False Negative/Positive Control for SAM on Noisy Medical Images

The Segment Anything Model (SAM) is a recently developed all-range foundation model for image segmentation. It can use sparse manual prompts such as bounding boxes to generate pixel-level segmentation in natural images but struggles in medical images such as low-contrast, noisy ultrasound images. We propose a refined test-phase prompt augmentation technique designed to improve SAM's performance in medical image segmentation. The method couples multi-box prompt augmentation and an aleatoric uncertainty-based false-negative (FN) and false-positive (FP) correction (FNPC) strategy. We evaluate the method on two ultrasound datasets and show improvement in SAM's performance and robustness to inaccurate prompts, without the necessity for further training or tuning. Moreover, we present the Single-Slice-to-Volume (SS2V) method, enabling 3D pixel-level segmentation using only the bounding box annotation from a single 2D slice. Our results allow efficient use of SAM in even noisy, low-contrast medical images. The source code will be released soon.

CATS v2: Hybrid encoders for robust medical segmentation

Convolutional Neural Networks (CNNs) have exhibited strong performance in medical image segmentation tasks by capturing high-level (local) information, such as edges and textures. However, due to the limited field of view of convolution kernel, it is hard for CNNs to fully represent global information. Recently, transformers have shown good performance for medical image segmentation due to their ability to better model long-range dependencies. Nevertheless, transformers struggle to capture high-level spatial features as effectively as CNNs. A good segmentation model should learn a better representation from local and global features to be both precise and semantically accurate. In our previous work, we proposed CATS, which is a U-shaped segmentation network augmented with transformer encoder. In this work, we further extend this model and propose CATS v2 with hybrid encoders. Specifically, hybrid encoders consist of a CNN-based encoder path paralleled to a transformer path with a shifted window, which better leverage both local and global information to produce robust 3D medical image segmentation. We fuse the information from the convolutional encoder and the transformer at the skip connections of different resolutions to form the final segmentation. The proposed method is evaluated on two public challenge datasets: Cross-Modality Domain Adaptation (CrossMoDA) and task 5 of Medical Segmentation Decathlon (MSD-5), to segment vestibular schwannoma (VS) and prostate, respectively. Compared with the state-of-the-art methods, our approach demonstrates superior performance in terms of higher Dice scores.

When GPT Meets Program Analysis: Towards Intelligent Detection of Smart Contract Logic Vulnerabilities in GPTScan

Smart contracts are prone to various vulnerabilities, leading to substantial financial losses over time. Current analysis tools mainly target vulnerabilities with fixed control or dataflow patterns, such as re-entrancy and integer overflow. However, a recent study on Web3 security bugs revealed that about 80% of these bugs cannot be audited by existing tools due to the lack of domain-specific property description and checking. Given recent advances in Generative Pretraining Transformer (GPT), it is worth exploring how GPT could aid in detecting logic vulnerabilities in smart contracts. In this paper, we propose GPTScan, the first tool combining GPT with static analysis for smart contract logic vulnerability detection. Instead of relying solely on GPT to identify vulnerabilities, which can lead to high false positives and is limited by GPT's pre-trained knowledge, we utilize GPT as a versatile code understanding tool. By breaking down each logic vulnerability type into scenarios and properties, GPTScan matches candidate vulnerabilities with GPT. To enhance accuracy, GPTScan further instructs GPT to intelligently recognize key variables and statements, which are then validated by static confirmation. Evaluation on diverse datasets with around 400 contract projects and 3K Solidity files shows that GPTScan achieves high precision (over 90%) for token contracts and acceptable precision (57.14%) for large projects like Web3Bugs. It effectively detects groundtruth logic vulnerabilities with a recall of over 80%, including 9 new vulnerabilities missed by human auditors. GPTScan is fast and cost-effective, taking an average of 14.39 seconds and 0.01 USD to scan per thousand lines of Solidity code. Moreover, static confirmation helps GPTScan reduce two-thirds of false positives.

COLosSAL: A Benchmark for Cold-start Active Learning for 3D Medical Image Segmentation

Medical image segmentation is a critical task in medical image analysis. In recent years, deep learning based approaches have shown exceptional performance when trained on a fully-annotated dataset. However, data annotation is often a significant bottleneck, especially for 3D medical images. Active learning (AL) is a promising solution for efficient annotation but requires an initial set of labeled samples to start active selection. When the entire data pool is unlabeled, how do we select the samples to annotate as our initial set? This is also known as the cold-start AL, which permits only one chance to request annotations from experts without access to previously annotated data. Cold-start AL is highly relevant in many practical scenarios but has been under-explored, especially for 3D medical segmentation tasks requiring substantial annotation effort. In this paper, we present a benchmark named COLosSAL by evaluating six cold-start AL strategies on five 3D medical image segmentation tasks from the public Medical Segmentation Decathlon collection. We perform a thorough performance analysis and explore important open questions for cold-start AL, such as the impact of budget on different strategies. Our results show that cold-start AL is still an unsolved problem for 3D segmentation tasks but some important trends have been observed. The code repository, data partitions, and baseline results for the complete benchmark are publicly available at https://github.com/MedICL-VU/COLosSAL.

Efficient Action Robust Reinforcement Learning with Probabilistic Policy Execution Uncertainty

Robust reinforcement learning (RL) aims to find a policy that optimizes the worst-case performance in the face of uncertainties. In this paper, we focus on action robust RL with the probabilistic policy execution uncertainty, in which, instead of always carrying out the action specified by the policy, the agent will take the action specified by the policy with probability $1-\rho$ and an alternative adversarial action with probability $\rho$. We establish the existence of an optimal policy on the action robust MDPs with probabilistic policy execution uncertainty and provide the action robust Bellman optimality equation for its solution. Furthermore, we develop Action Robust Reinforcement Learning with Certificates (ARRLC) algorithm that achieves minimax optimal regret and sample complexity. Furthermore, we conduct numerical experiments to validate our approach's robustness, demonstrating that ARRLC outperforms non-robust RL algorithms and converges faster than the robust TD algorithm in the presence of action perturbations.

Learning Multiple Coordinated Agents under Directed Acyclic Graph Constraints

This paper proposes a novel multi-agent reinforcement learning (MARL) method to learn multiple coordinated agents under directed acyclic graph (DAG) constraints. Unlike existing MARL approaches, our method explicitly exploits the DAG structure between agents to achieve more effective learning performance. Theoretically, we propose a novel surrogate value function based on a MARL model with synthetic rewards (MARLM-SR) and prove that it serves as a lower bound of the optimal value function. Computationally, we propose a practical training algorithm that exploits new notion of leader agent and reward generator and distributor agent to guide the decomposed follower agents to better explore the parameter space in environments with DAG constraints. Empirically, we exploit four DAG environments including a real-world scheduling for one of Intel's high volume packaging and test factory to benchmark our methods and show it outperforms the other non-DAG approaches.

HrSegNet : Real-time High-Resolution Neural Network with Semantic Guidance for Crack Segmentation

Through extensive research on deep learning in recent years and its application in construction, crack detection has evolved rapidly from rough detection at the image-level and patch-level to fine-grained detection at the pixel-level, which better suits the nature of this field. Despite numerous existing studies utilizing off-the-shelf deep learning models or enhancing them, these models are not always effective or efficient in real-world applications. In order to bridge this gap, we propose a High-resolution model with Semantic guidance, specifically designed for real-time crack segmentation, referred to as HrSegNet. Our model maintains high resolution throughout the entire process, as opposed to recovering from low-resolution features to high-resolution ones, thereby maximizing the preservation of crack details. Moreover, to enhance the context information, we use low-resolution semantic features to guide the reconstruction of high-resolution features. To ensure the efficiency of the algorithm, we design a simple yet effective method to control the computation cost of the entire model by controlling the capacity of high-resolution channels, while providing the model with extremely strong scalability. Extensive quantitative and qualitative evaluations demonstrate that our proposed HrSegNet has exceptional crack segmentation capabilities, and that maintaining high resolution and semantic guidance are crucial to the final prediction. Compared to state-of-the-art segmentation models, HrSegNet achieves the best trade-off between efficiency and effectiveness. Specifically, on the crack dataset CrackSeg9k, our fastest model HrSegNet-B16 achieves a speed of 182 FPS with 78.43% mIoU, while our most accurate model HrSegNet-B48 achieves 80.32% mIoU with an inference speed of 140.3 FPS.

VesselMorph: Domain-Generalized Retinal Vessel Segmentation via Shape-Aware Representation

Due to the absence of a single standardized imaging protocol, domain shift between data acquired from different sites is an inherent property of medical images and has become a major obstacle for large-scale deployment of learning-based algorithms. For retinal vessel images, domain shift usually presents as the variation of intensity, contrast and resolution, while the basic tubular shape of vessels remains unaffected. Thus, taking advantage of such domain-invariant morphological features can greatly improve the generalizability of deep models. In this study, we propose a method named VesselMorph which generalizes the 2D retinal vessel segmentation task by synthesizing a shape-aware representation. Inspired by the traditional Frangi filter and the diffusion tensor imaging literature, we introduce a Hessian-based bipolar tensor field to depict the morphology of the vessels so that the shape information is taken into account. We map the intensity image and the tensor field to a latent space for feature extraction. Then we fuse the two latent representations via a weight-balancing trick and feed the result to a segmentation network. We evaluate on six public datasets of fundus and OCT angiography images from diverse patient populations. VesselMorph achieves superior generalization performance compared with competing methods in different domain shift scenarios.

DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates $28$ distinct datasets across $7$ tasks, with input lengths ranging from $70$ to $1000$. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with $21 \times$ fewer parameters and approximately $56 \times$ less GPU time in pre-training.

Feature Programming for Multivariate Time Series Prediction

We introduce the concept of programmable feature engineering for time series modeling and propose a feature programming framework. This framework generates large amounts of predictive features for noisy multivariate time series while allowing users to incorporate their inductive bias with minimal effort. The key motivation of our framework is to view any multivariate time series as a cumulative sum of fine-grained trajectory increments, with each increment governed by a novel spin-gas dynamical Ising model. This fine-grained perspective motivates the development of a parsimonious set of operators that summarize multivariate time series in an abstract fashion, serving as the foundation for large-scale automated feature engineering. Numerically, we validate the efficacy of our method on several synthetic and real-world noisy time series datasets.