OpenRaiser/Intern-Atlas huggingface dataset:
Self-Normalizing Foundation Model for Enhanced Multi-Omics Data Analysis in Oncology
Venue: arXiv cs.LG 2024
Year: 2024

Multi-omics research has enhanced our understanding of cancer heterogeneity and progression. Investigating molecular data through multi-omics approaches is crucial for unraveling the complex biological mechanisms underlying cancer, thereby enabling more effective diagnosis, treatment, and prevention strategies. However, predicting patient outcomes through the integration of all available multi-omics data is still an under-study research direction. Here, we present SeNMo, a foundation model that has been trained on multi-omics data across 33 cancer types. SeNMo is particularly efficient in handling multi-omics data characterized by high-width and low-length attributes. We trained SeNMo for the task of overall survival of patients using pan-cancer multi-omics data involving 33 cancer sites from the GDC. The training multi-omics data includes gene expression, DNA methylation, miRNA expression, DNA mutations, protein expression modalities, and clinical data. SeNMo was validated on two independent cohorts: Moffitt Cancer Center and CPTAC lung squamous cell carcinoma. We evaluated the model's performance in predicting patient's overall survival using the C-Index. SeNMo performed consistently well in the training regime, reflected by the validation C-Index of 0.76 on GDC's public data. In the testing regime, SeNMo performed with a C-Index of 0.758 on a held-out test set. The model showed an average accuracy of 99.8% on the task of classifying the primary cancer type on the pan-cancer test cohort. SeNMo demonstrated robust performance on the classification task of predicting the primary cancer type of patients. SeNMo further demonstrated significant performance in predicting tertiary lymph structures from multi-omics data, showing generalizability across cancer types, molecular data types, and clinical endpoints.
A predictive learning model can simulate temporal dynamics and context effects found in neural representations of continuous speech
Venue: arXiv cs.CL 2024
Year: 2024

Speech perception involves storing and integrating sequentially presented items. Recent work in cognitive neuroscience has identified temporal and contextual characteristics in humans' neural encoding of speech that may facilitate this temporal processing. In this study, we simulated similar analyses with representations extracted from a computational model that was trained on unlabelled speech with the learning objective of predicting upcoming acoustics. Our simulations revealed temporal dynamics similar to those in brain signals, implying that these properties can arise without linguistic knowledge. Another property shared between brains and the model is that the encoding patterns of phonemes support some degree of cross-context generalization. However, we found evidence that the effectiveness of these generalizations depends on the specific contexts, which suggests that this analysis alone is insufficient to support the presence of context-invariant encoding.
Progressive enhancement and restoration for mural images under low-light and defected conditions based on multi-receptive field strategy
Venue: arXiv cs.CV 2024
Year: 2024

Ancient murals are valuable cultural heritage with great archaeological value. They provide insights into ancient religions, ceremonies, folklore, among other things through their content. However, due to long-term oxidation and inadequate protection, ancient murals have suffered continuous damage, including peeling and mold etc. Additionally, since ancient murals were typically painted indoors, the light intensity in images captured by digital devices is often low. The poor visibility hampers the further restoration of damaged areas. To address the escalating damage to ancient murals and facilitate batch restoration at archaeological sites, we propose a two-stage restoration model with automatic defect area detection strategy which called MER(Mural Enhancement and Restoration net) for ancient murals that are damaged and have been captured in low light. Our two-stage model not only enhances the visual quality of restored images but also achieves commendable results in relevant metric evaluations compared with other competitors. Furthermore, we have launched a website dedicated to the restoration of ancient mural paintings, utilizing the proposed model. Code is available at https://gitee.com/bbfan2024/MER.git.
Palette-based Color Transfer between Images
Venue: arXiv cs.CV 2024
Year: 2024

As an important subtopic of image enhancement, color transfer aims to enhance the color scheme of a source image according to a reference one while preserving the semantic context. To implement color transfer, the palette-based color mapping framework was proposed. \textcolor{black}{It is a classical solution that does not depend on complex semantic analysis to generate a new color scheme. However, the framework usually requires manual settings, blackucing its practicality.} The quality of traditional palette generation depends on the degree of color separation. In this paper, we propose a new palette-based color transfer method that can automatically generate a new color scheme. With a redesigned palette-based clustering method, pixels can be classified into different segments according to color distribution with better applicability. {By combining deep learning-based image segmentation and a new color mapping strategy, color transfer can be implemented on foreground and background parts independently while maintaining semantic consistency.} The experimental results indicate that our method exhibits significant advantages over peer methods in terms of natural realism, color consistency, generality, and robustness.
Towards Multi-Task Generative-AI Edge Services with an Attention-based Diffusion DRL Approach
Venue: arXiv cs.NI 2024
Year: 2024

As an emerging paradigm of content creation, AI-Generated Content (AIGC) has been widely adopted by a large number of edge end users. However, the requests for generated content from AIGC users have obvious diversity, and there remains a notable lack of research addressing the variance in user demands for AIGC services. This gap underscores a critical need for suitable AIGC service selection mechanisms satisfying various AIGC user requirements under resource-constrained edge environments. To address this challenge, this paper proposes a novel Attention-based Diffusion Soft Actor-Critic (ADSAC) algorithm to select the appropriate AIGC model in response to heterogeneous AIGC user requests. Specifically, the ADSAC algorithm integrates a diffusion model as the policy network in the off-policy reinforcement learning (RL) framework, to capture the intricate relationships between the characteristics of AIGC tasks and the integrated edge network states. Furthermore, an attention mechanism is utilized to harness the contextual long-range dependencies present in state feature vectors, enhancing the decision-making process. Extensive experiments validate the effectiveness of our algorithm in enhancing the overall user utility and reducing the crash rate of servers. Compared to the existing methods, the proposed ADSAC algorithm outperforms existing methods, reducing the overall user utility loss and the server crash rate by at least 58.3% and 58.4%, respectively. These results demonstrate our ADSAC algorithm is a robust solution to the challenges of diverse and dynamic user requirements in edge-based AIGC application environments.
Achieving Resolution-Agnostic DNN-based Image Watermarking: A Novel Perspective of Implicit Neural Representation
Venue: arXiv cs.CR 2024
Year: 2024

DNN-based watermarking methods are rapidly developing and delivering impressive performances. Recent advances achieve resolution-agnostic image watermarking by reducing the variant resolution watermarking problem to a fixed resolution watermarking problem. However, such a reduction process can potentially introduce artifacts and low robustness. To address this issue, we propose the first, to the best of our knowledge, Resolution-Agnostic Image WaterMarking (RAIMark) framework by watermarking the implicit neural representation (INR) of image. Unlike previous methods, our method does not rely on the previous reduction process by directly watermarking the continuous signal instead of image pixels, thus achieving resolution-agnostic watermarking. Precisely, given an arbitrary-resolution image, we fit an INR for the target image. As a continuous signal, such an INR can be sampled to obtain images with variant resolutions. Then, we quickly fine-tune the fitted INR to get a watermarked INR conditioned on a binary secret message. A pre-trained watermark decoder extracts the hidden message from any sampled images with arbitrary resolutions. By directly watermarking INR, we achieve resolution-agnostic watermarking with increased robustness. Extensive experiments show that our method outperforms previous methods with significant improvements: averagely improved bit accuracy by 7%$\sim$29%. Notably, we observe that previous methods are vulnerable to at least one watermarking attack (e.g. JPEG, crop, resize), while ours are robust against all watermarking attacks.
Multi-Robot Rendezvous in Unknown Environment with Limited Communication
Venue: arXiv cs.RO 2024
Year: 2024

Rendezvous aims at gathering all robots at a specific location, which is an important collaborative behavior for multi-robot systems. However, in an unknown environment, it is challenging to achieve rendezvous. Previous researches mainly focus on special scenarios where communication is not allowed and each robot executes a random searching strategy, which is highly time-consuming, especially in large-scale environments. In this work, we focus on rendezvous in unknown environments where communication is available. We divide this task into two steps: rendezvous based environment exploration with relative pose (RP) estimation and rendezvous point selection. A new strategy called partitioned and incomplete exploration for rendezvous (PIER) is proposed to efficiently explore the unknown environment, where lightweight topological maps are constructed and shared among robots for RP estimation with very few communications. Then, a rendezvous point selection algorithm based on the merged topological map is proposed for efficient rendezvous for multi-robot systems. The effectiveness of the proposed methods is validated in both simulations and real-world experiments.
KG-EmpiRE: A Community-Maintainable Knowledge Graph for a Sustainable Literature Review on the State and Evolution of Empirical Research in Requirements Engineering
Venue: arXiv cs.SE 2024
Year: 2024

In the last two decades, several researchers provided snapshots of the "current" state and evolution of empirical research in requirements engineering (RE) through literature reviews. However, these literature reviews were not sustainable, as none built on or updated previous works due to the unavailability of the extracted and analyzed data. KG-EmpiRE is a Knowledge Graph (KG) of empirical research in RE based on scientific data extracted from currently 680 papers published in the IEEE International Requirements Engineering Conference (1994-2022). KG-EmpiRE is maintained in the Open Research Knowledge Graph (ORKG), making all data openly and long-term available according to the FAIR data principles. Our long-term goal is to constantly maintain KG-EmpiRE with the research community to synthesize a comprehensive, up-to-date, and long-term available overview of the state and evolution of empirical research in RE. Besides KG-EmpiRE, we provide its analysis with all supplementary materials in a repository. This repository contains all files with instructions for replicating and (re-)using the analysis locally or via executable environments and for repeating the research approach. Since its first release based on 199 papers (2014-2022), KG-EmpiRE and its analysis have been updated twice, currently covering over 650 papers. KG-EmpiRE and its analysis demonstrate how innovative infrastructures, such as the ORKG, can be leveraged to make data from literature reviews FAIR, openly available, and maintainable for the research community in the long term. In this way, we can enable replicable, (re-)usable, and thus sustainable literature reviews to ensure the quality, reliability, and timeliness of their research results.
Seal-Tools: Self-Instruct Tool Learning Dataset for Agent Tuning and Detailed Benchmark
Venue: arXiv cs.CL 2024
Year: 2024

This paper presents a new tool learning dataset Seal-Tools, which contains self-instruct API-like tools. Seal-Tools not only offers a large number of tools, but also includes instances which demonstrate the practical application of tools. Seeking to generate data on a large scale while ensuring reliability, we propose a self-instruct method to generate tools and instances, allowing precise control over the process. Moreover, our Seal-Tools contains hard instances that call multiple tools to complete the job, among which some are nested tool callings. For precise and comprehensive evaluation, we use strict format control and design three metrics from different dimensions. Therefore, Seal-Tools can serve as a new benchmark to evaluate the tool-calling ability of LLMs. Finally, we evaluate several prevalent LLMs and our finetuned model on Seal-Tools. The results show that current systems are far from perfect. The code, data and experiment results are available at https://github.com/fairyshine/Seal-Tools .
Cross-Blockchain Communication Using Oracles With an Off-Chain Aggregation Mechanism Based on zk-SNARKs
Venue: arXiv cs.CR 2024
Year: 2024

The closed architecture of prevailing blockchain systems renders the usage of this technology mostly infeasible for a wide range of real-world problems. Most blockchains trap users and applications in their isolated space without the possibility of cooperating or switching to other blockchains. Therefore, blockchains need additional mechanisms for seamless communication and arbitrary data exchange between each other and external systems. Unfortunately, current approaches for cross-blockchain communication are resource-intensive or require additional blockchains or tailored solutions depending on the applied consensus mechanisms of the connected blockchains. Therefore, we propose an oracle with an off-chain aggregation mechanism based on ZeroKnowledge Succinct Non-interactive Arguments of Knowledge (zk-SNARKs) to facilitate cross-blockchain communication. The oracle queries data from another blockchain and applies a rollup-like mechanism to move state and computation off-chain. The zkOracle contract only expects the transferred data, an updated state root, and proof of the correct execution of the aggregation mechanism. The proposed solution only requires constant 378 kgas to submit data on the Ethereum blockchain and is primarily independent of the underlying technology of the queried blockchains.
Stylometric Watermarks for Large Language Models
Venue: arXiv cs.CL 2024
Year: 2024

The rapid advancement of large language models (LLMs) has made it increasingly difficult to distinguish between text written by humans and machines. Addressing this, we propose a novel method for generating watermarks that strategically alters token probabilities during generation. Unlike previous works, this method uniquely employs linguistic features such as stylometry. Concretely, we introduce acrostica and sensorimotor norms to LLMs. Further, these features are parameterized by a key, which is updated every sentence. To compute this key, we use semantic zero shot classification, which enhances resilience. In our evaluation, we find that for three or more sentences, our method achieves a false positive and false negative rate of 0.02. For the case of a cyclic translation attack, we observe similar results for seven or more sentences. This research is of particular of interest for proprietary LLMs to facilitate accountability and prevent societal harm.
Realtime Global Optimization of a Fail-Safe Emergency Stop Maneuver for Arbitrary Electrical / Electronical Failures in Automated Driving
Venue: arXiv cs.RO 2024
Year: 2024

In the event of a critical system failures in auto-mated vehicles, fail-operational or fail-safe measures provide minimum guarantees for the vehicle's performance, depending on which of its subsystems remain operational. Various such methods have been proposed which, upon failure, use different remaining sets of operational subsystems to execute maneuvers that bring the vehicle into a safe state under different environmental conditions. One particular such method proposes a fail-safe emergency stop system that requires no particular electric or electronic subsystem to be available after failure, and still provides a basic situation-dependent emergency stop maneuver. This is achieved by preemptively setting parameters to a hydraulic / mechanical system prior to failure, which after failure executes the preset maneuver "blindly". The focus of this paper is the particular challenge of implementing a lightweight planning algorithm that can cope with the complex uncertainties of the given task while still providing a globally optimal solution at regular intervals, based on the perceived and predicted environment of the automated vehicle.
AI-Resilient Interfaces
Venue: arXiv cs.HC 2024
Year: 2024

AI is powerful, but it can make choices that result in objective errors, contextually inappropriate outputs, and disliked options. We need AI-resilient interfaces that help people be resilient to the AI choices that are not right, or not right for them. To support this goal, interfaces need to help users notice and have the context to appropriately judge those AI choices. Existing human-AI interaction guidelines recommend efficient user dismissal, modification, or otherwise efficient recovery from AI choices that a user does not like. However, in order to recover from AI choices, the user must notice them first. This can be difficult. For example, when generating summaries of long documents, a system's exclusion of a detail that is critically important to the user is hard for the user to notice. That detail can be hiding in a wall of text in the original document, and the existence of a summary may tempt the user not to read the original document as carefully. Once noticed, judging AI choices well can also be challenging. The interface may provide very little information that contextualizes the choices, and the user may fall back on assumptions when deciding whether to dismiss, modify, or otherwise recover from an AI choice. Building on prior work, this paper defines key aspects of AI-resilient interfaces, illustrated with examples. Designing interfaces for increased AI-resilience of users will improve AI safety, usability, and utility. This is especially critical where AI-powered systems are used for context- and preference-dominated open-ended AI-assisted tasks, like ideating, summarizing, searching, sensemaking, and the reading and writing of text or code.
Work-in-Progress: Crash Course: Can (Under Attack) Autonomous Driving Beat Human Drivers?
Venue: arXiv cs.CR 2024
Year: 2024

Autonomous driving is a research direction that has gained enormous traction in the last few years thanks to advancements in Artificial Intelligence (AI). Depending on the level of independence from the human driver, several studies show that Autonomous Vehicles (AVs) can reduce the number of on-road crashes and decrease overall fuel emissions by improving efficiency. However, security research on this topic is mixed and presents some gaps. On one hand, these studies often neglect the intrinsic vulnerabilities of AI algorithms, which are known to compromise the security of these systems. On the other, the most prevalent attacks towards AI rely on unrealistic assumptions, such as access to the model parameters or the training dataset. As such, it is unclear if autonomous driving can still claim several advantages over human driving in real-world applications. This paper evaluates the inherent risks in autonomous driving by examining the current landscape of AVs and establishing a pragmatic threat model. Through our analysis, we develop specific claims highlighting the delicate balance between the advantages of AVs and potential security challenges in real-world scenarios. Our evaluation serves as a foundation for providing essential takeaway messages, guiding both researchers and practitioners at various stages of the automation pipeline. In doing so, we contribute valuable insights to advance the discourse on the security and viability of autonomous driving in real-world applications.
Representing Information on DNA using Patterns Induced by Enzymatic Labeling
Venue: arXiv cs.IT 2024
Year: 2024

Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a formal framework for modeling DNA labeling in strings, specifically tailored for data storage purposes. Our approach involves a known DNA molecule as a template for labeling, employing patterns induced by a set of designed labels to represent information. One hypothetical implementation can use CRISPR-Cas9 and gRNA reagents for labeling. Various aspects of the general labeling channel, including fixed-length labels, are explored, and upper bounds on the maximal size of the corresponding codes are given. The study includes the development of an efficient encoder-decoder pair that is proven optimal in terms of maximum code size under specific conditions.
Gradient Boosting Mapping for Dimensionality Reduction and Feature Extraction
Venue: arXiv cs.LG 2024
Year: 2024

A fundamental problem in supervised learning is to find a good set of features or distance measures. If the new set of features is of lower dimensionality and can be obtained by a simple transformation of the original data, they can make the model understandable, reduce overfitting, and even help to detect distribution drift. We propose a supervised dimensionality reduction method Gradient Boosting Mapping (GBMAP), where the outputs of weak learners -- defined as one-layer perceptrons -- define the embedding. We show that the embedding coordinates provide better features for the supervised learning task, making simple linear models competitive with the state-of-the-art regressors and classifiers. We also use the embedding to find a principled distance measure between points. The features and distance measures automatically ignore directions irrelevant to the supervised learning task. We also show that we can reliably detect out-of-distribution data points with potentially large regression or classification errors. GBMAP is fast and works in seconds for dataset of million data points or hundreds of features. As a bonus, GBMAP provides a regression and classification performance comparable to the state-of-the-art supervised learning methods.