OpenRaiser/Intern-Atlas huggingface dataset:
RoCP-GNN: Robust Conformal Prediction for Graph Neural Networks in Node-Classification
Venue: arXiv cs.LG 2024
Year: 2024

Graph Neural Networks (GNNs) have emerged as powerful tools for predicting outcomes in graph-structured data. However, a notable limitation of GNNs is their inability to provide robust uncertainty estimates, which undermines their reliability in contexts where errors are costly. One way to address this issue is by providing prediction sets that contain the true label with a predefined probability margin. Our approach builds upon conformal prediction (CP), a framework that promises to construct statistically robust prediction sets or intervals. There are two primary challenges: first, given dependent data like graphs, it is unclear whether the critical assumption in CP - exchangeability - still holds when applied to node classification. Second, even if the exchangeability assumption is valid for conformalized link prediction, we need to ensure high efficiency, i.e., the resulting prediction set or the interval length is small enough to provide useful information. In this article, we propose a novel approach termed Robust Conformal Prediction for GNNs (RoCP-GNN), which integrates conformal prediction (CP) directly into the GNN training process. This method generates prediction sets, instead of just point predictions, that are valid at a user-defined confidence level, assuming only exchangeability. Our approach robustly predicts outcomes with any predictive GNN model while quantifying the uncertainty in predictions within the realm of graph-based semi-supervised learning (SSL). Experimental results demonstrate that GNN models with size loss provide a statistically significant increase in performance. We validate our approach on standard graph benchmark datasets by coupling it with various state-of-the-art GNNs in node classification. The code will be made available after publication.
Biomedical Large Languages Models Seem not to be Superior to Generalist Models on Unseen Medical Data
Venue: arXiv cs.CL 2024
Year: 2024

Large language models (LLMs) have shown potential in biomedical applications, leading to efforts to fine-tune them on domain-specific data. However, the effectiveness of this approach remains unclear. This study evaluates the performance of biomedically fine-tuned LLMs against their general-purpose counterparts on a variety of clinical tasks. We evaluated their performance on clinical case challenges from the New England Journal of Medicine (NEJM) and the Journal of the American Medical Association (JAMA) and on several clinical tasks (e.g., information extraction, document summarization, and clinical coding). Using benchmarks specifically chosen to be likely outside the fine-tuning datasets of biomedical models, we found that biomedical LLMs mostly perform inferior to their general-purpose counterparts, especially on tasks not focused on medical knowledge. While larger models showed similar performance on case tasks (e.g., OpenBioLLM-70B: 66.4% vs. Llama-3-70B-Instruct: 65% on JAMA cases), smaller biomedical models showed more pronounced underperformance (e.g., OpenBioLLM-8B: 30% vs. Llama-3-8B-Instruct: 64.3% on NEJM cases). Similar trends were observed across the CLUE (Clinical Language Understanding Evaluation) benchmark tasks, with general-purpose models often performing better on text generation, question answering, and coding tasks. Our results suggest that fine-tuning LLMs to biomedical data may not provide the expected benefits and may potentially lead to reduced performance, challenging prevailing assumptions about domain-specific adaptation of LLMs and highlighting the need for more rigorous evaluation frameworks in healthcare AI. Alternative approaches, such as retrieval-augmented generation, may be more effective in enhancing the biomedical capabilities of LLMs without compromising their general knowledge.
An NP-hard generalization of Nim
Venue: arXiv cs.GT 2024
Year: 2024

A new combinatorial game is given. It generalizes both Substraction and Nim. It is proved the computation of Nash equilibrium points in this new game is NP-hard.
Tangram: Benchmark for Evaluating Geometric Element Recognition in Large Multimodal Models
Venue: arXiv cs.CV 2024
Year: 2024

Significant advancements in Large Multimodal Models (LMMs) have enabled them to tackle complex problems involving visual-mathematical reasoning. However, their ability to identify geometric elements remains underexplored. To address this gap, we introduce Tangram, a novel benchmark designed to evaluate the performance of LMMs on geometric element recognition. Tangram comprises 1,080 diverse geometric diagrams sourced from primary and secondary school exams, competitions, and textbooks, ranging from simple geometric shapes to complex combinations. Each diagram is paired with four questions, resulting in 4,320 visual-question-answer pairs. Unlike existing benchmarks that emphasize higher-level cognition and reasoning, Tangram focuses on understanding geometric elements, requiring models to perform a ``simple yet challenging" counting task. Systematic evaluation of 13 prominent LMMs, such as GPT-4o and Claude 3.5 Sonnet, reveals that these models face significant challenges even in seemingly straightforward tasks. The top-performing model achieves an accuracy of only 53.0%, highlighting a substantial gap compared to human performance. These findings underscore the limitations of current multimodal AI systems in handling basic perception tasks and serve to inspire the development of the next generation of expert-level multimodal foundational models. The data and code will be released soon.
SpeechCaps: Advancing Instruction-Based Universal Speech Models with Multi-Talker Speaking Style Captioning
Venue: arXiv cs.CL 2024
Year: 2024

Instruction-based speech processing is becoming popular. Studies show that training with multiple tasks boosts performance, but collecting diverse, large-scale tasks and datasets is expensive. Thus, it is highly desirable to design a fundamental task that benefits other downstream tasks. This paper introduces a multi-talker speaking style captioning task to enhance the understanding of speaker and prosodic information. We used large language models to generate descriptions for multi-talker speech. Then, we trained our model with pre-training on this captioning task followed by instruction tuning. Evaluation on Dynamic-SUPERB shows our model outperforming the baseline pre-trained only on single-talker tasks, particularly in speaker and emotion recognition. Additionally, tests on a multi-talker QA task reveal that current models struggle with attributes such as gender, pitch, and speaking rate. The code and dataset are available at https://github.com/cyhuang-tw/speechcaps.
SimpleSpeech 2: Towards Simple and Efficient Text-to-Speech with Flow-based Scalar Latent Transformer Diffusion Models
Venue: arXiv cs.SD 2024
Year: 2024

Scaling Text-to-speech (TTS) to large-scale datasets has been demonstrated as an effective method for improving the diversity and naturalness of synthesized speech. At the high level, previous large-scale TTS models can be categorized into either Auto-regressive (AR) based (\textit{e.g.}, VALL-E) or Non-auto-regressive (NAR) based models (\textit{e.g.}, NaturalSpeech 2/3). Although these works demonstrate good performance, they still have potential weaknesses. For instance, AR-based models are plagued by unstable generation quality and slow generation speed; meanwhile, some NAR-based models need phoneme-level duration alignment information, thereby increasing the complexity of data pre-processing, model design, and loss design. In this work, we build upon our previous publication by implementing a simple and efficient non-autoregressive (NAR) TTS framework, termed SimpleSpeech 2. SimpleSpeech 2 effectively combines the strengths of both autoregressive (AR) and non-autoregressive (NAR) methods, offering the following key advantages: (1) simplified data preparation; (2) straightforward model and loss design; and (3) stable, high-quality generation performance with fast inference speed. Compared to our previous publication, we present ({\romannumeral1}) a detailed analysis of the influence of speech tokenizer and noisy label for TTS performance; ({\romannumeral2}) four distinct types of sentence duration predictors; ({\romannumeral3}) a novel flow-based scalar latent transformer diffusion model. With these improvement, we show a significant improvement in generation performance and generation speed compared to our previous work and other state-of-the-art (SOTA) large-scale TTS models. Furthermore, we show that SimpleSpeech 2 can be seamlessly extended to multilingual TTS by training it on multilingual speech datasets. Demos are available on: {https://dongchaoyang.top/SimpleSpeech2\_demo/}.
Time Series Analysis for Education: Methods, Applications, and Future Directions
Venue: arXiv cs.LG 2024
Year: 2024

Recent advancements in the collection and analysis of sequential educational data have brought time series analysis to a pivotal position in educational research, highlighting its essential role in facilitating data-driven decision-making. However, there is a lack of comprehensive summaries that consolidate these advancements. To the best of our knowledge, this paper is the first to provide a comprehensive review of time series analysis techniques specifically within the educational context. We begin by exploring the landscape of educational data analytics, categorizing various data sources and types relevant to education. We then review four prominent time series methods-forecasting, classification, clustering, and anomaly detection-illustrating their specific application points in educational settings. Subsequently, we present a range of educational scenarios and applications, focusing on how these methods are employed to address diverse educational tasks, which highlights the practical integration of multiple time series methods to solve complex educational problems. Finally, we conclude with a discussion on future directions, including personalized learning analytics, multimodal data fusion, and the role of large language models (LLMs) in educational time series. The contributions of this paper include a detailed taxonomy of educational data, a synthesis of time series techniques with specific educational applications, and a forward-looking perspective on emerging trends and future research opportunities in educational analysis. The related papers and resources are available and regularly updated at the project page.
Shifted Window Fourier Transform And Retention For Image Captioning
Venue: arXiv cs.CV 2024
Year: 2024

Image Captioning is an important Language and Vision task that finds application in a variety of contexts, ranging from healthcare to autonomous vehicles. As many real-world applications rely on devices with limited resources, much effort in the field was put into the development of lighter and faster models. However, much of the current optimizations focus on the Transformer architecture in contrast to the existence of more efficient methods. In this work, we introduce SwiFTeR, an architecture almost entirely based on Fourier Transform and Retention, to tackle the main efficiency bottlenecks of current light image captioning models, being the visual backbone's onerosity, and the decoder's quadratic cost. SwiFTeR is made of only 20M parameters, and requires 3.1 GFLOPs for a single forward pass. Additionally, it showcases superior scalability to the caption length and its small memory requirements enable more images to be processed in parallel, compared to the traditional transformer-based architectures. For instance, it can generate 400 captions in one second. Although, for the time being, the caption quality is lower (110.2 CIDEr-D), most of the decrease is not attributed to the architecture but rather an incomplete training practice which currently leaves much room for improvements. Overall, SwiFTeR points toward a promising direction to new efficient architectural design. The implementation code will be released in the future.
Law and Order for Typestate with Borrowing
Venue: arXiv cs.PL 2024
Year: 2024

Typestate systems are notoriously complex as they require sophisticated machinery for tracking aliasing. We propose a new, transition-oriented foundation for typestate in the setting of impure functional programming. Our approach relies on ordered types for simple alias tracking and its formalization draws on work on bunched implications. Yet, we support a flexible notion of borrowing in the presence of typestate. Our core calculus comes with a notion of resource types indexed by an ordered partial monoid that models abstract state transitions. We prove syntactic type soundness with respect to a resource-instrumented semantics. We give an algorithmic version of our type system and prove its soundness. Algorithmic typing facilitates a simple surface language that does not expose tedious details of ordered types. We implemented a typechecker for the surface language along with an interpreter for the core language.
Beyond Detection: Leveraging Large Language Models for Cyber Attack Prediction in IoT Networks
Venue: arXiv cs.CR 2024
Year: 2024

In recent years, numerous large-scale cyberattacks have exploited Internet of Things (IoT) devices, a phenomenon that is expected to escalate with the continuing proliferation of IoT technology. Despite considerable efforts in attack detection, intrusion detection systems remain mostly reactive, responding to specific patterns or observed anomalies. This work proposes a proactive approach to anticipate and mitigate malicious activities before they cause damage. This paper proposes a novel network intrusion prediction framework that combines Large Language Models (LLMs) with Long Short Term Memory (LSTM) networks. The framework incorporates two LLMs in a feedback loop: a fine-tuned Generative Pre-trained Transformer (GPT) model for predicting network traffic and a fine-tuned Bidirectional Encoder Representations from Transformers (BERT) for evaluating the predicted traffic. The LSTM classifier model then identifies malicious packets among these predictions. Our framework, evaluated on the CICIoT2023 IoT attack dataset, demonstrates a significant improvement in predictive capabilities, achieving an overall accuracy of 98%, offering a robust solution to IoT cybersecurity challenges.
Let Video Teaches You More: Video-to-Image Knowledge Distillation using DEtection TRansformer for Medical Video Lesion Detection
Venue: arXiv cs.CV 2024
Year: 2024

AI-assisted lesion detection models play a crucial role in the early screening of cancer. However, previous image-based models ignore the inter-frame contextual information present in videos. On the other hand, video-based models capture the inter-frame context but are computationally expensive. To mitigate this contradiction, we delve into Video-to-Image knowledge distillation leveraging DEtection TRansformer (V2I-DETR) for the task of medical video lesion detection. V2I-DETR adopts a teacher-student network paradigm. The teacher network aims at extracting temporal contexts from multiple frames and transferring them to the student network, and the student network is an image-based model dedicated to fast prediction in inference. By distilling multi-frame contexts into a single frame, the proposed V2I-DETR combines the advantages of utilizing temporal contexts from video-based models and the inference speed of image-based models. Through extensive experiments, V2I-DETR outperforms previous state-of-the-art methods by a large margin while achieving the real-time inference speed (30 FPS) as the image-based model.
Using the SOCIO Chatbot for UML Modelling: A Family of Experiments
Venue: arXiv cs.SE 2024
Year: 2024

Context: Recent developments in natural language processing have facilitated the adoption of chatbots in typically collaborative software engineering tasks (such as diagram modelling). Families of experiments can assess the performance of tools and processes and, at the same time, alleviate some of the typical shortcomings of individual experiments (e.g., inaccurate and potentially biased results due to a small number of participants). Objective: Compare the usability of a chatbot for collaborative modelling (i.e., SOCIO) and an online web tool (i.e., Creately). Method: We conducted a family of three experiments to evaluate the usability of SOCIO against the Creately online collaborative tool in academic settings. Results: The student participants were faster at building class diagrams using the chatbot than with the online collaborative tool and more satisfied with SOCIO. Besides, the class diagrams built using the chatbot tended to be more concise -albeit slightly less complete. Conclusion: Chatbots appear to be helpful for building class diagrams. In fact, our study has helped us to shed light on the future direction for experimentation in this field and lays the groundwork for researching the applicability of chatbots in diagramming.
Rorqual: Speeding up Narwhal with TEEs
Venue: arXiv cs.DC 2024
Year: 2024

In this paper, we introduce Rorqual, a protocol designed to enhance the performance of the Narwhal Mempool by integrating Trusted Execution Environments (TEEs). Both Narwhal and Roqual are protocols based on a Directed Acyclic Graph (DAG). Compared to Narwhal, Rorqual achieves significant reductions in latency and increases throughput by streamlining the steps required to include a vertex in the DAG. The use of TEEs also reduces the communication complexity of the protocol while maintaining low computational costs. Through rigorous analysis, we demonstrate the protocol's robustness under both normal and adversarial conditions, highlighting its improvements in throughput, latency, and security.
ShapeMamba-EM: Fine-Tuning Foundation Model with Local Shape Descriptors and Mamba Blocks for 3D EM Image Segmentation
Venue: arXiv cs.CV 2024
Year: 2024

Electron microscopy (EM) imaging offers unparalleled resolution for analyzing neural tissues, crucial for uncovering the intricacies of synaptic connections and neural processes fundamental to understanding behavioral mechanisms. Recently, the foundation models have demonstrated impressive performance across numerous natural and medical image segmentation tasks. However, applying these foundation models to EM segmentation faces significant challenges due to domain disparities. This paper presents ShapeMamba-EM, a specialized fine-tuning method for 3D EM segmentation, which employs adapters for long-range dependency modeling and an encoder for local shape description within the original foundation model. This approach effectively addresses the unique volumetric and morphological complexities of EM data. Tested over a wide range of EM images, covering five segmentation tasks and 10 datasets, ShapeMamba-EM outperforms existing methods, establishing a new standard in EM image segmentation and enhancing the understanding of neural tissue architecture.
Towards Lifelong Learning Embeddings: An Algorithmic Approach to Dynamically Extend Embeddings
Venue: arXiv cs.LG 2024
Year: 2024

The rapid evolution of technology has transformed business operations and customer interactions worldwide, with personalization emerging as a key opportunity for e-commerce companies to engage customers more effectively. The application of machine learning, particularly that of deep learning models, has gained significant traction due to its ability to rapidly recognize patterns in large datasets, thereby offering numerous possibilities for personalization. These models use embeddings to map discrete information, such as product IDs, into a latent vector space, a method increasingly popular in recent years. However, e-commerce's dynamic nature, characterized by frequent new product introductions, poses challenges for these embeddings, which typically require fixed dimensions and inputs, leading to the need for periodic retraining from scratch. This paper introduces a modular algorithm that extends embedding input size while preserving learned knowledge, addressing the challenges posed by e-commerce's dynamism. The proposed algorithm also incorporates strategies to mitigate the cold start problem associated with new products. The results of initial experiments suggest that this method outperforms traditional embeddings.
GenFormer -- Generated Images are All You Need to Improve Robustness of Transformers on Small Datasets
Venue: arXiv cs.CV 2024
Year: 2024

Recent studies showcase the competitive accuracy of Vision Transformers (ViTs) in relation to Convolutional Neural Networks (CNNs), along with their remarkable robustness. However, ViTs demand a large amount of data to achieve adequate performance, which makes their application to small datasets challenging, falling behind CNNs. To overcome this, we propose GenFormer, a data augmentation strategy utilizing generated images, thereby improving transformer accuracy and robustness on small-scale image classification tasks. In our comprehensive evaluation we propose Tiny ImageNetV2, -R, and -A as new test set variants of Tiny ImageNet by transferring established ImageNet generalization and robustness benchmarks to the small-scale data domain. Similarly, we introduce MedMNIST-C and EuroSAT-C as corrupted test set variants of established fine-grained datasets in the medical and aerial domain. Through a series of experiments conducted on small datasets of various domains, including Tiny ImageNet, CIFAR, EuroSAT and MedMNIST datasets, we demonstrate the synergistic power of our method, in particular when combined with common train and test time augmentations, knowledge distillation, and architectural design choices. Additionally, we prove the effectiveness of our approach under challenging conditions with limited training data, demonstrating significant improvements in both accuracy and robustness, bridging the gap between CNNs and ViTs in the small-scale dataset domain.
Foodfusion: A Novel Approach for Food Image Composition via Diffusion Models
Venue: arXiv cs.CV 2024
Year: 2024

Food image composition requires the use of existing dish images and background images to synthesize a natural new image, while diffusion models have made significant advancements in image generation, enabling the construction of end-to-end architectures that yield promising results. However, existing diffusion models face challenges in processing and fusing information from multiple images and lack access to high-quality publicly available datasets, which prevents the application of diffusion models in food image composition. In this paper, we introduce a large-scale, high-quality food image composite dataset, FC22k, which comprises 22,000 foreground, background, and ground truth ternary image pairs. Additionally, we propose a novel food image composition method, Foodfusion, which leverages the capabilities of the pre-trained diffusion models and incorporates a Fusion Module for processing and integrating foreground and background information. This fused information aligns the foreground features with the background structure by merging the global structural information at the cross-attention layer of the denoising UNet. To further enhance the content and structure of the background, we also integrate a Content-Structure Control Module. Extensive experiments demonstrate the effectiveness and scalability of our proposed method.