In this article, we propose a new metaheuristic inspired by the morphogenetic cellular movements of endothelial cells (ECs) that occur during the tumor angiogenesis process. This algorithm starts with a random initial population. In each iteration, the best candidate selected as the tumor, while the other individuals in the population are treated as ECs migrating toward the tumor's direction following a coordinated dynamics through a spatial relationship between tip and follower ECs. This algorithm has an advantage compared to other similar optimization metaheuristics: the model parameters are already configured according to the tumor angiogenesis phenomenon modeling, preventing researchers from initializing them with arbitrary values. Subsequently, the algorithm is compared against well-known benchmark functions, and the results are validated through a comparative study with Particle Swarm Optimization (PSO). The results demonstrate that the algorithm is capable of providing highly competitive outcomes. Furthermore, the proposed algorithm is applied to real-world problems (cantilever beam design, pressure vessel design, tension/compression spring and sustainable explotation renewable resource). The results showed that the proposed algorithm worked effectively in solving constrained optimization problems. The results obtained were compared with several known algorithms.
We present a hierarchical Bayesian pipeline, BP3M, that measures positions, parallaxes, and proper motions (PMs) for cross-matched sources between Hubble~Space~Telescope (HST) images and Gaia -- even for sparse fields ($N_*<10$ per image) -- expanding from the recent GaiaHub tool. This technique uses Gaia-measured astrometry as priors to predict the locations of sources in HST images, and is therefore able to put the HST images onto a global reference frame without the use of background galaxies/QSOs. Testing our publicly-available code in the Fornax and Draco dSphs, we measure accurate PMs that are a median of 8-13 times more precise than Gaia DR3 alone for $20.5<G<21~\mathrm{mag}$. We are able to explore the effect of observation strategies on BP3M astrometry using synthetic data, finding an optimal strategy to improve parallax and position precision at no cost to the PM uncertainty. Using 1619 HST images in the sparse COSMOS field (median 9 Gaia sources per HST image), we measure BP3M PMs for 2640 unique sources in the $16<G<21.5~\mathrm{mag}$ range, 25% of which have no Gaia PMs; the median BP3M PM uncertainty for $20.25<G<20.75~\mathrm{mag}$ sources is $0.44~$mas/yr compared to $1.03~$mas/yr from Gaia, while the median BP3M PM uncertainty for sources without Gaia-measured PMs ($20.75<G<21.5~\mathrm{mag}$) is $1.16~$mas/yr. The statistics that underpin the BP3M pipeline are a generalized way of combining position measurements from different images, epochs, and telescopes, which allows information to be shared between surveys and archives to achieve higher astrometric precision than that from each catalog alone.
Metagenomics, the study of genome sequences of diverse organisms cohabiting in a shared environment, has experienced significant advancements across various medical and biological fields. Metagenomic analysis is crucial, for instance, in clinical applications such as infectious disease screening and the diagnosis and early detection of diseases such as cancer. A key task in metagenomics is to determine the species present in a sample and their relative abundances. Currently, the field is dominated by either alignment-based tools, which offer high accuracy but are computationally expensive, or alignment-free tools, which are fast but lack the needed accuracy for many applications. In response to this dichotomy, we introduce MetaFast, a tool based on heuristics, to achieve a fundamental improvement in accuracy-runtime tradeoff over existing methods. MetaFast delivers accuracy comparable to the alignment-based and highly accurate tool Metalign but with significantly enhanced efficiency. In MetaFast, we accelerate memory-frugal reference database indexing and filtering. We further employ heuristics to accelerate read mapping. Our evaluation demonstrates that MetaFast achieves a 4x speedup over Metalign without compromising accuracy. MetaFast is publicly available on: //github.com/CMU-SAFARI/MetaFast.
The evaluation of the fidelity of eXplainable Artificial Intelligence (XAI) methods to their underlying models is a challenging task, primarily due to the absence of a ground truth for explanations. However, assessing fidelity is a necessary step for ensuring a correct XAI methodology. In this study, we conduct a fair and objective comparison of the current state-of-the-art XAI methods by introducing three novel image datasets with reliable ground truth for explanations. The primary objective of this comparison is to identify methods with low fidelity and eliminate them from further research, thereby promoting the development of more trustworthy and effective XAI techniques. Our results demonstrate that XAI methods based on the backpropagation of output information to input yield higher accuracy and reliability compared to methods relying on sensitivity analysis or Class Activation Maps (CAM). However, the backpropagation method tends to generate more noisy saliency maps. These findings have significant implications for the advancement of XAI methods, enabling the elimination of erroneous explanations and fostering the development of more robust and reliable XAI.
Advancements in deep learning-based 3D object detection necessitate the availability of large-scale datasets. However, this requirement introduces the challenge of manual annotation, which is often both burdensome and time-consuming. To tackle this issue, the literature has seen the emergence of several weakly supervised frameworks for 3D object detection which can automatically generate pseudo labels for unlabeled data. Nevertheless, these generated pseudo labels contain noise and are not as accurate as those labeled by humans. In this paper, we present the first approach that addresses the inherent ambiguities present in pseudo labels by introducing an Evidential Deep Learning (EDL) based uncertainty estimation framework. Specifically, we propose MEDL-U, an EDL framework based on MTrans, which not only generates pseudo labels but also quantifies the associated uncertainties. However, applying EDL to 3D object detection presents three primary challenges: (1) relatively lower pseudolabel quality in comparison to other autolabelers; (2) excessively high evidential uncertainty estimates; and (3) lack of clear interpretability and effective utilization of uncertainties for downstream tasks. We tackle these issues through the introduction of an uncertainty-aware IoU-based loss, an evidence-aware multi-task loss function, and the implementation of a post-processing stage for uncertainty refinement. Our experimental results demonstrate that probabilistic detectors trained using the outputs of MEDL-U surpass deterministic detectors trained using outputs from previous 3D annotators on the KITTI val set for all difficulty levels. Moreover, MEDL-U achieves state-of-the-art results on the KITTI official test set compared to existing 3D automatic annotators.
Data pruning, which aims to downsize a large training set into a small informative subset, is crucial for reducing the enormous computational costs of modern deep learning. Though large-scale data collections invariably contain annotation noise and numerous robust learning methods have been developed, data pruning for the noise-robust learning scenario has received little attention. With state-of-the-art Re-labeling methods that self-correct erroneous labels while training, it is challenging to identify which subset induces the most accurate re-labeling of erroneous labels in the entire training set. In this paper, we formalize the problem of data pruning with re-labeling. We first show that the likelihood of a training example being correctly re-labeled is proportional to the prediction confidence of its neighborhood in the subset. Therefore, we propose a novel data pruning algorithm, Prune4Rel, that finds a subset maximizing the total neighborhood confidence of all training examples, thereby maximizing the re-labeling accuracy and generalization performance. Extensive experiments on four real and one synthetic noisy datasets show that \algname{} outperforms the baselines with Re-labeling models by up to 9.1% as well as those with a standard model by up to 21.6%.
Recently, graph neural networks have been gaining a lot of attention to simulate dynamical systems due to their inductive nature leading to zero-shot generalizability. Similarly, physics-informed inductive biases in deep-learning frameworks have been shown to give superior performance in learning the dynamics of physical systems. There is a growing volume of literature that attempts to combine these two approaches. Here, we evaluate the performance of thirteen different graph neural networks, namely, Hamiltonian and Lagrangian graph neural networks, graph neural ODE, and their variants with explicit constraints and different architectures. We briefly explain the theoretical formulation highlighting the similarities and differences in the inductive biases and graph architecture of these systems. We evaluate these models on spring, pendulum, gravitational, and 3D deformable solid systems to compare the performance in terms of rollout error, conserved quantities such as energy and momentum, and generalizability to unseen system sizes. Our study demonstrates that GNNs with additional inductive biases, such as explicit constraints and decoupling of kinetic and potential energies, exhibit significantly enhanced performance. Further, all the physics-informed GNNs exhibit zero-shot generalizability to system sizes an order of magnitude larger than the training system, thus providing a promising route to simulate large-scale realistic systems.
Although measuring held-out accuracy has been the primary approach to evaluate generalization, it often overestimates the performance of NLP models, while alternative approaches for evaluating models either focus on individual tasks or on specific behaviors. Inspired by principles of behavioral testing in software engineering, we introduce CheckList, a task-agnostic methodology for testing NLP models. CheckList includes a matrix of general linguistic capabilities and test types that facilitate comprehensive test ideation, as well as a software tool to generate a large and diverse number of test cases quickly. We illustrate the utility of CheckList with tests for three tasks, identifying critical failures in both commercial and state-of-art models. In a user study, a team responsible for a commercial sentiment analysis model found new and actionable bugs in an extensively tested model. In another user study, NLP practitioners with CheckList created twice as many tests, and found almost three times as many bugs as users without it.
In recent years, disinformation including fake news, has became a global phenomenon due to its explosive growth, particularly on social media. The wide spread of disinformation and fake news can cause detrimental societal effects. Despite the recent progress in detecting disinformation and fake news, it is still non-trivial due to its complexity, diversity, multi-modality, and costs of fact-checking or annotation. The goal of this chapter is to pave the way for appreciating the challenges and advancements via: (1) introducing the types of information disorder on social media and examine their differences and connections; (2) describing important and emerging tasks to combat disinformation for characterization, detection and attribution; and (3) discussing a weak supervision approach to detect disinformation with limited labeled data. We then provide an overview of the chapters in this book that represent the recent advancements in three related parts: (1) user engagements in the dissemination of information disorder; (2) techniques on detecting and mitigating disinformation; and (3) trending issues such as ethics, blockchain, clickbaits, etc. We hope this book to be a convenient entry point for researchers, practitioners, and students to understand the problems and challenges, learn state-of-the-art solutions for their specific needs, and quickly identify new research problems in their domains.
In this paper, we focus on three problems in deep learning based medical image segmentation. Firstly, U-net, as a popular model for medical image segmentation, is difficult to train when convolutional layers increase even though a deeper network usually has a better generalization ability because of more learnable parameters. Secondly, the exponential ReLU (ELU), as an alternative of ReLU, is not much different from ReLU when the network of interest gets deep. Thirdly, the Dice loss, as one of the pervasive loss functions for medical image segmentation, is not effective when the prediction is close to ground truth and will cause oscillation during training. To address the aforementioned three problems, we propose and validate a deeper network that can fit medical image datasets that are usually small in the sample size. Meanwhile, we propose a new loss function to accelerate the learning process and a combination of different activation functions to improve the network performance. Our experimental results suggest that our network is comparable or superior to state-of-the-art methods.
We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.