OpenRaiser/Intern-Atlas huggingface dataset:
Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning
Venue: arXiv cs.CV 2023
Year: 2023

Histology imaging is an important tool in medical diagnosis and research, enabling the examination of tissue structure and composition at the microscopic level. Understanding the underlying molecular mechanisms of tissue architecture is critical in uncovering disease mechanisms and developing effective treatments. Gene expression profiling provides insight into the molecular processes underlying tissue architecture, but the process can be time-consuming and expensive. We present BLEEP (Bi-modaL Embedding for Expression Prediction), a bi-modal embedding framework capable of generating spatially resolved gene expression profiles of whole-slide Hematoxylin and eosin (H&E) stained histology images. BLEEP uses contrastive learning to construct a low-dimensional joint embedding space from a reference dataset using paired image and expression profiles at micrometer resolution. With this approach, the gene expression of any query image patch can be imputed using the expression profiles from the reference dataset. We demonstrate BLEEP's effectiveness in gene expression prediction by benchmarking its performance on a human liver tissue dataset captured using the 10x Visium platform, where it achieves significant improvements over existing methods. Our results demonstrate the potential of BLEEP to provide insights into the molecular mechanisms underlying tissue architecture, with important implications in diagnosis and research of various diseases. The proposed approach can significantly reduce the time and cost associated with gene expression profiling, opening up new avenues for high-throughput analysis of histology images for both research and clinical applications.
Cooperative Collision Avoidance in a Connected Vehicle Environment
Venue: arXiv cs.RO 2023
Year: 2023

Connected vehicle (CV) technology is among the most heavily researched areas in both the academia and industry. The vehicle to vehicle (V2V), vehicle to infrastructure (V2I) and vehicle to pedestrian (V2P) communication capabilities enable critical situational awareness. In some cases, these vehicle communication safety capabilities can overcome the shortcomings of other sensor safety capabilities because of external conditions such as 'No Line of Sight' (NLOS) or very harsh weather conditions. Connected vehicles will help cities and states reduce traffic congestion, improve fuel efficiency and improve the safety of the vehicles and pedestrians. On the road, cars will be able to communicate with one another, automatically transmitting data such as speed, position, and direction, and send alerts to each other if a crash seems imminent. The main focus of this paper is the implementation of Cooperative Collision Avoidance (CCA) for connected vehicles. It leverages the Vehicle to Everything (V2X) communication technology to create a real-time implementable collision avoidance algorithm along with decision-making for a vehicle that communicates with other vehicles. Four distinct collision risk environments are simulated on a cost effective Connected Autonomous Vehicle (CAV) Hardware in the Loop (HIL) simulator to test the overall algorithm in real-time with real electronic control and communication hardware.
Synaptic motor adaptation: A three-factor learning rule for adaptive robotic control in spiking neural networks
Venue: arXiv cs.RO 2023
Year: 2023

Legged robots operating in real-world environments must possess the ability to rapidly adapt to unexpected conditions, such as changing terrains and varying payloads. This paper introduces the Synaptic Motor Adaptation (SMA) algorithm, a novel approach to achieving real-time online adaptation in quadruped robots through the utilization of neuroscience-derived rules of synaptic plasticity with three-factor learning. To facilitate rapid adaptation, we meta-optimize a three-factor learning rule via gradient descent to adapt to uncertainty by approximating an embedding produced by privileged information using only locally accessible onboard sensing data. Our algorithm performs similarly to state-of-the-art motor adaptation algorithms and presents a clear path toward achieving adaptive robotics with neuromorphic hardware.
Recent Advances of Local Mechanisms in Computer Vision: A Survey and Outlook of Recent Work
Venue: arXiv cs.CV 2023
Year: 2023

Inspired by the fact that human brains can emphasize discriminative parts of the input and suppress irrelevant ones, substantial local mechanisms have been designed to boost the development of computer vision. They can not only focus on target parts to learn discriminative local representations, but also process information selectively to improve the efficiency. In terms of application scenarios and paradigms, local mechanisms have different characteristics. In this survey, we provide a systematic review of local mechanisms for various computer vision tasks and approaches, including fine-grained visual recognition, person re-identification, few-/zero-shot learning, multi-modal learning, self-supervised learning, Vision Transformers, and so on. Categorization of local mechanisms in each field is summarized. Then, advantages and disadvantages for every category are analyzed deeply, leaving room for exploration. Finally, future research directions about local mechanisms have also been discussed that may benefit future works. To the best our knowledge, this is the first survey about local mechanisms on computer vision. We hope that this survey can shed light on future research in the computer vision field.
Optimal Control for Articulated Soft Robots
Venue: arXiv cs.RO 2023
Year: 2023

Soft robots can execute tasks with safer interactions. However, control techniques that can effectively exploit the systems' capabilities are still missing. Differential dynamic programming (DDP) has emerged as a promising tool for achieving highly dynamic tasks. But most of the literature deals with applying DDP to articulated soft robots by using numerical differentiation, in addition to using pure feed-forward control to perform explosive tasks. Further, underactuated compliant robots are known to be difficult to control and the use of DDP-based algorithms to control them is not yet addressed. We propose an efficient DDP-based algorithm for trajectory optimization of articulated soft robots that can optimize the state trajectory, input torques, and stiffness profile. We provide an efficient method to compute the forward dynamics and the analytical derivatives of series elastic actuators (SEA)/variable stiffness actuators (VSA) and underactuated compliant robots. We present a state-feedback controller that uses locally optimal feedback policies obtained from DDP. We show through simulations and experiments that the use of feedback is crucial in improving the performance and stabilization properties of various tasks. We also show that the proposed method can be used to plan and control underactuated compliant robots, with varying degrees of underactuation effectively.
AI Transparency in the Age of LLMs: A Human-Centered Research Roadmap
Venue: arXiv cs.HC 2023
Year: 2023

The rise of powerful large language models (LLMs) brings about tremendous opportunities for innovation but also looming risks for individuals and society at large. We have reached a pivotal moment for ensuring that LLMs and LLM-infused applications are developed and deployed responsibly. However, a central pillar of responsible AI -- transparency -- is largely missing from the current discourse around LLMs. It is paramount to pursue new approaches to provide transparency for LLMs, and years of research at the intersection of AI and human-computer interaction (HCI) highlight that we must do so with a human-centered perspective: Transparency is fundamentally about supporting appropriate human understanding, and this understanding is sought by different stakeholders with different goals in different contexts. In this new era of LLMs, we must develop and design approaches to transparency by considering the needs of stakeholders in the emerging LLM ecosystem, the novel types of LLM-infused applications being built, and the new usage patterns and challenges around LLMs, all while building on lessons learned about how people process, interact with, and make use of information. We reflect on the unique challenges that arise in providing transparency for LLMs, along with lessons learned from HCI and responsible AI research that has taken a human-centered perspective on AI transparency. We then lay out four common approaches that the community has taken to achieve transparency -- model reporting, publishing evaluation results, providing explanations, and communicating uncertainty -- and call out open questions around how these approaches may or may not be applied to LLMs. We hope this provides a starting point for discussion and a useful roadmap for future research.
A Survey on Explainability of Graph Neural Networks
Venue: arXiv cs.LG 2023
Year: 2023

Graph neural networks (GNNs) are powerful graph-based deep-learning models that have gained significant attention and demonstrated remarkable performance in various domains, including natural language processing, drug discovery, and recommendation systems. However, combining feature information and combinatorial graph structures has led to complex non-linear GNN models. Consequently, this has increased the challenges of understanding the workings of GNNs and the underlying reasons behind their predictions. To address this, numerous explainability methods have been proposed to shed light on the inner mechanism of the GNNs. Explainable GNNs improve their security and enhance trust in their recommendations. This survey aims to provide a comprehensive overview of the existing explainability techniques for GNNs. We create a novel taxonomy and hierarchy to categorize these methods based on their objective and methodology. We also discuss the strengths, limitations, and application scenarios of each category. Furthermore, we highlight the key evaluation metrics and datasets commonly used to assess the explainability of GNNs. This survey aims to assist researchers and practitioners in understanding the existing landscape of explainability methods, identifying gaps, and fostering further advancements in interpretable graph-based machine learning.
COBRA Frames: Contextual Reasoning about Effects and Harms of Offensive Statements
Venue: arXiv cs.CL 2023
Year: 2023

Warning: This paper contains content that may be offensive or upsetting. Understanding the harms and offensiveness of statements requires reasoning about the social and situational context in which statements are made. For example, the utterance "your English is very good" may implicitly signal an insult when uttered by a white man to a non-white colleague, but uttered by an ESL teacher to their student would be interpreted as a genuine compliment. Such contextual factors have been largely ignored by previous approaches to toxic language detection. We introduce COBRA frames, the first context-aware formalism for explaining the intents, reactions, and harms of offensive or biased statements grounded in their social and situational context. We create COBRACORPUS, a dataset of 33k potentially offensive statements paired with machine-generated contexts and free-text explanations of offensiveness, implied biases, speaker intents, and listener reactions. To study the contextual dynamics of offensiveness, we train models to generate COBRA explanations, with and without access to the context. We find that explanations by context-agnostic models are significantly worse than by context-aware ones, especially in situations where the context inverts the statement's offensiveness (29% accuracy drop). Our work highlights the importance and feasibility of contextualized NLP by modeling social factors.
Lightweight Structure-aware Transformer Network for VHR Remote Sensing Image Change Detection
Venue: arXiv cs.CV 2023
Year: 2023

Popular Transformer networks have been successfully applied to remote sensing (RS) image change detection (CD) identifications and achieve better results than most convolutional neural networks (CNNs), but they still suffer from two main problems. First, the computational complexity of the Transformer grows quadratically with the increase of image spatial resolution, which is unfavorable to very high-resolution (VHR) RS images. Second, these popular Transformer networks tend to ignore the importance of fine-grained features, which results in poor edge integrity and internal tightness for largely changed objects and leads to the loss of small changed objects. To address the above issues, this Letter proposes a Lightweight Structure-aware Transformer (LSAT) network for RS image CD. The proposed LSAT has two advantages. First, a Cross-dimension Interactive Self-attention (CISA) module with linear complexity is designed to replace the vanilla self-attention in visual Transformer, which effectively reduces the computational complexity while improving the feature representation ability of the proposed LSAT. Second, a Structure-aware Enhancement Module (SAEM) is designed to enhance difference features and edge detail information, which can achieve double enhancement by difference refinement and detail aggregation so as to obtain fine-grained features of bi-temporal RS images. Experimental results show that the proposed LSAT achieves significant improvement in detection accuracy and offers a better tradeoff between accuracy and computational costs than most state-of-the-art CD methods for VHR RS images.
BandwidthBreach: Unleashing Covert and Side Channels through Cache Bandwidth Exploitation
Venue: arXiv cs.CR 2023
Year: 2023

In the modern CPU architecture, enhancements such as the Line Fill Buffer (LFB) and Super Queue (SQ), which are designed to track pending cache requests, have significantly boosted performance. To exploit this structures, we deliberately engineered blockages in the L2 to L1d route by controlling LFB conflict and triggering prefetch prediction failures, while consciously dismissing other plausible influencing factors. This approach was subsequently extended to the L3 to L2 and L2 to L1i pathways, resulting in three potent covert channels, termed L2CC, L3CC, and LiCC, with capacities of 10.02 Mbps, 10.37 Mbps, and 1.83 Mbps, respectively. Strikingly, the capacities of L2CC and L3CC surpass those of earlier non-shared-memory-based covert channels, reaching a level comparable to their shared memory-dependent equivalents. Leveraging this congestion further facilitated the extraction of key bits from RSA and EdDSA implementations. Coupled with SpectreV1 and V2, our covert channels effectively evade the majority of traditional Spectre defenses. Their confluence with Branch Prediction (BP) Timing assaults additionally undercuts balanced branch protections, hence broadening their capability to infiltrate a wide range of cryptography libraries.
GAT-GAN : A Graph-Attention-based Time-Series Generative Adversarial Network
Venue: arXiv cs.LG 2023
Year: 2023

Generative Adversarial Networks (GANs) have proven to be a powerful tool for generating realistic synthetic data. However, traditional GANs often struggle to capture complex relationships between features which results in generation of unrealistic multivariate time-series data. In this paper, we propose a Graph-Attention-based Generative Adversarial Network (GAT-GAN) that explicitly includes two graph-attention layers, one that learns temporal dependencies while the other captures spatial relationships. Unlike RNN-based GANs that struggle with modeling long sequences of data points, GAT-GAN generates long time-series data of high fidelity using an adversarially trained autoencoder architecture. Our empirical evaluations, using a variety of real-time-series datasets, show that our framework consistently outperforms state-of-the-art benchmarks based on \emph{Frechet Transformer distance} and \emph{Predictive score}, that characterizes (\emph{Fidelity, Diversity}) and \emph{predictive performance} respectively. Moreover, we introduce a Frechet Inception distance-like (FID) metric for time-series data called Frechet Transformer distance (FTD) score (lower is better), to evaluate the quality and variety of generated data. We also found that low FTD scores correspond to the best-performing downstream predictive experiments. Hence, FTD scores can be used as a standardized metric to evaluate synthetic time-series data.
Does Microservices Adoption Impact the Development Velocity? A Cohort Study. A Registered Report
Venue: arXiv cs.SE 2023
Year: 2023

[Context] Microservices enable the decomposition of applications into small and independent services connected together. The independence between services could positively affect the development velocity of a project, which is considered an important metric measuring the time taken to implement features and fix bugs. However, no studies have investigated the connection between microservices and development velocity. [Objective and Method] The goal of this study plan is to investigate the effect microservices have on development velocity. The study compares GitHub projects adopting microservices from the beginning and similar projects using monolithic architectures. We designed this study using a cohort study method, to enable obtaining a high level of evidence. [Results] The result of this work enables the confirmation of the effective improvement of the development velocity of microservices. Moreover, this study will contribute to the body of knowledge of empirical methods being among the first works adopting the cohort study methodology.
Segment Anything Meets Semantic Communication
Venue: arXiv cs.CV 2023
Year: 2023

In light of the diminishing returns of traditional methods for enhancing transmission rates, the domain of semantic communication presents promising new frontiers. Focusing on image transmission, this paper explores the application of foundation models, particularly the Segment Anything Model (SAM) developed by Meta AI Research, to improve semantic communication. SAM is a promptable image segmentation model that has gained attention for its ability to perform zero-shot segmentation tasks without explicit training or domain-specific knowledge. By employing SAM's segmentation capability and lightweight neural network architecture for semantic coding, we propose a practical approach to semantic communication. We demonstrate that this approach retains critical semantic features, achieving higher image reconstruction quality and reducing communication overhead. This practical solution eliminates the resource-intensive stage of training a segmentation model and can be applied to any semantic coding architecture, paving the way for real-world applications.
Graph Mover's Distance: An Efficiently Computable Distance Measure for Geometric Graphs
Venue: arXiv cs.CG 2023
Year: 2023

Many applications in pattern recognition represent patterns as a geometric graph. The geometric graph distance (GGD) has recently been studied as a meaningful measure of similarity between two geometric graphs. Since computing the GGD is known to be $\mathcal{NP}$-hard, the distance measure proves an impractical choice for applications. As a computationally tractable alternative, we propose in this paper the Graph Mover's Distance (GMD), which has been formulated as an instance of the earth mover's distance. The computation of the GMD between two geometric graphs with at most $n$ vertices takes only $O(n^3)$-time. Alongside studying the metric properties of the GMD, we investigate the stability of the GGD and GMD. The GMD also demonstrates extremely promising empirical evidence at recognizing letter drawings from the {\tt LETTER} dataset \cite{da_vitoria_lobo_iam_2008}.
Buying Time: Latency Racing vs. Bidding in Transaction Ordering
Venue: arXiv cs.GT 2023
Year: 2023

We design TimeBoost: a practical transaction ordering policy for rollup sequencers that takes into account both transaction timestamps and bids; it works by creating a score from timestamps and bids, and orders transactions based on this score. TimeBoost is transaction-data-independent (i.e., can work with encrypted transactions) and supports low transaction finalization times similar to a first-come first-serve (FCFS or pure-latency) ordering policy. At the same time, it avoids the inefficient latency competition created by an FCFS policy. It further satisfies useful economic properties of first-price auctions that come with a pure-bidding policy. We show through rigorous economic analyses how TimeBoost allows players to compete on arbitrage opportunities in a way that results in better guarantees compared to both pure-latency and pure-bidding approaches.
brainlife.io: A decentralized and open source cloud platform to support neuroscience research
Venue: arXiv cs.DC 2023
Year: 2023

Neuroscience research has expanded dramatically over the past 30 years by advancing standardization and tool development to support rigor and transparency. Consequently, the complexity of the data pipeline has also increased, hindering access to FAIR (Findable, Accessible, Interoperabile, and Reusable) data analysis to portions of the worldwide research community. brainlife.io was developed to reduce these burdens and democratize modern neuroscience research across institutions and career levels. Using community software and hardware infrastructure, the platform provides open-source data standardization, management, visualization, and processing and simplifies the data pipeline. brainlife.io automatically tracks the provenance history of thousands of data objects, supporting simplicity, efficiency, and transparency in neuroscience research. Here brainlife.io's technology and data services are described and evaluated for validity, reliability, reproducibility, replicability, and scientific utility. Using data from 4 modalities and 3,200 participants, we demonstrate that brainlife.io's services produce outputs that adhere to best practices in modern neuroscience research.
Detector Guidance for Multi-Object Text-to-Image Generation
Venue: arXiv cs.CV 2023
Year: 2023

Diffusion models have demonstrated impressive performance in text-to-image generation. They utilize a text encoder and cross-attention blocks to infuse textual information into images at a pixel level. However, their capability to generate images with text containing multiple objects is still restricted. Previous works identify the problem of information mixing in the CLIP text encoder and introduce the T5 text encoder or incorporate strong prior knowledge to assist with the alignment. We find that mixing problems also occur on the image side and in the cross-attention blocks. The noisy images can cause different objects to appear similar, and the cross-attention blocks inject information at a pixel level, leading to leakage of global object understanding and resulting in object mixing. In this paper, we introduce Detector Guidance (DG), which integrates a latent object detection model to separate different objects during the generation process. DG first performs latent object detection on cross-attention maps (CAMs) to obtain object information. Based on this information, DG then masks conflicting prompts and enhances related prompts by manipulating the following CAMs. We evaluate the effectiveness of DG using Stable Diffusion on COCO, CC, and a novel multi-related object benchmark, MRO. Human evaluations demonstrate that DG provides an 8-22\% advantage in preventing the amalgamation of conflicting concepts and ensuring that each object possesses its unique region without any human involvement and additional iterations. Our implementation is available at \url{https://github.com/luping-liu/Detector-Guidance}.