New learning algorithm mimics biological neural networks.
problem Biologically implausible backpropagation for directed neural networks.
method Introduces new neuronal dynamics and learning rule for arbitrary architectures, sparsity-inducing pruning method, and dynamical-systems characterization.
result Prunes irrelevant connections and improves learning efficiency.
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex multi-level systems. We go one step further and advocate for the consideration of …
DCNs mimic neuronal networks for improved neural classification.
problem Lack of topological similarity between DNNs and biological neural networks.
method Developed DCNs with topologies inspired by real-world neuronal networks.
result High classification accuracy achieved by DCNs.
Proposes a novel network-based neighborhood regression for biological systems.
problem Lack of comprehensive analysis on biological modules using both global and local network data.
method Develops a community-wise least square optimization approach to analyze gene modules and their regulatory strength.
result Achieves exact minimax optimality and linear consistency in identifying gene module associations.
New learning rules for wide neural networks without backpropagation.
problem Training wide neural networks efficiently and without backpropagation.
method Input-weight alignment driven by gradient descent in the NTK regime.
result Biologically-motivated learning rules equivalent to backpropagation in wide networks.
DeepSIBA predicts biological effects of chemical structures using graph neural networks.
problem Predicting biological effects of chemical structures for drug discovery.
method Siamese Graph Convolutional Neural Networks for structure-biological effect mapping.
result Highly accurate predictions of biological effects for structurally dissimilar compounds.
Graph auto-encoder predicts unobserved node features from biological networks and omics data.
problem Integrating biological networks and continuous node features for better prediction.
method Graph neural networks and feature auto-encoders trained on feature reconstruction.
result Graph feature auto-encoder outperforms auto-encoders trained on graph reconstruction for predicting unobserved node features.
Oja's rule improves neural network training without engineered tricks.
problem Training deep neural networks with biological constraints.
method Incorporating Oja's plasticity rule into error-driven training.
result Stable, efficient learning in feedforward and recurrent architectures.
Fault-tolerant neural networks inspired by biological error correction codes.
problem Achieving reliable computation with unreliable neurons.
method Using biological error correction codes from grid cells in the mammalian cortex to develop a fault-tolerant neural network.
result Noisy biological neurons operate below a fault-tolerance threshold, suggesting a mechanism for reliable computation in the brain.
Biological neural network mimics CCA for multi-channel data.
problem Implementing CCA in a biologically plausible neural network.
method Derive an online CCA algorithm with local synaptic updates for multi-compartmental neurons.
result The derived neural network architecture and synaptic updates resemble cortical pyramidal neuron behavior.
We introduce bio-inspired artificial neural networks consisting of neurons that are additionally characterized by spatial positions. To simulate properties of biological systems we add the costs penalizing long connections and the proximity of neurons in a two-dimensional space. Our experiments show that in the case wh…
In this work, we perform an exploratory study on synthesizing deep neural networks using biological synaptic strength distributions, and the potential influence of different distributions on modelling performance particularly for the scenario associated with small data sets. Surprisingly, a CNN with convolutional layer…
Deep learning applied to biological data mining.
problem Mining complex biological data from diverse sources.
method Artificial neural networks, deep learning architectures.
result Deep learning techniques improve pattern recognition in biological data.
Training deep neural networks with the error backpropagation algorithm is considered implausible from a biological perspective. Numerous recent publications suggest elaborate models for biologically plausible variants of deep learning, typically defining success as reaching around 98% test accuracy on the MNIST data se…
Derives a biologically plausible neural network for Slow Feature Analysis.
problem Learning latent features from time series data.
method Starting from an SFA objective, derives Bio-SFA with a biologically plausible neural network implementation.
result Validates Bio-SFA on naturalistic stimuli, reproducing interesting properties of brain cells.
Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological observations might be heterogeneous and correspond to different biological mechanisms. Seco…
FsNet selects features for high-dimensional biological data efficiently.
problem Efficient feature selection for high-dimensional biological data.
method FsNet combines selection and reconstruction layers with tiny networks for weight prediction.
result FsNet outperforms standard DNNs on high-dimensional biological datasets.
New learning rules from information bottleneck improve deep learning without precise labels.
problem Training deep neural networks with backpropagation is biologically implausible.
method Kernelized information bottleneck principle with 3-factor Hebbian structure.
result The new learning rules perform nearly as well as backpropagation on image classification tasks.
Deep neural networks (DNNs) transform stimuli across multiple processing stages to produce representations that can be used to solve complex tasks, such as object recognition in images. However, a full understanding of how they achieve this remains elusive. The complexity of biological neural networks substantially exc…
Unified framework improves gene prioritization in disease studies.
problem Identifying genes involved in diseases using heterogeneous biological data.
method Network propagation-based gene prioritization with integrated biological information.
result Significant improvements in prioritizing genes not identified by traditional methods.
AR algorithm simplifies backpropagation with improved scalability and biological plausibility.
problem Improving backpropagation algorithms for complex neural networks and biological plausibility.
method Introducing learnable backwards weights and avoiding nonlinear derivative computations; relaxing frozen feedforward pass assumption.
result Simplified AR algorithm maintains performance on complex CNN architectures and challenging datasets.
New algorithm shows neural networks can learn without full backpropagation.
problem Stochastic gradient descent with backpropagation is non-biologically plausible.
method Random and fixed backpropagation weights in a feedback alignment algorithm.
result Error converges to zero exponentially fast in overparameterized networks.
Stochastic RNNs classify biological neural network paths with robust error bounds.
problem Classifying biological neural network paths.
method Modelled as a continuous-time stochastic recurrent neural network (RNN) with identity activation function, analysed in the robust regime.
result Generalisation error bound holds with high probability, showing the empirical risk minimiser is the best-in-class hypothesis.
Backpropagation is explained as a diffusion process in neural networks.
problem The biological plausibility of Backpropagation is questioned.
method Demonstrated that time-delayed neurons and forward-backward waves approximate the gradient in deep networks.
result Backpropagation can be interpreted as a diffusion process, approximating the gradient for non-fast inputs.
Develops DSD for analyzing multiscale biological networks.
problem Analyzing multiscale structure in biological networks.
method Data-driven diffusion process with multitemporal analysis.
result Parameter-free inference of intrinsic data structure.
Neural network models of early sensory processing typically reduce the dimensionality of streaming input data. Such networks learn the principal subspace, in the sense of principal component analysis (PCA), by adjusting synaptic weights according to activity-dependent learning rules. When derived from a principled cost…
GAIT-prop derives a biologically plausible learning rule from backpropagation.
problem Biological implausibility in traditional backpropagation for neural networks.
method GAIT-prop uses a top-down model to convert output error into plausible targets for weight updates.
result GAIT-prop and backpropagation give identical weight updates under certain conditions.
A new learning framework mimics biological STDP for neural networks.
problem To create a neural network that learns like biological systems.
method Developed MSTDP framework using Spike-timing dependent plasticity rules.
result Framework can learn and generate patterns without additional supervision.
Understanding biological network dynamics is a fundamental issue in various scientific and engineering fields. Network theory is capable of revealing the relationship between elements and their propagation; however, for complex collective motions, the network properties often transiently and complexly change. A fundame…
A new model uses 'ghost units' to enable efficient backpropagation in deep neural networks.
problem How to achieve efficient backpropagation in deep neural networks with biological plausibility.
method Introduces 'ghost units' to cancel feedback, enabling efficient error backpropagation.
result Demonstrates that the model can approximate error gradients and achieve good performance on classification tasks.
Sparse neural networks visualize paired transcriptomic and electrophysiological data.
problem Efficiently analyzing and visualizing paired multivariate neuroscientific data.
method Sparse deep neural networks with a two-dimensional bottleneck and group lasso penalty.
result Biologically interpretable two-dimensional visualizations of paired data.
TNDE quantifies dynamic gene drivers from single-cell snapshots.
problem Reconstructing time-resolved regulatory effects in biological processes.
method Time-varying Network Driver Estimation (TNDE) using shared graph attention encoder and partial optimal transport.
result TNDE identifies stage-specific driver genes in mouse erythropoiesis.
Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are locally co-regulated by shared biological mechanisms. To do this, we de…
Proposes a new neural network approach to credit assignment.
problem Credit assignment problem in deep neural networks.
method Contrastive similarity matching objective function.
result Deep networks learn to match similarity between layers.
Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various measurements. Two main supervised frameworks have been proposed: the local appro…
engGNN combines external and generated graphs to improve disease classification and biomarker discovery.
problem Challenges in integrating omics data due to high dimensionality and small sample sizes.
method Dual-graph framework that integrates external biological networks with data-driven generated graphs.
result engGNN outperforms state-of-the-art methods in disease classification and biomarker discovery.
New algorithm for online training of Spiking Neural Networks (SNNs).
problem Training Spiking Neural Networks (SNNs) online with BPTT-equivalent gradients.
method Clear separation of spatial and temporal gradient components, derived from biological insights.
result Online training of SNNs with BPTT-equivalent gradients and low time complexity.
A new theory explains large associative memory with biological plausibility.
problem Large associative memory in neurobiology and machine learning.
method Microscopic theory with hidden neurons and two-body interactions.
result Valid model of large associative memory with biological plausibility.
Deep neural networks (DNNs) are known for extracting useful information from large amounts of data. However, the representations learned in DNNs are typically hard to interpret, especially in dense layers. One crucial issue of the classical DNN model such as multilayer perceptron (MLP) is that neurons in the same layer…
New method identifies key genes affecting phenotypes in biological systems.
problem Identifying genes that drive specific phenotypes in complex biological systems.
method Data-driven observability decomposition using Koopman operators.
result Koopman operator representation identifies genes that drive phenotypes.
The power law has been observed in the degree distributions of many biological neural networks. Sparse deep neural networks, which learn an economical representation from the data, resemble biological neural networks in many ways. In this paper, we study if these artificial networks also exhibit properties of the power…
Finding biologically plausible alternatives to back-propagation of errors is a fundamentally important challenge in artificial neural network research. In this paper, we propose a learning algorithm called error-driven Local Representation Alignment (LRA-E), which has strong connections to predictive coding, a theory t…
DASH simplifies neural networks for gene regulatory dynamics using domain knowledge.
problem Pruning neural networks for gene regulatory dynamics lacks biologically meaningful structure learning.
method DASH uses domain-specific structural information to guide network pruning, leading to sparser, better interpretable models.
result DASH outperforms general pruning methods in gene regulatory network inference, yielding deeper insights.
This paper explores adaptive neural activation in RNNs for better learning.
problem Fixed neural activation functions limit the performance and adaptability of RNNs.
method Developed a novel parametric family of nonlinear activation functions inspired by biological neurons.
result Adaptive neural activation improves learning speed and performance in RNNs.
Defines metrics to compare neural network representations.
problem Comparing neural network representations across different architectures and tasks.
method Developed a family of metric spaces and modified existing measures to quantify representational dissimilarity.
result Identified relationships between neural representations and anatomical features.
Spiking neural networks perform similarly to deep networks on occluded images.
problem Robust object recognition in partially occluded images.
method Developed a two-layer spiking neural network trained on natural scenes with a biologically plausible learning rule, compared to deep convolutional networks.
result Spiking neural networks achieve good accuracy and robustness on stepwise pixel erasement tasks.
One conjecture in both deep learning and classical connectionist viewpoint is that the biological brain implements certain kinds of deep networks as its back-end. However, to our knowledge, a detailed correspondence has not yet been set up, which is important if we want to bridge between neuroscience and machine learni…
Log-Normal Multiplicative Dynamics improves low-precision training of neural networks.
problem Training large neural networks with low precision is unstable.
method Derive a Bayesian learning rule with log-normal posterior distributions and multiplicative updates.
result LMD achieves stable and accurate training for Vision Transformer and GPT-2.