AIMC Topic: Software

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Deep learning approaches for automated classification and segmentation of head and neck cancers and brain tumors in magnetic resonance images: a meta-analysis study.

International journal of computer assisted radiology and surgery
PURPOSE: Deep learning (DL) has led to widespread changes in automated segmentation and classification for medical purposes. This study is an attempt to use statistical methods to analyze studies related to segmentation and classification of head and...

seqQscorer: automated quality control of next-generation sequencing data using machine learning.

Genome biology
Controlling quality of next-generation sequencing (NGS) data files is a necessary but complex task. To address this problem, we statistically characterize common NGS quality features and develop a novel quality control procedure involving tree-based ...

Hands-on training about overfitting.

PLoS computational biology
Overfitting is one of the critical problems in developing models by machine learning. With machine learning becoming an essential technology in computational biology, we must include training about overfitting in all courses that introduce this techn...

Attention based GRU-LSTM for software defect prediction.

PloS one
Software defect prediction (SDP) can be used to produce reliable, high-quality software. The current SDP is practiced on program granular components (such as file level, class level, or function level), which cannot accurately predict failures. To so...

DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation.

PLoS computational biology
We present DeepMIB, a new software package that is capable of training convolutional neural networks for segmentation of multidimensional microscopy datasets on any workstation. We demonstrate its successful application for segmentation of 2D and 3D ...

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.

Genome biology
Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long reads reveals the true complexity of processing. However, the relatively high error rates of long-read sequencing technolog...

The EU medical device regulation: Implications for artificial intelligence-based medical device software in medical physics.

Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB)
Medical device manufacturers are increasingly applying artificial intelligence (AI) to innovate their products and to improve patient outcomes. Health institutions are also developing their own algorithms, to address specific needs for which no comme...

An effective SteinGLM initialization scheme for training multi-layer feedforward sigmoidal neural networks.

Neural networks : the official journal of the International Neural Network Society
Network initialization is the first and critical step for training neural networks. In this paper, we propose a novel network initialization scheme based on the celebrated Stein's identity. By viewing multi-layer feedforward sigmoidal neural networks...

Design of experiment (DOE) applied to artificial neural network architecture enables rapid bioprocess improvement.

Bioprocess and biosystems engineering
Modern bioprocess development employs statistically optimized design of experiments (DOE) and regression modeling to find optimal bioprocess set points. Using modeling software, such as JMP Pro, it is possible to leverage artificial neural networks (...

Androgen Receptor Binding Category Prediction with Deep Neural Networks and Structure-, Ligand-, and Statistically Based Features.

Molecules (Basel, Switzerland)
Substances that can modify the androgen receptor pathway in humans and animals are entering the environment and food chain with the proven ability to disrupt hormonal systems and leading to toxicity and adverse effects on reproduction, brain developm...