Artificial Intelligence for Microbiology and Microbiome Research

Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine learning and deep learning applications. This review provides a comprehensive overview of AI-driven approaches tailored for microbiology and microbiome studies, emphasizing both technical advancements and biological insights. We begin with an introduction to foundational AI techniques, including primary machine learning paradigms and various deep learning architectures, and offer guidance on choosing between machine learning and deep learning methods based on specific research goals. The primary section on application scenarios spans diverse research areas, from taxonomic profiling, functional annotation & prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, clinical microbiology, to prevention & therapeutics. Finally, we discuss challenges unique to this field, including the balance between interpretability and complexity, the "small n, large p" problem, and the critical need for standardized benchmarking datasets to validate and compare models. Together, this review underscores AI's transformative role in microbiology and microbiome research, paving the way for innovative methodologies and applications that enhance our understanding of microbial life and its impact on our planet and our health.

Improving Decision Sparsity

Sparsity is a central aspect of interpretability in machine learning. Typically, sparsity is measured in terms of the size of a model globally, such as the number of variables it uses. However, this notion of sparsity is not particularly relevant for decision-making; someone subjected to a decision does not care about variables that do not contribute to the decision. In this work, we dramatically expand a notion of decision sparsity called the Sparse Explanation Value(SEV) so that its explanations are more meaningful. SEV considers movement along a hypercube towards a reference point. By allowing flexibility in that reference and by considering how distances along the hypercube translate to distances in feature space, we can derive sparser and more meaningful explanations for various types of function classes. We present cluster-based SEV and its variant tree-based SEV, introduce a method that improves credibility of explanations, and propose algorithms that optimize decision sparsity in machine learning models.

BFA-YOLO: Balanced multiscale object detection network for multi-view building facade attachments detection

Detection of building facade attachments such as doors, windows, balconies, air conditioner units, billboards, and glass curtain walls plays a pivotal role in numerous applications. Building facade attachments detection aids in vbuilding information modeling (BIM) construction and meeting Level of Detail 3 (LOD3) standards. Yet, it faces challenges like uneven object distribution, small object detection difficulty, and background interference. To counter these, we propose BFA-YOLO, a model for detecting facade attachments in multi-view images. BFA-YOLO incorporates three novel innovations: the Feature Balanced Spindle Module (FBSM) for addressing uneven distribution, the Target Dynamic Alignment Task Detection Head (TDATH) aimed at improving small object detection, and the Position Memory Enhanced Self-Attention Mechanism (PMESA) to combat background interference, with each component specifically designed to solve its corresponding challenge. Detection efficacy of deep network models deeply depends on the dataset's characteristics. Existing open source datasets related to building facades are limited by their single perspective, small image pool, and incomplete category coverage. We propose a novel method for building facade attachments detection dataset construction and construct the BFA-3D dataset for facade attachments detection. The BFA-3D dataset features multi-view, accurate labels, diverse categories, and detailed classification. BFA-YOLO surpasses YOLOv8 by 1.8% and 2.9% in mAP@0.5 on the multi-view BFA-3D and street-view Facade-WHU datasets, respectively. These results underscore BFA-YOLO's superior performance in detecting facade attachments.

From Model Explanation to Data Misinterpretation: Uncovering the Pitfalls of Post Hoc Explainers in Business Research

Machine learning models have been increasingly used in business research. However, most state-of-the-art machine learning models, such as deep neural networks and XGBoost, are black boxes in nature. Therefore, post hoc explainers that provide explanations for machine learning models by, for example, estimating numerical importance of the input features, have been gaining wide usage. Despite the intended use of post hoc explainers being explaining machine learning models, we found a growing trend in business research where post hoc explanations are used to draw inferences about the data. In this work, we investigate the validity of such use. Specifically, we investigate with extensive experiments whether the explanations obtained by the two most popular post hoc explainers, SHAP and LIME, provide correct information about the true marginal effects of X on Y in the data, which we call data-alignment. We then identify what factors influence the alignment of explanations. Finally, we propose a set of mitigation strategies to improve the data-alignment of explanations and demonstrate their effectiveness with real-world data in an econometric context. In spite of this effort, we nevertheless conclude that it is often not appropriate to infer data insights from post hoc explanations. We articulate appropriate alternative uses, the most important of which is to facilitate the proposition and subsequent empirical investigation of hypotheses. The ultimate goal of this paper is to caution business researchers against translating post hoc explanations of machine learning models into potentially false insights and understanding of data.

TextMastero: Mastering High-Quality Scene Text Editing in Diverse Languages and Styles

Scene text editing aims to modify texts on images while maintaining the style of newly generated text similar to the original. Given an image, a target area, and target text, the task produces an output image with the target text in the selected area, replacing the original. This task has been studied extensively, with initial success using Generative Adversarial Networks (GANs) to balance text fidelity and style similarity. However, GAN-based methods struggled with complex backgrounds or text styles. Recent works leverage diffusion models, showing improved results, yet still face challenges, especially with non-Latin languages like CJK characters (Chinese, Japanese, Korean) that have complex glyphs, often producing inaccurate or unrecognizable characters. To address these issues, we present \emph{TextMastero} - a carefully designed multilingual scene text editing architecture based on latent diffusion models (LDMs). TextMastero introduces two key modules: a glyph conditioning module for fine-grained content control in generating accurate texts, and a latent guidance module for providing comprehensive style information to ensure similarity before and after editing. Both qualitative and quantitative experiments demonstrate that our method surpasses all known existing works in text fidelity and style similarity.

Using Advanced LLMs to Enhance Smaller LLMs: An Interpretable Knowledge Distillation Approach

Advanced Large language models (LLMs) like GPT-4 or LlaMa 3 provide superior performance in complex human-like interactions. But they are costly, or too large for edge devices such as smartphones and harder to self-host, leading to security and privacy concerns. This paper introduces a novel interpretable knowledge distillation approach to enhance the performance of smaller, more economical LLMs that firms can self-host. We study this problem in the context of building a customer service agent aimed at achieving high customer satisfaction through goal-oriented dialogues. Unlike traditional knowledge distillation, where the "student" model learns directly from the "teacher" model's responses via fine-tuning, our interpretable "strategy" teaching approach involves the teacher providing strategies to improve the student's performance in various scenarios. This method alternates between a "scenario generation" step and a "strategies for improvement" step, creating a customized library of scenarios and optimized strategies for automated prompting. The method requires only black-box access to both student and teacher models; hence it can be used without manipulating model parameters. In our customer service application, the method improves performance, and the learned strategies are transferable to other LLMs and scenarios beyond the training set. The method's interpretabilty helps safeguard against potential harms through human audit.

Explore the LiDAR-Camera Dynamic Adjustment Fusion for 3D Object Detection

Camera and LiDAR serve as informative sensors for accurate and robust autonomous driving systems. However, these sensors often exhibit heterogeneous natures, resulting in distributional modality gaps that present significant challenges for fusion. To address this, a robust fusion technique is crucial, particularly for enhancing 3D object detection. In this paper, we introduce a dynamic adjustment technology aimed at aligning modal distributions and learning effective modality representations to enhance the fusion process. Specifically, we propose a triphase domain aligning module. This module adjusts the feature distributions from both the camera and LiDAR, bringing them closer to the ground truth domain and minimizing differences. Additionally, we explore improved representation acquisition methods for dynamic fusion, which includes modal interaction and specialty enhancement. Finally, an adaptive learning technique that merges the semantics and geometry information for dynamical instance optimization. Extensive experiments in the nuScenes dataset present competitive performance with state-of-the-art approaches. Our code will be released in the future.

SEED: A Simple and Effective 3D DETR in Point Clouds

Recently, detection transformers (DETRs) have gradually taken a dominant position in 2D detection thanks to their elegant framework. However, DETR-based detectors for 3D point clouds are still difficult to achieve satisfactory performance. We argue that the main challenges are twofold: 1) How to obtain the appropriate object queries is challenging due to the high sparsity and uneven distribution of point clouds; 2) How to implement an effective query interaction by exploiting the rich geometric structure of point clouds is not fully explored. To this end, we propose a simple and effective 3D DETR method (SEED) for detecting 3D objects from point clouds, which involves a dual query selection (DQS) module and a deformable grid attention (DGA) module. More concretely, to obtain appropriate queries, DQS first ensures a high recall to retain a large number of queries by the predicted confidence scores and then further picks out high-quality queries according to the estimated quality scores. DGA uniformly divides each reference box into grids as the reference points and then utilizes the predicted offsets to achieve a flexible receptive field, allowing the network to focus on relevant regions and capture more informative features. Extensive ablation studies on DQS and DGA demonstrate its effectiveness. Furthermore, our SEED achieves state-of-the-art detection performance on both the large-scale Waymo and nuScenes datasets, illustrating the superiority of our proposed method. The code is available at https://github.com/happinesslz/SEED

OPEN: Object-wise Position Embedding for Multi-view 3D Object Detection

Accurate depth information is crucial for enhancing the performance of multi-view 3D object detection. Despite the success of some existing multi-view 3D detectors utilizing pixel-wise depth supervision, they overlook two significant phenomena: 1) the depth supervision obtained from LiDAR points is usually distributed on the surface of the object, which is not so friendly to existing DETR-based 3D detectors due to the lack of the depth of 3D object center; 2) for distant objects, fine-grained depth estimation of the whole object is more challenging. Therefore, we argue that the object-wise depth (or 3D center of the object) is essential for accurate detection. In this paper, we propose a new multi-view 3D object detector named OPEN, whose main idea is to effectively inject object-wise depth information into the network through our proposed object-wise position embedding. Specifically, we first employ an object-wise depth encoder, which takes the pixel-wise depth map as a prior, to accurately estimate the object-wise depth. Then, we utilize the proposed object-wise position embedding to encode the object-wise depth information into the transformer decoder, thereby producing 3D object-aware features for final detection. Extensive experiments verify the effectiveness of our proposed method. Furthermore, OPEN achieves a new state-of-the-art performance with 64.4% NDS and 56.7% mAP on the nuScenes test benchmark.

Dance of the ADS: Orchestrating Failures through Historically-Informed Scenario Fuzzing

As autonomous driving systems (ADS) advance towards higher levels of autonomy, orchestrating their safety verification becomes increasingly intricate. This paper unveils ScenarioFuzz, a pioneering scenario-based fuzz testing methodology. Designed like a choreographer who understands the past performances, it uncovers vulnerabilities in ADS without the crutch of predefined scenarios. Leveraging map road networks, such as OPENDRIVE, we extract essential data to form a foundational scenario seed corpus. This corpus, enriched with pertinent information, provides the necessary boundaries for fuzz testing in the absence of starting scenarios. Our approach integrates specialized mutators and mutation techniques, combined with a graph neural network model, to predict and filter out high-risk scenario seeds, optimizing the fuzzing process using historical test data. Compared to other methods, our approach reduces the time cost by an average of 60.3%, while the number of error scenarios discovered per unit of time increases by 103%. Furthermore, we propose a self-supervised collision trajectory clustering method, which aids in identifying and summarizing 54 high-risk scenario categories prone to inducing ADS faults. Our experiments have successfully uncovered 58 bugs across six tested systems, emphasizing the critical safety concerns of ADS.