We developed a rapid scanning optical microscope, termed "BlurryScope", that leverages continuous image acquisition and deep learning to provide a cost-effective and compact solution for automated inspection and analysis of tissue sections. BlurryScope integrates specialized hardware with a neural network-based model to quickly process motion-blurred histological images and perform automated pathology classification. This device offers comparable speed to commercial digital pathology scanners, but at a significantly lower price point and smaller size/weight, making it ideal for fast triaging in small clinics, as well as for resourcelimited settings. To demonstrate the proof-of-concept of BlurryScope, we implemented automated classification of human epidermal growth factor receptor 2 (HER2) scores on immunohistochemically (IHC) stained breast tissue sections, achieving concordant results with those obtained from a high-end digital scanning microscope. We evaluated this approach by scanning HER2-stained tissue microarrays (TMAs) at a continuous speed of 5,000 µm/s, which introduces bidirectional motion blur artifacts. These compromised images were then used to train our network models. Using a test set of 284 unique patient cores, we achieved blind testing accuracies of 79.3% and 89.7% for 4-class (0, 1+, 2+, 3+) and 2-class (0/1+, 2+/3+) HER2 score classification, respectively. BlurryScope automates the entire workflow, from image scanning to stitching and cropping of regions of interest, as well as HER2 score classification. We believe BlurryScope has the potential to enhance the current pathology infrastructure in resource-scarce environments, save diagnostician time and bolster cancer identification and classification across various clinical environments.

This paper conducts a comprehensive study of the learning curves of kernel ridge regression (KRR) under minimal assumptions. Our contributions are three-fold: 1) we analyze the role of key properties of the kernel, such as its spectral eigen-decay, the characteristics of the eigenfunctions, and the smoothness of the kernel; 2) we demonstrate the validity of the Gaussian Equivalent Property (GEP), which states that the generalization performance of KRR remains the same when the whitened features are replaced by standard Gaussian vectors, thereby shedding light on the success of previous analyzes under the Gaussian Design Assumption; 3) we derive novel bounds that improve over existing bounds across a broad range of setting such as (in)dependent feature vectors and various combinations of eigen-decay rates in the over/underparameterized regimes.

Safety is a paramount concern of large language models (LLMs) in their open deployment. To this end, safeguard methods aim to enforce the ethical and responsible use of LLMs through safety alignment or guardrail mechanisms. However, we found that the malicious attackers could exploit false positives of safeguards, i.e., fooling the safeguard model to block safe content mistakenly, leading to a new denial-of-service (DoS) attack on LLMs. Specifically, by software or phishing attacks on user client software, attackers insert a short, seemingly innocuous adversarial prompt into to user prompt templates in configuration files; thus, this prompt appears in final user requests without visibility in the user interface and is not trivial to identify. By designing an optimization process that utilizes gradient and attention information, our attack can automatically generate seemingly safe adversarial prompts, approximately only 30 characters long, that universally block over 97\% of user requests on Llama Guard 3. The attack presents a new dimension of evaluating LLM safeguards focusing on false positives, fundamentally different from the classic jailbreak.

Federated learning (FL) is a promising machine learning paradigm that collaborates with client models to capture global knowledge. However, deploying FL models in real-world scenarios remains unreliable due to the coexistence of in-distribution data and unexpected out-of-distribution (OOD) data, such as covariate-shift and semantic-shift data. Current FL researches typically address either covariate-shift data through OOD generalization or semantic-shift data via OOD detection, overlooking the simultaneous occurrence of various OOD shifts. In this work, we propose FOOGD, a method that estimates the probability density of each client and obtains reliable global distribution as guidance for the subsequent FL process. Firstly, SM3D in FOOGD estimates score model for arbitrary distributions without prior constraints, and detects semantic-shift data powerfully. Then SAG in FOOGD provides invariant yet diverse knowledge for both local covariate-shift generalization and client performance generalization. In empirical validations, FOOGD significantly enjoys three main advantages: (1) reliably estimating non-normalized decentralized distributions, (2) detecting semantic shift data via score values, and (3) generalizing to covariate-shift data by regularizing feature extractor. The prejoct is open in https://github.com/XeniaLLL/FOOGD-main.git.

Over the past two decades, tools from network science have been leveraged to characterize the organization of both structural and functional networks of the brain. One such measure of network organization is hub node identification. Hubs are specialized nodes within a network that link distinct brain units corresponding to specialized functional processes. Conventional methods for identifying hub nodes utilize different types of centrality measures and participation coefficient to profile various aspects of nodal importance. These methods solely rely on the functional connectivity networks constructed from functional magnetic resonance imaging (fMRI), ignoring the structure-function coupling in the brain. In this paper, we introduce a graph signal processing (GSP) based hub detection framework that utilizes both the structural connectivity and the functional activation to identify hub nodes. The proposed framework models functional activity as graph signals on the structural connectivity. Hub nodes are then detected based on the premise that hub nodes are sparse, have higher level of activity compared to their neighbors, and the non-hub nodes' activity can be modeled as the output of a graph-based filter. Based on these assumptions, an optimization framework, GraFHub, is formulated to learn the coefficients of the optimal polynomial graph filter and detect the hub nodes. The proposed framework is evaluated on both simulated data and resting state fMRI (rs-fMRI) data from Human Connectome Project (HCP).

We introduce VEMOCLAP: Video EMOtion Classifier using Pretrained features, the first readily available and open-source web application that analyzes the emotional content of any user-provided video. We improve our previous work, which exploits open-source pretrained models that work on video frames and audio, and then efficiently fuse the resulting pretrained features using multi-head cross-attention. Our approach increases the state-of-the-art classification accuracy on the Ekman-6 video emotion dataset by 4.3% and offers an online application for users to run our model on their own videos or YouTube videos. We invite the readers to try our application at serkansulun.com/app.

This study investigates the risks of exposing confidential chemical structures when machine learning models trained on these structures are made publicly available. We use membership inference attacks, a common method to assess privacy that is largely unexplored in the context of drug discovery, to examine neural networks for molecular property prediction in a black-box setting. Our results reveal significant privacy risks across all evaluated datasets and neural network architectures. Combining multiple attacks increases these risks. Molecules from minority classes, often the most valuable in drug discovery, are particularly vulnerable. We also found that representing molecules as graphs and using message-passing neural networks may mitigate these risks. We provide a framework to assess privacy risks of classification models and molecular representations. Our findings highlight the need for careful consideration when sharing neural networks trained on proprietary chemical structures, informing organisations and researchers about the trade-offs between data confidentiality and model openness.

Following the advancement of large language models (LLMs), the development of LLM-based autonomous agents has become increasingly prevalent. As a result, the need to understand the security vulnerabilities of these agents has become a critical task. We examine how ReAct agents can be exploited using a straightforward yet effective method we refer to as the foot-in-the-door attack. Our experiments show that indirect prompt injection attacks, prompted by harmless and unrelated requests (such as basic calculations) can significantly increase the likelihood of the agent performing subsequent malicious actions. Our results show that once a ReAct agents thought includes a specific tool or action, the likelihood of executing this tool in the subsequent steps increases significantly, as the agent seldom re-evaluates its actions. Consequently, even random, harmless requests can establish a foot-in-the-door, allowing an attacker to embed malicious instructions into the agents thought process, making it more susceptible to harmful directives. To mitigate this vulnerability, we propose implementing a simple reflection mechanism that prompts the agent to reassess the safety of its actions during execution, which can help reduce the success of such attacks.

Deep Neural Networks (DNNs) have been shown to be vulnerable to adversarial examples. While numerous successful adversarial attacks have been proposed, defenses against these attacks remain relatively understudied. Existing defense approaches either focus on negating the effects of perturbations caused by the attacks to restore the DNNs' original predictions or use a secondary model to detect adversarial examples. However, these methods often become ineffective due to the continuous advancements in attack techniques. We propose a novel universal and lightweight method to detect adversarial examples by analyzing the layer outputs of DNNs. Through theoretical justification and extensive experiments, we demonstrate that our detection method is highly effective, compatible with any DNN architecture, and applicable across different domains, such as image, video, and audio. Goodfellow et al. (2014) demonstrated that deep neural networks (DNNs) are vulnerable to adversarial examples and proposed the Fast Gradient Sign Method (FGSM) to craft these adversarial examples by adding perturbations to the model inputs, leveraging the linear nature of DNNs. After the initial introduction of FGSM, various adversarial attacks were proposed across different domains. However, compared to the vast diversity among attack techniques, existing defense methods are built on a few different strategies.

Explainable Artificial Intelligence (AI) focuses on helping humans understand the working of AI systems or their decisions and has been a cornerstone of AI for decades. Recent research in explainability has focused on explaining the workings of AI models or model explainability. There have also been several position statements and review papers detailing the needs of end-users for user-centered explainability but fewer implementations. Hence, this thesis seeks to bridge some gaps between model and user-centered explainability. We create an explanation ontology (EO) to represent literature-derived explanation types via their supporting components. We implement a knowledge-augmented question-answering (QA) pipeline to support contextual explanations in a clinical setting. Finally, we are implementing a system to combine explanations from different AI methods and data modalities. Within the EO, we can represent fifteen different explanation types, and we have tested these representations in six exemplar use cases. We find that knowledge augmentations improve the performance of base large language models in the contextualized QA, and the performance is variable across disease groups. In the same setting, clinicians also indicated that they prefer to see actionability as one of the main foci in explanations. In our explanations combination method, we plan to use similarity metrics to determine the similarity of explanations in a chronic disease detection setting. Overall, through this thesis, we design methods that can support knowledge-enabled explanations across different use cases, accounting for the methods in today's AI era that can generate the supporting components of these explanations and domain knowledge sources that can enhance them.