Develops a new model for deep structured prediction with non-linear output transformations.
problem Limited neighborhood structure and inability to transform output space in deep structured models.
method Introduces a novel model that generalizes existing approaches and maintains applicability of inference techniques.
result Demonstrates improved flexibility and applicability of deep structured models through non-linear output transformations.
Torch-Struct simplifies structured prediction for deep learning.
problem Difficulty in integrating structured prediction algorithms with deep learning frameworks.
method Develops a library (Torch-Struct) that integrates structured prediction with vectorized, auto-differentiation-based frameworks.
result Significant performance gains over fast baselines and cross-algorithm efficiency.
E2Efold predicts RNA secondary structures better than previous methods.
problem RNA secondary structure prediction with constraints.
method End-to-end deep learning model using unrolled algorithms to enforce constraints.
result E2Efold predicts significantly better structures, especially for pseudoknotted structures.
Deep learning predicts protein structures accurately.
problem Predicting the 3D structure of proteins from amino acid sequences.
method Embeddings and deep learning models for backbone atom distance matrices and torsion angles.
result Competitive results in CASP13 and CASP12, surpassing previous winners.
Deep neural networks for structured prediction using kernel-induced losses.
problem Structured prediction tasks for images and texts.
method Designing a novel family of deep neural architectures that predict in a finite-dimensional subspace derived from the kernel-induced loss.
result Gradient descent algorithms can be used for structured prediction with deep neural networks.
Deep learning predicts stress fields in cantilevered structures accurately.
problem Accurate and fast structural analysis for cantilevered structures.
method Convolutional Neural Networks (CNN) for predicting von Mises stress fields.
result StressNet outperforms SCSNet with a mean relative error of 2.04%.
Deep learning uses layers of transformations to predict structured data with uncertainty.
problem Predicting structured high-dimensional data efficiently and with uncertainty.
method Applying layers of semi-affine input transformations to find features for probabilistic statistical methods.
result Achieves scalable prediction rules with uncertainty quantification and feature selection.
We introduce structured prediction energy networks (SPENs), a flexible framework for structured prediction. A deep architecture is used to define an energy function of candidate labels, and then predictions are produced by using back-propagation to iteratively optimize the energy with respect to the labels. This deep a…
dGAP learns feature dependencies and predicts targets simultaneously.
problem Learning task-agnostic statistical dependencies and missing explicit feature dependencies.
method Jointly optimizes a neural dependency graph and target prediction loss.
result dGAP can recover correct feature dependencies and improve prediction accuracy.
Machine learning improves RNA secondary structure prediction.
problem Stagnant performance of RNA secondary structure prediction methods.
method Machine learning, especially deep learning, is used to predict RNA secondary structures.
result Machine learning methods have improved the prediction of RNA secondary structures.
Study shows structured reservoirs improve deep ESN performance.
problem Improving performance of deep reservoir computing networks.
method Investigated structured reservoir topologies in deep ESNs.
result Structured reservoirs significantly enhance predictive performance.
PS8-Net improves eight-state protein secondary structure prediction accuracy.
problem Precise prediction of eight-state protein secondary structure (PSS) is crucial in bioinformatics.
method PS8-Net is a new deep convolutional neural network (DCNN) that uses a PS8 module with skip connections to enhance accuracy.
result PS8-Net achieves 76.89% Q8 accuracy on benchmark datasets.
SSH-Net: A Deep Neural Network for Predicting Failure Time Distribution Functions under Competing Risks with GPU Data
problem Predicting failure time distribution functions under competing risks
method Structured Segmented Hazard Deep Neural Network (SSH-Net)
result Prediction accuracy validated through simulation studies and GPU data
Deep learning predicts lung cancer prognosis by controlling collider effects.
problem Unbiased survival predictions for lung cancer patients.
method Dual task network predicting both outcome and collider, enforcing independence with OLS.
result Unbiased individual prognosis predictions are possible with deep learning.
Proposes a deep tree-ensemble model for multi-output prediction.
problem Lack of efficient solutions for multi-output prediction.
method Integrates tree-embeddings into deep tree-ensembles for structured output prediction.
result Superior performance in multi-label classification and multi-target regression tasks.
Survey on deep learning methods for stock market prediction.
problem Lack of comprehensive survey on deep learning methods for stock market prediction.
method Propose a novel taxonomy summarizing state-of-the-art models based on deep neural networks.
result Provide detailed statistics on datasets and evaluation metrics.
Deep learning model predicts protein-ligand binding modes from docking data.
problem Improving protein-ligand binding mode prediction accuracy.
method Dual-graph architecture with separate sub-networks for ligand topology and protein-ligand interactions.
result Deep learning model outperforms docking programs in binding mode prediction.
SDREM models complex network data with deep learning, improving link prediction.
problem Modeling latent structures in relational data with high-order node dependence.
method Scalable deep generative relational model (SDREM) incorporating high-order neighbourhood structure and novel data augmentation.
result Improved link prediction performance on real-world datasets.
Combines deep and statistical learning for structured data.
problem Structured high-dimensional data challenges.
method Generates nonlinear features via sparse regularization and stochastic optimisation, uses probabilistic output layer for uncertainty.
result Achieves best of scalability and uncertainty quantification.
A new framework enhances IDW models for complex industrial datasets.
problem Low performance of IDW models in complex industrial datasets.
method Deep reinforcement learning network to enhance IDW models and learn hyperparameters.
result The proposed framework achieves differential spatial prediction and is more accurate than current IDW models.
Novel GNN predicts drug-target interactions using protein-ligand 3D structures.
problem Accurate prediction of drug-target interactions for in silico drug design.
method 3D structure-embedded graph representations and distance-aware graph attention algorithm with gate augmentation.
result Our model outperforms docking and other deep learning methods in virtual screening and pose prediction.
Deep convolutional neural networks comprise a subclass of deep neural networks (DNN) with a constrained architecture that leverages the spatial and temporal structure of the domain they model. Convolutional networks achieve the best predictive performance in areas such as speech and image recognition by hierarchically …
GTDL methods fail to accurately model feature interactions in tabular data.
problem Accurate modeling of feature interactions in tabular data.
method Graph-based tabular deep learning methods using attention mechanisms and message-passing schemes.
result Current GTDL methods fail to recover meaningful feature interactions due to poor edge recovery.
In this paper, we tackle the real-world problem of predicting Yelp star-review rating based on business features (such as images, descriptions), user features (average previous ratings), and, of particular interest, network properties (which businesses has a user rated before). We compare multiple models on different s…
Enhanced mortality prediction model using EHR and free-text data.
problem Predicting one-year mortality in AMI patients.
method Used deep learning models with word embedding features from free-text discharge summaries.
result Significant improvement in model performance (92.89% accuracy, 0.928 F-measure).
Transforms ensemble predictions to maintain interpretability.
problem Loss of interpretability in deep ensembles.
method Proposes transformation ensembles that aggregate predictions while preserving interpretability.
result Transformation ensembles yield better predictions than individual models and maintain interpretability.
Compact Gaussian model approximates deep ensemble predictions.
problem Efficiently approximating deep ensemble models for image prediction.
method Sparse-structured multivariate Gaussian with Cholesky parameterization trained to match pre-trained ensemble outputs.
result Compact representation captures uncertainty and structured correlations explicitly.
This thesis improves protein contact prediction using unsupervised and supervised methods.
problem Improving accuracy of protein contact prediction.
method Unsupervised and supervised deep learning methods.
result A scoring system called diversity score for measuring contact novelty.
A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design. Current widely-adopted methods use physics-based energy functions to evaluate s…
New framework interprets deep neural networks through input structure.
problem Limited understanding of how input structure, network parameters, and optimization algorithms work together.
method Introducing a novel theoretical framework based on the compositional structure of piecewise linear activation functions.
result Shows that input instances can be grouped based on their similarity in the internal representation of the neural network.
DSPPs improve predictive distributions in scalable regression tasks.
problem Improving predictive distributions in scalable regression tasks.
method Inspired by DGPs, DSPPs use mini-batch training and kernel basis functions for uncertainty control.
result DSPPs provide significantly better calibrated predictive distributions than other methods.
Improved protein structure classification using weighted graphlets and deep neural networks.
problem Protein structure classification for function prediction.
method Developed a weighted network and graphlet-based measure, combined with a deep neural network.
result Significantly improved performance on 36 real datasets compared to existing methods.
Deep learning model integrates SMILES and molecular descriptors for EGFR inhibitor prediction.
problem Improving drug discovery by integrating structural and property data.
method Attention-based deep learning architecture trained on SMILES and molecular descriptors.
result Max MCC 0.58 and AUC 90% on EGFR inhibitors dataset, outperforming reference model.
Proposes FATTNN for tensor-on-tensor regression with improved prediction and reduced computation.
problem Tensor-on-tensor regression with complex tensor structures and nonlinear relationships.
method Integrates tensor factor models into deep neural networks to handle nonlinearity and reduce data dimensionality.
result Significant improvements in prediction accuracy and computational efficiency over traditional methods.
Multimodal deep learning improves toxicity prediction accuracy.
problem Improving prediction accuracy of chemical compound toxicity.
method Combining multiple neural network types and data representations.
result Significantly better accuracy on a toxicity benchmark.
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.
Recently, link prediction has attracted more attentions from various disciplines such as computer science, bioinformatics and economics. In this problem, unknown links between nodes are discovered based on numerous information such as network topology, profile information and user generated contents. Most of the previo…
Deep single-index Fréchet regression for metric space-valued outputs
problem Predicting outputs in non-Euclidean spaces
method DeSI (Deep Single-Index Fréchet Regression)
result Interpretable index direction for inputs
We introduce a deep learning architecture for structure-based virtual screening that generates fixed-sized fingerprints of proteins and small molecules by applying learnable atom convolution and softmax operations to each compound separately. These fingerprints are further transformed non-linearly, their inner-product …
Paper proposes an alternative to set losses for predicting unordered variables without imposing structure.
problem Learning unordered variables with unknown interrelations without imposing structure.
method Viewing set prediction as conditional density estimation and using deep energy-based models with gradient-guided sampling.
result Empirically demonstrates capability to learn multi-modal densities and produce different plausible predictions.
MiME learns EHR data structure for predictive healthcare tasks.
problem Data insufficiency in EHR for predictive healthcare tasks.
method Leverages multilevel structure of EHR data and learns multilevel embedding.
result MiME outperforms baseline methods in diverse evaluation settings.
Novel deep Gaussian process improves predictive uncertainty.
problem Flexible probabilistic data representations with tractable inference.
method Structured Gaussian variational family with marginalisation.
result Improved accuracy and calibrated uncertainty estimates.
Deep learning predicts heart failure readmission from clinical notes.
problem Predicting and preventing heart failure readmission.
method Convolutional Neural Networks (CNN) trained on clinical notes.
result Deep learning models outperform traditional machine learning methods in readmission prediction.
We describe \textit{deep exponential families} (DEFs), a class of latent variable models that are inspired by the hidden structures used in deep neural networks. DEFs capture a hierarchy of dependencies between latent variables, and are easily generalized to many settings through exponential families. We perform infere…
SARD improves deep learning clinical prediction performance.
problem Deep learning models struggle to match linear models in healthcare predictions.
method Reverse Distillation to initialize deep models, combined with contextual and temporal embeddings.
result SARD outperforms state-of-the-art methods on clinical prediction outcomes.
Study uses deep learning to predict stock trends with superior performance.
problem Predicting short-term equity trends with high accuracy.
method Dual-task multilayer perceptron (MLP) integrating technical signals and deep learning.
result Deep learning model outperforms linear baselines in multi-factor stock selection.
ISAAC audits deep models for drug-target interactions, revealing structural differences.
problem Deep models for DTI often use irrelevant features, making them hard to evaluate.
method ISAAC uses intervention-based structural auditing to evaluate model sensitivity.
result ISAAC reveals significant structural differences in DTI models' reasoning.
Deep learning predicts traffic flow on Sydney motorways.
problem Challenging traffic flow prediction due to inter-dependencies.
method Advanced deep learning framework using CNN-LSTM.
result Deep learning models outperform traditional methods.