A new reinforcement learning framework for multi-reward processing.
problem Understanding and modeling multi-reward interactions in complex systems.
method Two-stream reward processing with biological associations.
result Agents can react differently to different types of rewards.
New AI learns like neurons, generalizing from sparse rewards.
problem Designing AI that learns without explicit instructions and applies that learning to sparse reward scenarios.
method Combining neuroscience principles with computational efficiency, creating the Neurons-in-a-Box architecture.
result The architecture can learn efficiently and generalize across various tasks, including challenging environments.
Paper tackles zero-shot policy learning for agents in new environments.
problem Learning in one environment and generalizing to unseen environments without additional data.
method Decomposes sparse rewards into spatial-temporal regions and uses Model Predictive Control (MPC).
result Method achieves natural generalization to new environments, demonstrated on various tasks.
New metrics improve scRNA-seq perturbation modeling by reducing mode collapse.
problem Outperformed by simple mean prediction in scRNA-seq perturbation modeling.
method Introduce DEG-aware metrics (WMSE, Rw2(Δ)) and negative/positive baselines. result WMSE loss function reduces mode collapse and improves model performance.
BRAID fine-tunes diffusion models to optimize reward models in offline scenarios.
problem Combining generative modeling and model-based optimization in offline scenarios.
method Conservative fine-tuning of diffusion models using RL to optimize reward models.
result BRAID outperforms existing methods in offline data, avoiding invalid designs.
Despite its size and complexity, the human cortex exhibits striking anatomical regularities, suggesting there may simple meta-algorithms underlying cortical learning and computation. We expect such meta-algorithms to be of interest since they need to operate quickly, scalably and effectively with little-to-no specializ…
This study proposes hidden state curiosity to enhance RL models' resilience against noise.
problem Curiosity traps in RL models distract agents from discovering novel experiences.
method Proposed hidden state curiosity based on the Free Energy Principle to reward agents for KL divergence between predictive priors and posteriors.
result Agents with hidden state curiosity are more resilient against curiosity traps compared to those with prediction error curiosity.
This work improves online fine-tuning of diffusion models for specific properties.
problem Efficiently fine-tuning diffusion models to maximize specific properties.
method A novel reinforcement learning procedure that efficiently explores feasible samples.
result The method provides a regret guarantee and empirical validation across multiple domains.
New method steers protein design towards desired properties.
problem Challenges in designing proteins with specific structures and properties.
method Feynman-Kac framework applied to RFdiffusion models with guiding potentials.
result Significant improvement in predicted interface energetics and binder designability.
Deep active inference agents learn complex environments using Monte-Carlo methods.
problem Understanding and modeling biological intelligence in complex, continuous state-spaces.
method Neural architecture for deep active inference agents using multiple forms of Monte-Carlo sampling.
result Deep active inference agents can learn environmental dynamics and plan future actions.
Optimal algorithm selects biological models without prior info.
problem Determining the correct biological model without prior knowledge.
method Systems biology models and likelihood-free inference.
result Improved model selection performance over conventional methods.
Researchers develop flexible kernels for biological sequences with guaranteed reliability.
problem Challenges in applying machine learning to biological sequences, including unreliable methods.
method Theoretical analysis and development of modified kernels to ensure reliability and accuracy.
result Developed kernels that are universal, characteristic, and metrize the space of distributions for biological sequences.
Skip connections improve biologically-inspired learning rules.
problem Biologically-inspired learning rules often underperform compared to backpropagation.
method Introduced skip connections between intermediate layers in biologically-motivated learning rules.
result Skip connections can match the performance of backpropagation and are robust to hyper-parameters.
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.
Spatially positioned neurons in neural networks mimic biological systems.
problem Creating neural networks that can perform multiple tasks efficiently.
method Added spatial positions and proximity penalties to artificial neurons.
result Neurons naturally cluster, each responsible for a specific task.
SENA-discrepancy-VAE interprets latent causal factors in biological pathways.
problem Interpreting latent causal factors in biological pathways.
method SENA-discrepancy-VAE, a model based on discrepancy-VAE, that produces interpretable latent causal factors.
result Sena-discrepancy-VAE achieves comparable predictive performance with non-interpretable counterparts while providing biologically meaningful causal factors.
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.
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 …
Scalable GPLVM reduces complexity in scRNA-seq data, accounting for technical and biological confounders.
problem Complexity and confounders in scRNA-seq data hamper interpretation.
method Extended Gaussian process latent variable model (GPLVM) to handle large datasets.
result Framework reconstructs latent signatures and captures disease-specific gene expression.
Modulating masks improve lifelong reinforcement learning.
problem Catastrophic forgetting and task interference in lifelong reinforcement learning.
method Adapted modulating masks for deep lifelong reinforcement learning (LRL) with PPO and IMPALA agents.
result Superior performance in both discrete and continuous RL tasks compared to LRL baselines.
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.
New methods improve uncertainty quantification in dynamic biological systems.
problem Uncertainty in dynamic biological models due to nonlinearity and parameter sensitivity.
method Conformal inference methods for non-asymptotic guarantees.
result Enhanced robustness and scalability for diverse biological data structures.
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.
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.
We solve a lifecycle model in which the consumer's chronological age does not move in lockstep with calendar time. Instead, biological age increases at a stochastic non-linear rate in time like a broken clock that might occasionally move backwards. In other words, biological age could actually decline. Our paper is ins…
Minimum attention improves reinforcement learning performance in high-dimensional dynamics.
problem Improving reinforcement learning performance in high-dimensional nonlinear dynamics.
method Applying minimum attention as a regularization technique in reinforcement learning, including model-based and model-free approaches.
result Minimum attention outperforms state-of-the-art algorithms in few-shot adaptation and variance reduction.
Optimizes harvesting in biopharmaceutical fermentation with limited data.
problem High variability in fermentation outputs due to model risk with small data.
method Stochastic model, Bayesian approach, Markov decision process.
result Improves fermentation output and reduces variability.
Algorithm optimizes biological sequences using bootstrapped training with a score-conditioned generator.
problem Optimizing biological sequences for a black-box score function.
method Bootstrapped training of score-conditioned generator (BootGen) algorithm.
result Our method outperforms competitive baselines on biological sequential design tasks.
Parallelized bandit algorithms speed up decision-making.
problem Sequential exploration limits decision-making speed.
method Developed parallel contextual bandit algorithms.
result Regret nearly identical to sequential algorithms.
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.
This tutorial reviews RL-based methods for optimizing diffusion models to maximize specific metrics.
problem Optimizing diffusion models to generate samples that maximize specific metrics in practical applications.
method Various RL algorithms including PPO, differentiable optimization, reward-weighted MLE, value-weighted sampling, and path consistency learning.
result Exploration of strengths and limitations of RL-based fine-tuning algorithms and their benefits compared to non-RL-based approaches.
This thesis tackles data fusion issues across different biological scales and types.
problem Heterogeneity in data types and scales in systems biology.
method Developed statistical methods to fuse heterogeneous data sets.
result Advantages of proposed methods assessed through simulations and real data analysis.
Probabilistic graphical models (PGMs) have become a popular tool for computational analysis of biological data in a variety of domains. But, what exactly are they and how do they work? How can we use PGMs to discover patterns that are biologically relevant? And to what extent can PGMs help us formulate new hypotheses t…
DBNs improve accuracy of biological ODE models with missing data.
problem Uncertainty in biological ODE models with missing data.
method Converted ODE models to DBNs and used Particle Filtering for parameter estimation.
result DBNs can accurately infer model variables with missing data.
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.
Machine learning predicts biologic therapy outcomes in psoriasis patients.
problem Predicting long-term biologic therapy outcomes in psoriasis patients.
method Machine learning algorithms were used to predict drug discontinuation and treatment duration.
result Machine learning models accurately predict outcomes with high diagnostic accuracy and low MAE.
We present an analysis of the problem of identifying biological context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological context as descriptions of the species, tissue type and cell type that are associated …
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.
New approach tackles biological fluid adaptivity in AI.
problem Weak performance of AI in dynamic environments.
method Derives strategies from biological fluid adaptivity.
result Equips AI with fluid adaptivity similar to biology.
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.
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.
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.
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…
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…
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.
High-dimensional data acquired from biological experiments such as next generation sequencing are subject to a number of confounding effects. These effects include both technical effects, such as variation across batches from instrument noise or sample processing, or institution-specific differences in sample acquisiti…
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.
ODBAE detects complex phenotypes in biological data.
problem Challenges in identifying complex phenotypes from high-dimensional biological data.
method ODBAE (Outlier Detection using Balanced Autoencoders) identifies influential and high leverage points in latent relationships among multiple physiological parameters.
result ODBAE reveals novel metabolism-related genes and uncovers coordinated abnormalities across metabolic indicators.