2,101 research outputs found
Biomedical and Pharmacological Applications of Marine Collagen
Biomimetic polymers and materials have been widely used in a variety of biomedical and pharmacological applications. Particularly, collagen-based biomaterials have been extensively applied in various biomedical fields, such as scaffolds in tissue engineering. However, there are many challenges associated with the use of mammalian collagen, including the issues of religious constrains, allergic or autoimmune reactions, and the spread of animal diseases. Over the past few decades, marine collagen (MC) has emerged as a promising biomaterial for biomedical and pharmacological applications. Marine organisms are a rich source of structurally novel and biologically active compounds, and to date, many biological components have been isolated from various marine resources. MC offers advantages over mammalian collagen due to its water solubility, low immunogenicity, safety, biocompatibility, antimicrobial activity, functionality, and low production costs. Due to its characteristics and physicobiochemical properties, it has tremendous potential for use as a scaffold biomaterial in tissue engineering and regenerative medicine, in drug delivery systems, and as a therapeutic. In this Special Issue, we encourage submissions related to the recent developments, advancements, trends, challenges, and future perspectives in this new research field. We expect to receive contributions from different areas of multidisciplinary research, including—but not restricted to—extraction, purification, characterization, fabrication, and experimentation of MC, with a particular focus on their biotechnological, biomedical and pharmacological uses
LIPIcs, Volume 251, ITCS 2023, Complete Volume
LIPIcs, Volume 251, ITCS 2023, Complete Volum
Guided rewriting and constraint satisfaction for parallel GPU code generation
Graphics Processing Units (GPUs) are notoriously hard to optimise for manually due to their scheduling and memory hierarchies. What is needed are good automatic code generators and optimisers for such parallel hardware. Functional approaches such as Accelerate, Futhark and LIFT leverage a high-level algorithmic Intermediate Representation (IR) to expose parallelism and abstract the implementation details away from the user. However, producing efficient code for a given accelerator remains challenging. Existing code generators depend on the user input to choose a subset of hard-coded optimizations or automated exploration of implementation search space. The former suffers from the lack of extensibility, while the latter is too costly due to the size of the search space. A hybrid approach is needed, where a space of valid implementations is built automatically and explored with the aid of human expertise.
This thesis presents a solution combining user-guided rewriting and automatically generated constraints to produce high-performance code. The first contribution is an automatic tuning technique to find a balance between performance and memory consumption. Leveraging its functional patterns, the LIFT compiler is empowered to infer tuning constraints and limit the search to valid tuning combinations only.
Next, the thesis reframes parallelisation as a constraint satisfaction problem. Parallelisation constraints are extracted automatically from the input expression, and a solver is used to identify valid rewriting. The constraints truncate the search space to valid parallel mappings only by capturing the scheduling restrictions of the GPU in the context of a given program. A synchronisation barrier insertion technique is proposed to prevent data races and improve the efficiency of the generated parallel mappings.
The final contribution of this thesis is the guided rewriting method, where the user encodes a design space of structural transformations using high-level IR nodes called rewrite points. These strongly typed pragmas express macro rewrites and expose design choices as explorable parameters. The thesis proposes a small set of reusable rewrite points to achieve tiling, cache locality, data reuse and memory optimisation.
A comparison with the vendor-provided handwritten kernel ARM Compute Library and the TVM code generator demonstrates the effectiveness of this thesis' contributions. With convolution as a use case, LIFT-generated direct and GEMM-based convolution implementations are shown to perform on par with the state-of-the-art solutions on a mobile GPU. Overall, this thesis demonstrates that a functional IR yields well to user-guided and automatic rewriting for high-performance code generation
Automated Distinct Bone Segmentation from Computed Tomography Images using Deep Learning
Large-scale CT scans are frequently performed for forensic and diagnostic purposes, to plan and
direct surgical procedures, and to track the development of bone-related diseases. This often
involves radiologists who have to annotate bones manually or in a semi-automatic way, which is
a time consuming task. Their annotation workload can be reduced by automated segmentation
and detection of individual bones. This automation of distinct bone segmentation not only has
the potential to accelerate current workflows but also opens up new possibilities for processing
and presenting medical data for planning, navigation, and education.
In this thesis, we explored the use of deep learning for automating the segmentation of all
individual bones within an upper-body CT scan. To do so, we had to find a network architec-
ture that provides a good trade-off between the problem’s high computational demands and the
results’ accuracy. After finding a baseline method and having enlarged the dataset, we set out
to eliminate the most prevalent types of error. To do so, we introduced an novel method called
binary-prediction-enhanced multi-class (BEM) inference, separating the task into two: Distin-
guishing bone from non-bone is conducted separately from identifying the individual bones.
Both predictions are then merged, which leads to superior results. Another type of error is tack-
led by our developed architecture, the Sneaky-Net, which receives additional inputs with larger
fields of view but at a smaller resolution. We can thus sneak more extensive areas of the input
into the network while keeping the growth of additional pixels in check.
Overall, we present a deep-learning-based method that reliably segments most of the over
one hundred distinct bones present in upper-body CT scans in an end-to-end trained matter
quickly enough to be used in interactive software. Our algorithm has been included in our
groups virtual reality medical image visualisation software SpectoVR with the plan to be used
as one of the puzzle piece in surgical planning and navigation, as well as in the education of
future doctors
AI: Limits and Prospects of Artificial Intelligence
The emergence of artificial intelligence has triggered enthusiasm and promise of boundless opportunities as much as uncertainty about its limits. The contributions to this volume explore the limits of AI, describe the necessary conditions for its functionality, reveal its attendant technical and social problems, and present some existing and potential solutions. At the same time, the contributors highlight the societal and attending economic hopes and fears, utopias and dystopias that are associated with the current and future development of artificial intelligence
Computational Approaches to Drug Profiling and Drug-Protein Interactions
Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a
long period of stagnation in drug approvals. Due to the extreme costs associated with
introducing a drug to the market, locating and understanding the reasons for clinical failure
is key to future productivity. As part of this PhD, three main contributions were made in
this respect. First, the web platform, LigNFam enables users to interactively explore
similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly,
two deep-learning-based binding site comparison tools were developed, competing with
the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the
open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold
relationships and has already been used in multiple projects, including integration into a
virtual screening pipeline to increase the tractability of ultra-large screening experiments.
Together, and with existing tools, the contributions made will aid in the understanding of
drug-protein relationships, particularly in the fields of off-target prediction and drug
repurposing, helping to design better drugs faster
Deep learning for unsupervised domain adaptation in medical imaging: Recent advancements and future perspectives
Deep learning has demonstrated remarkable performance across various tasks in
medical imaging. However, these approaches primarily focus on supervised
learning, assuming that the training and testing data are drawn from the same
distribution. Unfortunately, this assumption may not always hold true in
practice. To address these issues, unsupervised domain adaptation (UDA)
techniques have been developed to transfer knowledge from a labeled domain to a
related but unlabeled domain. In recent years, significant advancements have
been made in UDA, resulting in a wide range of methodologies, including feature
alignment, image translation, self-supervision, and disentangled representation
methods, among others. In this paper, we provide a comprehensive literature
review of recent deep UDA approaches in medical imaging from a technical
perspective. Specifically, we categorize current UDA research in medical
imaging into six groups and further divide them into finer subcategories based
on the different tasks they perform. We also discuss the respective datasets
used in the studies to assess the divergence between the different domains.
Finally, we discuss emerging areas and provide insights and discussions on
future research directions to conclude this survey.Comment: Under Revie
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Multi-scale pedestrian intent prediction using 3D joint information as spatio-temporal representation
Data availability: Only publicly available data were used.Copyright © 2023 The Author(s). There has been a rise of use of Autonomous Vehicles on public roads. With the predicted rise of road traffic accidents over the coming years, these vehicles must be capable of safely operate in the public domain. The field of pedestrian detection has significantly advanced in the last decade, providing high-level accuracy, with some technique reaching near-human level accuracy. However, there remains further work required for pedestrian intent prediction to reach human-level performance. One of the challenges facing current pedestrian intent predictors are the varying scales of pedestrians, particularly smaller pedestrians. This is because smaller pedestrians can blend into the background, making them difficult to detect, track or apply pose estimations techniques. Therefore, in this work, we present a novel intent prediction approach for multi-scale pedestrians using 2D pose estimation and a Long Short-term memory (LSTM) architecture. The pose estimator predicts keypoints for the pedestrian along the video frames. Based on the accumulation of these keypoints along the frames, spatio-temporal data is generated. This spatio-temporal data is fed to the LSTM for classifying the crossing behaviour of the pedestrians. We evaluate the performance of the proposed techniques on the popular Joint Attention in Autonomous Driving (JAAD) dataset and the new larger-scale Pedestrian Intention Estimation (PIE) dataset. Using data generalisation techniques, we show that the proposed technique outperformed the state-of-the-art techniques by up to 7%, reaching up to 94% accuracy while maintaining a comparable run-time of 6.1 ms
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