nodes in the degenerate core as we systematically remove periphery nodes (by repeated peeling off $k$-cores)? We discover three patterns w.r.t. instability in degenerate-core embeddings across a variety of popular graph embedding algorithms and datasets. We use regression to quantify the change point in graph embedding stability. Furthermore, we present the STABLE algorithm, which takes an existing graph embedding algorithm and makes it stable. We show the effectiveness of STABLE in terms of making the degenerate-core embedding stable and still producing state-of-the-art link prediction performance.

Vision transformer (ViT) and its variants have achieved remarkable successes in various visual tasks. The key characteristic of these ViT models is to adopt different aggregation strategies of spatial patch information within the artificial neural networks (ANNs). However, there is still a key lack of unified representation of different ViT architectures for systematic understanding and assessment of model representation performance. Moreover, how those well-performing ViT ANNs are similar to real biological neural networks (BNNs) is largely unexplored. To answer these fundamental questions, we, for the first time, propose a unified and biologically-plausible relational graph representation of ViT models. Specifically, the proposed relational graph representation consists of two key sub-graphs: aggregation graph and affine graph. The former one considers ViT tokens as nodes and describes their spatial interaction, while the latter one regards network channels as nodes and reflects the information communication between channels. Using this unified relational graph representation, we found that: a) a sweet spot of the aggregation graph leads to ViTs with significantly improved predictive performance; b) the graph measures of clustering coefficient and average path length are two effective indicators of model prediction performance, especially when applying on the datasets with small samples; c) our findings are consistent across various ViT architectures and multiple datasets; d) the proposed relational graph representation of ViT has high similarity with real BNNs derived from brain science data. Overall, our work provides a novel unified and biologically-plausible paradigm for more interpretable and effective representation of ViT ANNs., Comment: 11 pages,7 figures, submitted to 36th Conference on Neural Information Processing Systems (NeurIPS 2022)

Learning with little data is challenging but often inevitable in various application scenarios where the labeled data is limited and costly. Recently, few-shot learning (FSL) gained increasing attention because of its generalizability of prior knowledge to new tasks that contain only a few samples. However, for data-intensive models such as vision transformer (ViT), current fine-tuning based FSL approaches are inefficient in knowledge generalization and thus degenerate the downstream task performances. In this paper, we propose a novel mask-guided vision transformer (MG-ViT) to achieve an effective and efficient FSL on ViT model. The key idea is to apply a mask on image patches to screen out the task-irrelevant ones and to guide the ViT to focus on task-relevant and discriminative patches during FSL. Particularly, MG-ViT only introduces an additional mask operation and a residual connection, enabling the inheritance of parameters from pre-trained ViT without any other cost. To optimally select representative few-shot samples, we also include an active learning based sample selection method to further improve the generalizability of MG-ViT based FSL. We evaluate the proposed MG-ViT on both Agri-ImageNet classification task and ACFR apple detection task with gradient-weighted class activation mapping (Grad-CAM) as the mask. The experimental results show that the MG-ViT model significantly improves the performance when compared with general fine-tuning based ViT models, providing novel insights and a concrete approach towards generalizing data-intensive and large-scale deep learning models for FSL., Comment: 11 pages,4 figures, submitted to 36th Conference on Neural Information Processing Systems (NeurIPS 2022)