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Artificial intelligence for anticancer drug discovery from natural products of macroalgae and sponges: A systematic review.

Marine natural products (MNPs) from macroalgae and marine sponges have inspired clinically important anticancer agents, including the cytarabine pharmacophore and the eribulin scaffold, while cyanobacterial dolastatin chemistry supplies the auristatin payloads of several marine-inspired antibody-drug conjugates (ADCs) such as brentuximab vedotin. Artificial intelligence (AI) methods, encompassing both classical machine learning (ML) with hand-engineered features and modern deep learning (DL) with many-layered neural networks, are increasingly supporting key decisions in natural-product anticancer drug discovery, including bioactivity prediction, target identification, absorption, distribution, metabolism, excretion and toxicity (ADMET) filtering, generative analogue design, and the selection of preclinical candidates. DL architectures relevant to this field include graph neural networks, transformer-based molecular generators, diffusion models for protein-ligand docking, and convolutional networks for mass spectrometry, while classical ML contributes interpretable fingerprint-based bioactivity models and molecular networking for dereplication. This review follows a systematic literature review methodology to organize the landscape of AI methods now applied to MNP anticancer discovery, distinguishing ML and DL approaches where relevant, situating them within the chemical context of macroalgal and sponge-derived oncology leads, and critically examining published case studies, including validation level (computational, in vitro, in vivo, clinical). The principal bottleneck for medical translation has shifted partly from algorithmic capability toward data infrastructure and experimental validation. Sparse, heterogeneous, and taxonomically biased bioactivity records limit what current models can learn and reduce the reliability of AI-prioritized candidates entering the preclinical pipeline. A roadmap is proposed that prioritizes open MNP-specific benchmarks, symbiont-aware modeling, and active learning loops with synthesizability and ADMET constraints. These AI workflows may accelerate the prioritization of marine-derived anticancer leads and support earlier, more evidence-based translational decisions in oncology drug development.

Biological Products↗

Blind source separation and deconvolution: the dynamic component analysis algorithm.

We derive a novel family of unsupervised learning algorithms for blind separation of mixed and convolved sources. Our approach is based on formulating the separation problem as a learning task of a spatiotemporal generative model, whose parameters are adapted iteratively to minimize suitable error functions, thus ensuring stability of the algorithms. The resulting learning rules achieve separation by exploiting high-order spatiotemporal statistics of the mixture data. Different rules are obtained by learning generative models in the frequency and time domains, whereas a hybrid frequency-time model leads to the best performance. These algorithms generalize independent component analysis to the case of convolutive mixtures and exhibit superior performance on instantaneous mixtures. An extension of the relative-gradient concept to the spatiotemporal case leads to fast and efficient learning rules with equivariant properties. Our approach can incorporate information about the mixing situation when available, resulting in a "semiblind" separation method. The spatiotemporal redundancy reduction performed by our algorithms is shown to be equivalent to information-rate maximization through a simple network. We illustrate the performance of these algorithms by successfully separating instantaneous and convolutive mixtures of speech and noise signals.

Algorithms↗

Modelling human memory: connectionism and convolution.

The mathematical operation of convolution is used as an associative mechanism by several recent influential models of human memory. Convolution can be used to associate two vectors (representing items to be remembered) into a memory trace vector in one operation. An approximation to either of the input vectors can then be retrieved, using the other vector as a probe. Recent convolution-based memory models have accounted for a wide range of data. Connectionist models may have greater potential for providing developmental accounts, but the architectures that have been most widely used to account for developmental phenomena cannot perform one-trial learning and this has limited their use as models of human memory. We show that a connectionist-like architecture can learn, using a gradient-descent algorithm, to perform single-trial learning in a similar manner to convolution. The solution that the network finds leads to less variable retrieval than does convolution. Furthermore, the network can learn to carry out the convolution operation itself. This provides a link between connectionist and convolution approaches, and a basis for models with many of the attractions of both connectionist and convolution approaches.

Humans↗

Optimal design of connectivity in neural network training.

Many authors consider neural network (NN) supervised training as an optimization process during which the weights are iteratively adjusted in order to minimise an error (cost) function, which represents the difference between the obtained and the aimed output. The error function surface is usually nonconvex, can be highly convoluted, with many plateaux and long narrow troughs, and can encounter many saddle and local minima (LM) points. Because backpropagation (BP), which is widely used method for supervised learning, uses local methods for optimization, it can get stuck in LM. This can make learning very difficult and sometimes its convergence to optimal solution--not possible. In this paper we propose a stochastic method for global optimization (GO), which make use of a uniformly distributed LP tau sequence of points. The developed technique is tested with common benchmark problems and used for neural network supervised learning. The conducted tests show that the proposed method can be successfully used for an optimal supervised training of small size NN.

Neural Networks, Computer↗

An artificial neural network for estimating scatter exposures in portable chest radiography.

An adaptive linear element (Adaline) was developed to estimate the two-dimensional scatter exposure distribution in digital portable chest radiographs (DPCXR). DPCXRs and quantitative scatter exposure measurements at 64 locations throughout the chest were acquired for ten radiographically normal patients. The Adaline is an artificial neural network which has only a single node and linear thresholding. The Adaline was trained using DPCXR-scatter measurement pairs from five patients. The spatially invariant network would take a portion of the image as its input and estimate the scatter content as output. The trained network was applied to the other five images, and errors were evaluated between estimated and measured scatter values. Performance was compared against a convolution scatter estimation algorithm. The network was evaluated as a function of network size, initial values, and duration of training. Network performance was evaluated qualitatively by the correlation of network weights to physical models, and quantitatively by training and evaluation errors. Using DPCXRs as input, the network learned to describe known scatter exposures accurately (7% error) and estimate scatter in new images (< 8% error) slightly better than convolution methods. Regardless of size and initial shape, all networks adapted into radial exponentials with magnitude of 0.75, perhaps implying an ideal point spread function and average scatter fraction, respectively. To implement scatter compensation, the two-dimensional scatter distribution estimated by the neural network is subtracted from the original DPCXR.

Algorithms↗

An investigation into the usefulness of generalized regression neural network analysis in the development of level A in vitro-in vivo correlation.

Quantitative correlations between in vivo and in vitro data (IVIVC) reduce the number of human in vivo studies, thus decreasing the overall time and expenses necessary for the development of optimal drug product formulation. Although linear regression analysis represents the simplest relationship, it is recognized that IVIVC should not be limited to linear relationship. With regards to the implementation of non-linear IVIVC models and the ability of artificial neural network (ANN) computing to cope with non-linear relationships, the usefulness of ANN analysis in the development of IVIVC merits further evaluation. The present paper is an attempt to develop an IVIVC for model sustained release paracetamol matrix tablet formulations employing various correlation approaches based on linear and non-linear modeling of in vitro and in vivo data. Currently accepted compendial methodology was compared with the alternative approaches, involving general mixed effects model and generalized regression neural network (GRNN) analysis, in order to evaluate their usefulness for predicting the in vivo behavior of drug products. Although based on analogous approaches, data generated by GRNN were closer to those observed in vivo, leading to the higher level of IVIVC than obtained by convolution. It can be assumed that GRNN analysis was able to generalize complex relations between the output and input parameters and could account for the differences in drug release kinetics observed under various conditions in vitro, thus offering potential as a reliable and robust estimate of drug products in vivo behavior.

Acetaminophen↗

Mathematical and connectionist models of human memory: a comparison.

Recent convolution-based models of human memory (e.g. Lewandowsky & Murdock, 1989), have accounted for a wide range of data. However such models require the relevant mathematical operations to be provided to the network. Connectionist models, in contrast, have generally addressed different data, and not all architectures are appropriate for modelling single-trial learning. Furthermore, they tend to exhibit catastrophic interference in multiple list learning. In this paper we compare the ability of convolution-based models and DARNET (Developmental Associative Recall NETwork), to account for human memory data. DARNET is a connectionist approach to human memory in which the system gradually learns to associate vectors, in one trial, into a memory trace vector. Either of the vectors can than be retrieved. It is shown that the new associative mechanism can be used to account for a wide range of relevant experimental data as successfully as can convolution-based models with the same higher-level architectures. Limitations of the models are also addressed.

Computer Simulation↗

Robust sound classification through the representation of similarity using response fields derived from stimuli during early experience.

Models of auditory processing, particularly of speech, face many difficulties. Included in these are variability among speakers, variability in speech rate, and robustness to moderate distortions such as time compression. We constructed a system based on ensembles of feature detectors derived from fragments of an onset-sensitive sound representation. This method is based on the idea of 'spectro-temporal response fields' and uses convolution to measure the degree of similarity through time between the feature detectors and the stimulus. The output from the ensemble was used to derive segmentation cues and patterns of response, which were used to train an artificial neural network (ANN) classifier. This allowed us to estimate a lower bound for the mutual information between the class of the input and the class of the output. Our results suggest that there is significant information in the output of our system, and that this is robust with respect to the exact choice of feature set, time compression in the stimulus, and speaker variation. In addition, the robustness to time compression in the stimulus has features in common with human psychophysics. Similar experiments using feature detectors derived from fragments of non-speech sounds performed less well. This result is interesting in the light of results showing aberrant cortical development in animals exposed to impoverished auditory environments during the developmental phase.

Acoustic Stimulation↗

LeRec: a NN/HMM hybrid for on-line handwriting recognition.

We introduce a new approach for on-line recognition of handwritten words written in unconstrained mixed style. The preprocessor performs a word-level normalization by fitting a model of the word structure using the EM algorithm. Words are then coded into low resolution "annotated images" where each pixel contains information about trajectory direction and curvature. The recognizer is a convolution network that can be spatially replicated. From the network output, a hidden Markov model produces word scores. The entire system is globally trained to minimize word-level errors.

Algorithms↗

MRI-based individual 3D region-of-interest atlases of the human brain: a new method for analyzing functional data.

OBJECTIVES: Introduction of a new atlas-based method for analyzing functional data which takes into account the variability of individual human brains and the partial volume, effects of functional emission computed tomography, images in complex anatomical 3D regions, as well as, describing the underlying multi-modal image processing, principles. METHODS: 3D atlas extraction is done directly by automated segmentation of individual magnetic resonance images of the patient's head. This is done in two steps: voxel-based classification of T1-weighted images for tissue differentiation (low-level processing) is followed by knowledge-based analysis of the classified images for extraction of 3D anatomical regions (high-level processing). For atlas-based quantification of co-registered functional images, 3D anatomical regions can be convoluted with an idealized point spread function of the emission computed tomography system, after which a partial volume-dependent threshold can be determined. RESULTS: Quantitative evaluation studies, based on 50 realistic software head phantoms and 24 image data sets obtained from healthy subjects and patients, show low misclassification rates and stable results for the neural network-based classification approach (mean +/- SD 3.587 +/- 0.466%, range 2.726-4.927%) as well as for the adjustable parameters of the knowledge-based approach. Computation time is <5 min for classification, <1 min for most of the extraction algorithms. The influence of the partial volume-dependent threshold is shown for an activation study. CONCLUSIONS: This new method allows 3D atlas generation without the need to warp individual image data to an anatomical or statistical brain atlas. Going beyond the purely tissue-oriented approach, partial volume effects of emission computed tomography images can be analyzed in complex anatomical 3D regions.

Algorithms↗

Influence of glycosaminoglycans on neurite morphology and outgrowth patterns in vitro.

The neuritic growth patterns obtained on substrates made of several glycosaminoglycans (GAGs) bound to type I collagen were analysed and compared in primary cultures of chick embryo dorsal root ganglion grown in serum-free supplemented medium. In 2-day cultures grown on type I collagen or heparan sulphate (HS)-collagen surfaces, ganglionic explants exhibit a dense, symmetrical network of long, parallel neuritic processes and very few flat migrating non-neuronal cells. In contrast, on either dermatan sulphate (DS), chondroitin-6-sulphate (C6S) or hyaluronic acid (HA)-bound collagen substrates, neurons form irregular nerve fibre patterns; indeed, neurites follow convoluted paths and often, after abrupt turns, totally reverse their direction of extension. Experiments were carried out in which a choice was given to growing neural processes between collagen or GAG-collagen substrates. While growth cones elongating over type I collagen easily cross the border with HS-bound collagen surface and indiscriminately extend on this substrate, in contrast, neurites generally avoid surfaces coated with DS, C6S or HA and change their direction of growth in order to stay on collagen. The binding of DS, C6S or HA, but not HS, to type I collagen thus decreases its ability to promote neurite elongation. The interaction of neuronal cells with these extracellular matrix components by restricting neurites in their paths of extension may, therefore, play a role in the patterning of the nervous circuitry.

Animals↗

Convolutional face finder: a neural architecture for fast and robust face detection.

In this paper, we present a novel face detection approach based on a convolutional neural architecture, designed to robustly detect highly variable face patterns, rotated up to +/-20 degrees in image plane and turned up to +/-60 degrees, in complex real world images. The proposed system automatically synthesizes simple problem-specific feature extractors from a training set of face and nonface patterns, without making any assumptions or using any hand-made design concerning the features to extract or the areas of the face pattern to analyze. The face detection procedure acts like a pipeline of simple convolution and subsampling modules that treat the raw input image as a whole. We therefore show that an efficient face detection system does not require any costly local preprocessing before classification of image areas. The proposed scheme provides very high detection rate with a particularly low level of false positives, demonstrated on difficult test sets, without requiring the use of multiple networks for handling difficult cases. We present extensive experimental results illustrating the efficiency of the proposed approach on difficult test sets and including an in-depth sensitivity analysis with respect to the degrees of variability of the face patterns.

Algorithms↗

[Glossary of terms used by radiologists in image processing].

We give the definition of 166 words used in image processing. Adaptivity, aliazing, analog-digital converter, analysis, approximation, arc, artifact, artificial intelligence, attribute, autocorrelation, bandwidth, boundary, brightness, calibration, class, classification, classify, centre, cluster, coding, color, compression, contrast, connectivity, convolution, correlation, data base, decision, decomposition, deconvolution, deduction, descriptor, detection, digitization, dilation, discontinuity, discretization, discrimination, disparity, display, distance, distorsion, distribution dynamic, edge, energy, enhancement, entropy, erosion, estimation, event, extrapolation, feature, file, filter, filter floaters, fitting, Fourier transform, frequency, fusion, fuzzy, Gaussian, gradient, graph, gray level, group, growing, histogram, Hough transform, Houndsfield, image, impulse response, inertia, intensity, interpolation, interpretation, invariance, isotropy, iterative, JPEG, knowledge base, label, laplacian, learning, least squares, likelihood, matching, Markov field, mask, matching, mathematical morphology, merge (to), MIP, median, minimization, model, moiré, moment, MPEG, neural network, neuron, node, noise, norm, normal, operator, optical system, optimization, orthogonal, parametric, pattern recognition, periodicity, photometry, pixel, polygon, polynomial, prediction, pulsation, pyramidal, quantization, raster, reconstruction, recursive, region, rendering, representation space, resolution, restoration, robustness, ROC, thinning, transform, sampling, saturation, scene analysis, segmentation, separable function, sequential, smoothing, spline, split (to), shape, threshold, tree, signal, speckle, spectrum, spline, stationarity, statistical, stochastic, structuring element, support, syntaxic, synthesis, texture, truncation, variance, vision, voxel, windowing.

Diagnostic Imaging↗

Stochastic completion fields; a neural model of illusory contour shape and salience.

We describe an algorithm- and representation-level theory of illusory contour shape and salience. Unlike previous theories, our model is derived from a single assumption: that the prior probability distribution of boundary completion shape can be modeled by a random walk in a lattice whose points are positions and orientations in the image plane (i.e., the space that one can reasonably assume is represented by neurons of the mammalian visual cortex). Our model does not employ numerical relaxation or other explicit minimization, but instead relies on the fact that the probability that a particle following a random walk will pass through a given position and orientation on a path joining two boundary fragments can be computed directly as the product of two vector-field convolutions. We show that for the random walk we define, the maximum likelihood paths are curves of least energy, that is, on average, random walks follow paths commonly assumed to model the shape of illusory contours. A computer model is demonstrated on numerous illusory contour stimuli from the literature.

Algorithms↗

The structural organization of layer I of the adult human acoustic cortex. A Golgi and electron microscopy study.

The cellular morphology and the three dimensional cytoarchitecture of layer I of the adult human acoustic cortex were studied by using sagittal, transverse and tangential Golgi preparations and electron microscopy. The prominent neuron of layer I of the acoustic cortex is the Retzius-Cajal cell which is a solitary neuron accompanied by satellite astrocytes located mostly below the pial surface in the upper third of the layer. This neuron demonstrates a marked polymorphism in the various regions of the acoustic cortex. The anterior part of the Hessl convolutions contains Retzius-Cajal cells which are horizontal, multipolar forming dense dendritic arborization by extending long horizontal dendrites to all directions within a tangential plane parallel to the surface of the convolutions. The axon of the Retzius-Cajal cell is a long myelinated nerve fibre which mostly run horizontally, parallel to the pial surface, descending finally to the deeper parts of the layer and projecting a large number of axonic collaterals which radiate in all directions forming dense axonic networks. The Retzius-Cajal cell in the posterior part of the Hessl convolutions is a large polyhedral or triangular cell which extends a large number of dendrites, forming two dendritic networks: one in the upper third of the layer and another in middle part of it. Both of the networks communicate with the axonic collaterals of the Retzius-Cajal cells, forming numerous axodendritic synapses as can be clearly seen in electron microscopy.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

Learning optimized features for hierarchical models of invariant object recognition.

There is an ongoing debate over the capabilities of hierarchical neural feedforward architectures for performing real-world invariant object recognition. Although a variety of hierarchical models exists, appropriate supervised and unsupervised learning methods are still an issue of intense research. We propose a feedforward model for recognition that shares components like weight sharing, pooling stages, and competitive nonlinearities with earlier approaches but focuses on new methods for learning optimal feature-detecting cells in intermediate stages of the hierarchical network. We show that principles of sparse coding, which were previously mostly applied to the initial feature detection stages, can also be employed to obtain optimized intermediate complex features. We suggest a new approach to optimize the learning of sparse features under the constraints of a weight-sharing or convolutional architecture that uses pooling operations to achieve gradual invariance in the feature hierarchy. The approach explicitly enforces symmetry constraints like translation invariance on the feature set. This leads to a dimension reduction in the search space of optimal features and allows determining more efficiently the basis representatives, which achieve a sparse decomposition of the input. We analyze the quality of the learned feature representation by investigating the recognition performance of the resulting hierarchical network on object and face databases. We show that a hierarchy with features learned on a single object data set can also be applied to face recognition without parameter changes and is competitive with other recent machine learning recognition approaches. To investigate the effect of the interplay between sparse coding and processing nonlinearities, we also consider alternative feedforward pooling nonlinearities such as presynaptic maximum selection and sum-of-squares integration. The comparison shows that a combination of strong competitive nonlinearities with sparse coding offers the best recognition performance in the difficult scenario of segmentation-free recognition in cluttered surround. We demonstrate that for both learning and recognition, a precise segmentation of the objects is not necessary.

Learning↗

On neural blind separation with noise suppression and redundancy reduction.

Noise is an unavoidable factor in real sensor signals. We study how additive and convolutive noise can be reduced or even eliminated in the blind source separation (BSS) problem. Particular attention is paid to cases in which the number of sensors is larger than the number of sources. We propose various methods and associated adaptive learning algorithms for such an extended BSS problem. Performance and validity of the proposed approaches are demonstrated by extensive computer simulations.

Algorithms↗

MO-GCAN: multi-omics integration based on graph convolutional and attention networks.

MOTIVATION: Cancer subtypes play a critical role in disease progression, prognosis, and treatment, making their detection essential for tailoring precision medicine. Studies have shown that multi-omics integration outperforms single-omics approaches in cancer subtyping tasks. However, due to the high-dimensionality of multi-omics data, many existing studies either fail to capture the correlation between true labels and learned features, or lack sufficient capacity to model complex biological representations. These limitations hinder the full potential of leveraging the rich and complementary information embedded in multi-omics datasets. RESULT: We propose a framework that leverages supervised feature learning and classification based on a graph-based learning approach with attention mechanism for cancer subtyping. More specifically, we train graph convolutional network models on each omics dataset to extract latent representations, which are then concatenated to form a comprehensive multi-omics feature embedding. We further develop sample fusion network based on the omics-specific graphs, incorporating the derived features and feeding them into a graph attention model for subtype classification. This two-stage multi-omics framework is applied to eight cancer types, with performance evaluated in terms of test accuracy, training time, macro-averaged precision, recall, and F-score. Experimental results show that the proposed method outperforms state-of-the-art approaches across various cancer types. Additionally, we provide empirical evidence supporting the hypothesis that retaining a limited number of high-confidence edges and utilizing enriched embeddings from intermediate graph neural network layers can improve predictive performance. AVAILABILITY AND IMPLEMENTATION: Data and the code are available at https://github.com/YD-00/MO-GCAN-Updated.git.

Neoplasms↗