Towards accurate abdominal tumor segmentation: A 2D model with Position-Aware and Key Slice Feature Sharing.

Abdominal tumor segmentation is a crucial yet challenging step during the screening and diagnosis of tumors. While 3D segmentation models provide powerful performance, they demand substantial computational resources. Additionally, in 3D data, tumors often represent a small portion, leading to imbalanced data and potentially overlooking crucial information. Conversely, 2D segmentation models have a lightweight structure, but disregard the inter-slice correlation, risking the loss of tumor in edge slices. To address these challenges, this paper proposes a novel Position-Aware and Key Slice Feature Sharing 2D tumor segmentation model (PAKS-Net). Leveraging the Swin-Transformer, we effectively model the global features within each slice, facilitating essential information extraction. Furthermore, we introduce a Position-Aware module to capture the spatial relationship between tumors and their corresponding organs, mitigating noise and interference from surrounding organ tissues. To enhance the edge slice segmentation accuracy, we employ key slices to assist in the segmentation of other slices to prioritize tumor regions. Through extensive experiments on three abdominal tumor segmentation CT datasets and a lung tumor segmentation CT dataset, PAKS-Net demonstrates superior performance, reaching 0.893, 0.769, 0.598 and 0.738 tumor DSC on the KiTS19, LiTS17, pancreas and LOTUS datasets, surpassing 3D segmentation models, while remaining computationally efficient with fewer parameters.

Antibiotic usage patterns in COVID-19 patients in five tertiary hospitals from Bangladesh: A countrywide picture.

Objectives: Irrational and injudicious use of antibiotics in COVID-19 patients could be detrimental in a tropical country with a weak antibiotic stewardship policy such as Bangladesh. This study aimed to focus on the antibiotic usage patterns in COVID-19 patients in Bangladesh. Methods: This prospective observational study was performed from July 2020 to June 2021 in five tertiary hospitals in Bangladesh. Data on demographic profile, disease severity, and antibiotic usage were collected directly from the patients' hospital documents. Results: A total of 3486 (94.4%) patients were treated with at least one antibiotic; 3261 (93.6%) patients received a single antibiotic, and 225 (6.5%) received multiple antibiotics. The most used antibiotics were ceftriaxone (37.3%), co-amoxiclav (26.3%), azithromycin (10.6%), and meropenem (10.3%). According to the World Health Organization AWaRe categorization, most (2260; 69.6%) of the antibiotics prescribed in this study belonged to the "Watch" group. Culture and sensitivity reports were available in 111 cases from one center. Only 18.9% of the patients were found to be co-infected with multi-drug-resistant bacteria (52.4% yield from sputum, 28.6% from urine, and 14.3% from blood). Conclusions: Strict antibiotic prescribing policy and antibiotic stewardship should be implemented immediately to limit the future threat of antimicrobial resistance in countries such as Bangladesh.

Mutual learning with memory for semi-supervised pest detection.

Effectively monitoring pest-infested areas by computer vision is essential in precision agriculture in order to minimize yield losses and create early scientific preventative solutions. However, the scale variation, complex background, and dense distribution of pests bring challenges to accurate detection when utilizing vision technology. Simultaneously, supervised learning-based object detection heavily depends on abundant labeled data, which poses practical difficulties. To overcome these obstacles, in this paper, we put forward innovative semi-supervised pest detection, PestTeacher. The framework effectively mitigates the issues of confirmation bias and instability among detection results across different iterations. To address the issue of leakage caused by the weak features of pests, we propose the Spatial-aware Multi-Resolution Feature Extraction (SMFE) module. Furthermore, we introduce a Region Proposal Network (RPN) module with a cascading architecture. This module is specifically designed to generate higher-quality anchors, which are crucial for accurate object detection. We evaluated the performance of our method on two datasets: the corn borer dataset and the Pest24 dataset. The corn borer dataset encompasses data from various corn growth cycles, while the Pest24 dataset is a large-scale, multi-pest image dataset consisting of 24 classes and 25k images. Experimental results demonstrate that the enhanced model achieves approximately 80% effectiveness with only 20% of the training set supervised in both the corn borer dataset and Pest24 dataset. Compared to the baseline model SoftTeacher, our model improves mAP @0.5 (mean Average Precision) at 7.3 compared to that of SoftTeacher at 4.6. This method offers theoretical research and technical references for automated pest identification and management.

CP-Net: Instance-aware part segmentation network for biological cell parsing.

Instance segmentation of biological cells is important in medical image analysis for identifying and segmenting individual cells, and quantitative measurement of subcellular structures requires further cell-level subcellular part segmentation. Subcellular structure measurements are critical for cell phenotyping and quality analysis. For these purposes, instance-aware part segmentation network is first introduced to distinguish individual cells and segment subcellular structures for each detected cell. This approach is demonstrated on human sperm cells since the World Health Organization has established quantitative standards for sperm quality assessment. Specifically, a novel Cell Parsing Net (CP-Net) is proposed for accurate instance-level cell parsing. An attention-based feature fusion module is designed to alleviate contour misalignments for cells with an irregular shape by using instance masks as spatial cues instead of as strict constraints to differentiate various instances. A coarse-to-fine segmentation module is developed to effectively segment tiny subcellular structures within a cell through hierarchical segmentation from whole to part instead of directly segmenting each cell part. Moreover, a sperm parsing dataset is built including 320 annotated sperm images with five semantic subcellular part labels. Extensive experiments on the collected dataset demonstrate that the proposed CP-Net outperforms state-of-the-art instance-aware part segmentation networks.

Polymorphism-aware models in RevBayes: Species trees, disentangling Balancing Selection and CG-biased gene conversion.

The role of balancing selection is a long-standing evolutionary puzzle. Balancing selection is a crucial evolutionary process that maintains genetic variation (polymorphism) over extended periods of time; however, detecting it poses a significant challenge. Building upon the polymorphism-aware phylogenetic models (PoMos) framework rooted in the Moran model, we introduce PoMoBalance model. This novel approach is designed to disentangle the interplay of mutation, genetic drift, directional selection (GC-biased gene conversion), along with the previously unexplored balancing selection pressures on ultra-long timescales comparable with species divergence times by analysing multi-individual genomic and phylogenetic divergence data. Implemented in the open-source RevBayes Bayesian framework, PoMoBalance offers a versatile tool for inferring phylogenetic trees as well as quantifying various selective pressures. The novel aspect of our approach in studying balancing selection lies in PoMos' ability to account for ancestral polymorphisms and incorporate parameters that measure frequency-dependent selection, allowing us to determine the strength of the effect and exact frequencies under selection. We implemented validation tests and assessed the model on the data simulated with SLiM and a custom Moran model simulator. Real sequence analysis of Drosophila populations reveals insights into the evolutionary dynamics of regions subject to frequency-dependent balancing selection, particularly in the context of sex-limited colour dimorphism in Drosophila erecta.

Efficient context-aware computing: a systematic model for dynamic working memory updates in context-aware computing.

The expanding computer landscape leads us toward ubiquitous computing, in which smart gadgets seamlessly provide intelligent services anytime, anywhere. Smartphones and other smart devices with multiple sensors are at the vanguard of this paradigm, enabling context-aware computing. Similar setups are also known as smart spaces. Context-aware systems, primarily deployed on mobile and other resource-constrained wearable devices, use a variety of implementation approaches. Rule-based reasoning, noted for its simplicity, is based on a collection of assertions in working memory and a set of rules that regulate decision-making. However, controlling working memory capacity efficiently is a key challenge, particularly in the context of resource-constrained systems. The paper's main focus lies in addressing the dynamic working memory challenge in memory-constrained devices by introducing a systematic method for content removal. The initiative intends to improve the creation of intelligent systems for resource-constrained devices, optimize memory utilization, and enhance context-aware computing.

Prediction of steelmaking process variables using K-medoids and a time-aware LSTM network.

A new method is required to address the challenge of predicting process parameters in high-temperature, high-pressure industrial processes. This study proposes a multi-model Long Short-Term Memory (LSTM) network prediction algorithm with irregular time interval sequences to predict the silicon yield in converter steelmaking. The experimental results demonstrate that this algorithm performs better than comparable neural network models in classifying high-dimensional, redundant industrial production data with noise and outliers. The algorithm is evaluated using data from a steel plant. The proposed algorithm has lower errors for predicting the alloy yield than other neural network models. An average mean absolute error (MAE) of less than 0.01 confirms the algorithm's feasibility and practicality.

Consumption of antibiotics in Brazil - an analysis of sales data between 2014 and 2019.

BACKGROUND: Antibiotic consumption is a driver for the increase of antimicrobial resistance. The objective of this study is to analyze variations in antibiotic consumption and its appropriate use in Brazil from 2014 to 2019. METHODS: We conducted a time series study using the surveillance information system database (SNGPC) from the Brazilian Health Regulatory Agency. Antimicrobials sold in retail pharmacies were evaluated. All antimicrobials recorded for systemic use identified by the active ingredient were eligible. Compounded products and formulations for topic use (dermatological, gynecological, and eye/ear treatments) were excluded. The number of defined daily doses (DDDs)/1,000 inhabitants/day for each antibiotic was attributed. The number of DDDs per 1,000 inhabitants per day (DDIs) was used as a proxy for consumption. Results were stratified by regions and the average annual percentage change in the whole period studied was estimated. We used the WHO Access, Watch, and Reserve (AWaRe) framework to categorize antimicrobial drugs. RESULTS: An overall increase of 30% in consumption from 2014 to 2019 was observed in all Brazilian regions. Amoxicillin, azithromycin and cephalexin were the antimicrobials more consumed, with the Southeast region responsible for more than 50% of the antibiotic utilization. Among all antimicrobials analyzed 45.0% were classified as watch group in all Brazilian regions. CONCLUSION: We observed a significant increase in antibiotics consumption from 2014 to 2019 in Brazil restricted to the Northeast and Central West regions. Almost half of the antibiotics consumed in Brazil were classified as watch group, highlighting the importance to promote rational use in this country.

URCA: Uncertainty-based region clipping algorithm for semi-supervised medical image segmentation.

BACKGROUND AND OBJECTIVE: Training convolutional neural networks based on large amount of labeled data has made great progress in the field of image segmentation. However, in medical image segmentation tasks, annotating the data is expensive and time-consuming because pixel-level annotation requires experts in the relevant field. Currently, the combination of consistent regularization and pseudo labeling-based semi-supervised methods has shown good performance in image segmentation. However, in the training process, a portion of low-confidence pseudo labels are generated by the model. And the semi-supervised segmentation method still has the problem of distribution bias between labeled and unlabeled data. The objective of this study is to address the challenges of semi-supervised learning and improve the segmentation accuracy of semi-supervised models on medical images. METHODS: To address these issues, we propose an Uncertainty-based Region Clipping Algorithm for semi-supervised medical image segmentation, which consists of two main modules. A module is introduced to compute the uncertainty of two sub-networks predictions with diversity using Monte Carlo Dropout, allowing the model to gradually learn from more reliable targets. To retain model diversity, we use different loss functions for different branches and use Non-Maximum Suppression in one of the branches. The other module is proposed to generate new samples by masking the low-confidence pixels in the original image based on uncertainty information. New samples are fed into the model to facilitate the model to generate pseudo labels with high confidence and enlarge the training data distribution. RESULTS: Comprehensive experiments on the combination of two benchmarks ACDC and BraTS2019 show that our proposed model outperforms state-of-the-art methods in terms of Dice, HD95 and ASD. The results reach an average Dice score of 87.86 % and a HD95 score of 4.214 mm on ACDC dataset. For the brain tumor segmentation, the results reach an average Dice score of 84.79 % and a HD score of 10.13 mm. CONCLUSIONS: Our proposed method improves the accuracy of semi-supervised medical image segmentation. Extensive experiments on two public medical image datasets including 2D and 3D modalities demonstrate the superiority of our model. The code is available at: https://github.com/QuintinDong/URCA.

Lesion-aware cross-phase attention network for renal tumor subtype classification on multi-phase CT scans.

Multi-phase computed tomography (CT) has been widely used for the preoperative diagnosis of kidney cancer due to its non-invasive nature and ability to characterize renal lesions. However, since enhancement patterns of renal lesions across CT phases are different even for the same lesion type, the visual assessment by radiologists suffers from inter-observer variability in clinical practice. Although deep learning-based approaches have been recently explored for differential diagnosis of kidney cancer, they do not explicitly model the relationships between CT phases in the network design, limiting the diagnostic performance. In this paper, we propose a novel lesion-aware cross-phase attention network (LACPANet) that can effectively capture temporal dependencies of renal lesions across CT phases to accurately classify the lesions into five major pathological subtypes from time-series multi-phase CT images. We introduce a 3D inter-phase lesion-aware attention mechanism to learn effective 3D lesion features that are used to estimate attention weights describing the inter-phase relations of the enhancement patterns. We also present a multi-scale attention scheme to capture and aggregate temporal patterns of lesion features at different spatial scales for further improvement. Extensive experiments on multi-phase CT scans of kidney cancer patients from the collected dataset demonstrate that our LACPANet outperforms state-of-the-art approaches in diagnostic accuracy.

ESC-NAS: Environment Sound Classification Using Hardware-Aware Neural Architecture Search for the Edge.

The combination of deep-learning and IoT plays a significant role in modern smart solutions, providing the capability of handling task-specific real-time offline operations with improved accuracy and minimised resource consumption. This study provides a novel hardware-aware neural architecture search approach called ESC-NAS, to design and develop deep convolutional neural network architectures specifically tailored for handling raw audio inputs in environmental sound classification applications under limited computational resources. The ESC-NAS process consists of a novel cell-based neural architecture search space built with 2D convolution, batch normalization, and max pooling layers, and capable of extracting features from raw audio. A black-box Bayesian optimization search strategy explores the search space and the resulting model architectures are evaluated through hardware simulation. The models obtained from the ESC-NAS process achieved the optimal trade-off between model performance and resource consumption compared to the existing literature. The ESC-NAS models achieved accuracies of 85.78%, 81.25%, 96.25%, and 81.0% for the FSC22, UrbanSound8K, ESC-10, and ESC-50 datasets, respectively, with optimal model sizes and parameter counts for edge deployment.

Dual-Tower Counterfactual Session-Aware Recommender System.

In the complex dynamics of modern information systems such as e-commerce and streaming services, managing uncertainty and leveraging information theory are crucial in enhancing session-aware recommender systems (SARSs). This paper presents an innovative approach to SARSs that combines static long-term and dynamic short-term preferences within a counterfactual causal framework. Our method addresses the shortcomings of current prediction models that tend to capture spurious correlations, leading to biased recommendations. By incorporating a counterfactual viewpoint, we aim to elucidate the causal influences of static long-term preferences on next-item selections and enhance the overall robustness of predictive models. We introduce a dual-tower architecture with a novel data augmentation process and a self-supervised training strategy, tailored to tackle inherent biases and unreliable correlations. Extensive experiments demonstrate the effectiveness of our approach, outperforming existing benchmarks and paving the way for more accurate and reliable session-based recommendations.

A Context-Aware Navigation Framework for Ground Robots in Horticultural Environments.

Environmental mapping and robot navigation are the basis for realizing robot automation in modern agricultural production. This study proposes a new autonomous mapping and navigation method for gardening scene robots. First, a new LiDAR slam-based semantic mapping algorithm is proposed to enable the robots to analyze structural information from point cloud images and generate roadmaps from them. Secondly, a general robot navigation framework is proposed to enable the robot to generate the shortest global path according to the road map, and consider the local terrain information to find the optimal local path to achieve safe and efficient trajectory tracking; this method is equipped in apple orchards. The LiDAR was evaluated on a differential drive robotic platform. Experimental results show that this method can effectively process orchard environmental information. Compared with vnf and pointnet++, the semantic information extraction efficiency and time are greatly improved. The map feature extraction time can be reduced to 0.1681 s, and its MIoU is 0.812. The resulting global path planning achieved a 100% success rate, with an average run time of 4ms. At the same time, the local path planning algorithm can effectively generate safe and smooth trajectories to execute the global path, with an average running time of 36 ms.

Semantic-Aware Fusion Network Based on Super-Resolution.

The aim of infrared and visible image fusion is to generate a fused image that not only contains salient targets and rich texture details, but also facilitates high-level vision tasks. However, due to the hardware limitations of digital cameras and other devices, there are more low-resolution images in the existing datasets, and low-resolution images are often accompanied by the problem of losing details and structural information. At the same time, existing fusion algorithms focus too much on the visual quality of the fused images, while ignoring the requirements of high-level vision tasks. To address the above challenges, in this paper, we skillfully unite the super-resolution network, fusion network and segmentation network, and propose a super-resolution-based semantic-aware fusion network. First, we design a super-resolution network based on a multi-branch hybrid attention module (MHAM), which aims to enhance the quality and details of the source image, enabling the fusion network to integrate the features of the source image more accurately. Then, a comprehensive information extraction module (STDC) is designed in the fusion network to enhance the network's ability to extract finer-grained complementary information from the source image. Finally, the fusion network and segmentation network are jointly trained to utilize semantic loss to guide the semantic information back to the fusion network, which effectively improves the performance of the fused images on high-level vision tasks. Extensive experiments show that our method is more effective than other state-of-the-art image fusion methods. In particular, our fused images not only have excellent visual perception effects, but also help to improve the performance of high-level vision tasks.

3D EAGAN: 3D edge-aware attention generative adversarial network for prostate segmentation in transrectal ultrasound images.

Background: The segmentation of prostates from transrectal ultrasound (TRUS) images is a critical step in the diagnosis and treatment of prostate cancer. Nevertheless, the manual segmentation performed by physicians is a time-consuming and laborious task. To address this challenge, there is a pressing need to develop computerized algorithms capable of autonomously segmenting prostates from TRUS images, which sets a direction and form for future development. However, automatic prostate segmentation in TRUS images has always been a challenging problem since prostates in TRUS images have ambiguous boundaries and inhomogeneous intensity distribution. Although many prostate segmentation methods have been proposed, they still need to be improved due to the lack of sensibility to edge information. Consequently, the objective of this study is to devise a highly effective prostate segmentation method that overcomes these limitations and achieves accurate segmentation of prostates in TRUS images. Methods: A three-dimensional (3D) edge-aware attention generative adversarial network (3D EAGAN)-based prostate segmentation method is proposed in this paper, which consists of an edge-aware segmentation network (EASNet) that performs the prostate segmentation and a discriminator network that distinguishes predicted prostates from real prostates. The proposed EASNet is composed of an encoder-decoder-based U-Net backbone network, a detail compensation module (DCM), four 3D spatial and channel attention modules (3D SCAM), an edge enhancement module (EEM), and a global feature extractor (GFE). The DCM is proposed to compensate for the loss of detailed information caused by the down-sampling process of the encoder. The features of the DCM are selectively enhanced by the 3D spatial and channel attention module. Furthermore, an EEM is proposed to guide shallow layers in the EASNet to focus on contour and edge information in prostates. Finally, features from shallow layers and hierarchical features from the decoder module are fused through the GFE to predict the segmentation prostates. Results: The proposed method is evaluated on our TRUS image dataset and the open-source µRegPro dataset. Specifically, experimental results on two datasets show that the proposed method significantly improved the average segmentation Dice score from 85.33% to 90.06%, Jaccard score from 76.09% to 84.11%, Hausdorff distance (HD) score from 8.59 to 4.58 mm, Precision score from 86.48% to 90.58%, and Recall score from 84.79% to 89.24%. Conclusions: A novel 3D EAGAN-based prostate segmentation method is proposed. The proposed method consists of an EASNet and a discriminator network. Experimental results demonstrate that the proposed method has achieved satisfactory results on 3D TRUS image segmentation for prostates.

FetalBrainAwareNet: Bridging GANs with anatomical insight for fetal ultrasound brain plane synthesis.

Over the past decade, deep-learning (DL) algorithms have become a promising tool to aid clinicians in identifying fetal head standard planes (FHSPs) during ultrasound (US) examination. However, the adoption of these algorithms in clinical settings is still hindered by the lack of large annotated datasets. To overcome this barrier, we introduce FetalBrainAwareNet, an innovative framework designed to synthesize anatomically accurate images of FHSPs. FetalBrainAwareNet introduces a cutting-edge approach that utilizes class activation maps as a prior in its conditional adversarial training process. This approach fosters the presence of the specific anatomical landmarks in the synthesized images. Additionally, we investigate specialized regularization terms within the adversarial training loss function to control the morphology of the fetal skull and foster the differentiation between the standard planes, ensuring that the synthetic images faithfully represent real US scans in both structure and overall appearance. The versatility of our FetalBrainAwareNet framework is highlighted by its ability to generate high-quality images of three predominant FHSPs using a singular, integrated framework. Quantitative (Fréchet inception distance of 88.52) and qualitative (t-SNE) results suggest that our framework generates US images with greater variability compared to state-of-the-art methods. By using the synthetic images generated with our framework, we increase the accuracy of FHSP classifiers by 3.2% compared to training the same classifiers solely with real acquisitions. These achievements suggest that using our synthetic images to increase the training set could provide benefits to enhance the performance of DL algorithms for FHSPs classification that could be integrated in real clinical scenarios.

SpotSweeper: spatially-aware quality control for spatial transcriptomics.

Quality control (QC) is a crucial step to ensure the reliability and accuracy of the data obtained from RNA sequencing experiments, including spatially-resolved transcriptomics (SRT). Existing QC approaches for SRT that have been adopted from single-nucleus RNA sequencing (snRNA-seq) methods are confounded by spatial biology and are inappropriate for SRT data. In addition, no methods currently exist for identifying histological tissue artifacts unique to SRT. Here, we introduce SpotSweeper, spatially-aware QC methods for identifying local outliers and regional artifacts in SRT. SpotSweeper evaluates the quality of individual spots relative to their local neighborhood, thus minimizing bias due to biological heterogeneity, and uses multiscale methods to detect regional artifacts. Using SpotSweeper on publicly available data, we identified a consistent set of Visium barcodes/spots as systematically low quality and demonstrate that SpotSweeper accurately identifies two distinct types of regional artifacts, resulting in improved downstream clustering and marker gene detection for spatial domains.

"Obviously, Nothing's Gonna Happen in Five Minutes": How Adolescents and Young Adults Infrastructure Resources to Learn Type 1 Diabetes Management.

Learning personalized self-management routines is pivotal for people with type 1 diabetes (T1D), particularly early in diagnosis. Context-aware technologies, such as hybrid closed-loop (HCL) insulin pumps, are important tools for diabetes self-management. However, clinicians have observed that practices using these technologies involve significant individual differences. We conducted interviews with 20 adolescents and young adults who use HCL insulin pump systems for managing T1D, and we found that these individuals leverage both technological and non-technological means to maintain situational awareness about their condition. We discuss how these practices serve to infrastructure their self-management routines, including medical treatment, diet, and glucose measurement-monitoring routines. Our study provides insights into adolescents' and young adults' lived experiences of using HCL systems and related technology to manage diabetes, and contributes to a more nuanced understanding of how the HCI community can support the contextualized management of diabetes through technology design.

TinyNS: Platform-Aware Neurosymbolic Auto Tiny Machine Learning.

Machine learning at the extreme edge has enabled a plethora of intelligent, time-critical, and remote applications. However, deploying interpretable artificial intelligence systems that can perform high-level symbolic reasoning and satisfy the underlying system rules and physics within the tight platform resource constraints is challenging. In this paper, we introduce TinyNS, the first platform-aware neurosymbolic architecture search framework for joint optimization of symbolic and neural operators. TinyNS provides recipes and parsers to automatically write microcontroller code for five types of neurosymbolic models, combining the context awareness and integrity of symbolic techniques with the robustness and performance of machine learning models. TinyNS uses a fast, gradient-free, black-box Bayesian optimizer over discontinuous, conditional, numeric, and categorical search spaces to find the best synergy of symbolic code and neural networks within the hardware resource budget. To guarantee deployability, TinyNS talks to the target hardware during the optimization process. We showcase the utility of TinyNS by deploying microcontroller-class neurosymbolic models through several case studies. In all use cases, TinyNS outperforms purely neural or purely symbolic approaches while guaranteeing execution on real hardware.

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.

Despite having important biological implications, insertion, and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search. Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modeling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages. Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.