During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank has increased more than 15 fold since 1999, which …
Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a…
Article compares different machine learning techniques for protein classification.
problem Predicting enzyme class from unknown proteins is challenging.
method Implemented seven classification techniques on 4368 protein data.
result C5.0 classification technique gives highest accuracy and balanced performance.
Bayesian network models are finding success in characterizing enzyme-catalyzed reactions, slow conformational changes, predicting enzyme inhibition, and genomics. In this work, we apply them to statistical modeling of peptides by simultaneously identifying amino acid sequence motifs and using a motif-based model to cla…
Study tangle equations linking enzyme actions to knot theory.
problem Proving the Jones Unknot conjecture and understanding tangle solutions.
method Analyzing framed tangle equations and introducing Kauffman bracket ratios.
result Unique rational solutions for tangle equations imply the Jones Unknot conjecture.
Machine learning methods are used to discover complex nonlinear relationships in biological and medical data. However, sophisticated learning models are computationally unfeasible for data with millions of features. Here we introduce the first feature selection method for nonlinear learning problems that can scale up t…
This abstract reviews recent methods for predicting protein-ligand binding affinity.
problem Predicting protein-ligand binding affinity for various applications in life sciences.
method Traditional and deep learning models for binding affinity prediction.
result Improved predictive performance of AI-driven models.
In Biology, all motor enzymes operate on the same principle: they trap favourable brownian fluctuations in order to generate directed forces and to move. Whether it is possible or not to copy one such strategy to play the market was the starting point of our investigations. We found the answer is yes. In this paper we …
We present chemlambda (or the chemical concrete machine), an artificial chemistry with the following properties: (a) is Turing complete, (b) has a model of decentralized, distributed computing associated to it, (c) works at the level of individual (artificial) molecules, subject of reversible, but otherwise determinist…
New method learns diverse protein scaffolds for motif design.
problem Designing long, diverse protein scaffolds for specific motifs.
method E(3)-equivariant graph neural network for diffusion modeling.
result First to guarantee conditional sampling from diffusion models.
A new approach to protein language models combines latent space prediction with masked language modeling.
problem Improving protein language models by predicting amino acid identities at masked positions.
method A variant of masked language modeling that predicts latent targets only at masked positions, retaining the MLM cross-entropy.
result The new approach outperforms pure masked language modeling on 11 out of 16 downstream tasks.
Solving tangle equations is deeply connected with studying enzyme action on DNA. The main goal of this paper is to solve the system of tangle equations N(O+X1)=b1 and N(O+X2)=b2#b3, where X1 and X2 are rational tangles, and bi is a 2-bridge link, for i=1,2,3, with b2 and b3 nontrivial. We s…
Neural net reweighing improves selectivity in molecule binding studies.
problem Improving selectivity in neural net models for molecule binding studies.
method Greedy algorithm to reweight loss function based on Wasserstein distance.
result Proven to make neural net weights approach limiting distribution of another dataset.
Framework assesses treatment effects by risk groups in observational studies.
problem Evaluating treatment effects in observational studies with risk stratification.
method Five-step framework for risk-based assessment of treatment effect heterogeneity.
result Low-risk patients received negligible absolute benefits, while high-risk patients had pronounced effects.
This study connects prevalence and machine learning for diagnostic testing.
problem Uncertainty quantification in machine learning for diagnostic tests.
method Developed a numerical homotopy algorithm to estimate classification boundaries and quantify uncertainty.
result The proposed method stabilizes uncertainty quantification in machine learning for diagnostic tests.
New method detects RNA modifications without prior training, revealing novel sites.
problem Detecting RNA modifications with high accuracy and sensitivity.
method Anomaly detection using nanopore raw ionic current signals and nearest neighbor comparison.
result Detects diverse RNA modifications without prior training, including a novel 2'-O-methylated site in DENV.
Paper explores how unsupervised learning can be understood through linear algebra concepts.
problem Understanding unsupervised learning through linear algebra concepts.
method Introducing the concept of linearly independent populations and using them to solve for prevalence values.
result Unsupervised learning can be realized as a generalization of supervised learning.
Fuzzy prediction sets generalize binary predictions to include elements at varying confidence levels.
problem Binary prediction sets are limited; fuzzy prediction sets offer richer guarantees.
method Generalize prediction sets to fuzzy sets, showing they are e-values with merging properties.
result Optimal e-values lead to optimal fuzzy prediction sets, including optimal conformal prediction.
Paper defines predictive multiplicity and measures its severity in classification problems.
problem Challenges in machine learning due to competing models with conflicting predictions.
method Formal measures and integer programming tools for linear classification problems.
result Real-world datasets may admit competing models with wildly conflicting predictions.
A novel continual prediction model outperforms traditional one-time models in predicting AKI.
problem Optimally predicting AKI before it develops during a hospital stay.
method A novel continual prediction model that predicts AKI every time a patient's AKI-relevant variable changes in the EHR.
result The continual prediction model outperformed traditional one-time models, achieving a higher AUC of 0.724 compared to 0.653.
This paper re-examines conformal e-prediction and its advantages over conformal prediction.
problem The relationship between conformal prediction and conformal e-prediction.
method Systematic re-examination of conformal prediction and conformal e-prediction from a modern perspective.
result Conformal e-prediction has advantages such as ease of designing conditional predictors and guaranteed validity of cross-predictors.
Two new methods improve efficiency of conformal predictive systems.
problem Efficiency of conformal predictive systems in regression problems.
method Split conformal predictive systems and cross-conformal predictive systems.
result Cross-conformal predictive systems are more efficient but not guaranteed valid.
Self-calibrating conformal prediction improves interval efficiency and offers a practical alternative.
problem Improving the reliability and uncertainty quantification of machine learning predictions.
method Combines Venn-Abers calibration and conformal prediction for binary and regression problems.
result Improves interval efficiency through model calibration and offers practical alternatives.
Study uses deep learning to predict asset prices, finds complex target processes lead to meaningless predictions.
problem Complexity of successful price prediction models hinders understanding.
method Deep learning models for high-frequency price prediction, focusing on volatility and directional prediction.
result Inadequately defined target price process renders predictions meaningless.
The paper emphasizes the importance of joint predictions over marginal predictions for decision-making.
problem The need for accurate joint predictions in decision-making problems.
method The paper analyzes combinatorial decision problems, sequential predictions, and multi-armed bandits, introducing an approximate Thompson sampling algorithm and new regret bounds.
result Accurate joint predictions are essential for good performance in decision-making problems.
Behavior modification improves prediction accuracy by nudging user behavior.
problem Improving prediction accuracy using behavior modification techniques.
method Combining prediction and behavior modification with reinforcement learning algorithms.
result Behavior modification can make predictions more certain but may not generalize.
New adaptive conformal predictive systems developed.
problem Severe restrictions on adapting predictive distributions to test objects.
method Calibrating existing predictive systems to ensure full adaptability and validity.
result Developed fully adaptive split-conformal and cross-conformal predictive systems.
Predictions can shape outcomes, study helps predict these effects.
problem Understanding how predictions influence real-world outcomes.
method Causal identifiability analysis of prediction-covariate-outcome relationships.
result Standard supervised learning can identify transferable relationships from predictions.
Proposes feature conformal prediction for broader application in semantic feature spaces.
problem Establishing valid prediction intervals in semantic feature spaces.
method Extends conformal prediction to semantic feature spaces using deep representation learning.
result Feature conformal prediction outperforms regular conformal prediction under mild assumptions.
AutoCP automates the construction of accurate prediction intervals.
problem Creating valid and accurate prediction intervals for machine learning models.
method AutoML framework that optimizes prediction interval length for better accuracy and less conservatism.
result AutoCP significantly outperforms benchmark algorithms in constructing accurate prediction intervals.
Proposes a method to apply conformal prediction to probabilistic time series forecasting models.
problem Obtaining accurate prediction regions for multi-step time series forecasting with probabilistic models.
method Conformalises conditional normalising flows to generate potentially disjoint prediction regions.
result Improves predictive efficiency in time series forecasting with multimodal distributions.
ICP improves prediction intervals for continuous outcomes at lower computational cost.
problem Systematic bias in point predictions that undermines their use in decision-making.
method Develops Isotonic Conformal Prediction (ICP) framework to decouple calibration from prediction-set construction.
result SICP and TICP procedures match SC-CP coverage at lower computational cost.
Optimizes predictions for specific tasks using parametrized decision analysis.
problem Optimizing predictions for specific decision tasks of interest.
method Designs a class of parametrized actions for Bayesian decision analysis.
result Derives efficient and interpretable solutions for various action parametrizations and loss functions.
New measures for prediction validity and consonant plausibility introduced.
problem Challenges in predicting future observations and quantifying prediction uncertainty.
method Introducing Type-2 validity and using consonant plausibility measures and conformal prediction.
result Achieving both Type-1 and Type-2 validity through consonant plausibility measures and conformal prediction.
RFpredInterval package builds prediction intervals for random forests and boosted forests.
problem Quantifying uncertainty in random forest and boosted forest point predictions.
method 16 methods to build prediction intervals with random forests and boosted forests.
result The proposed method outperforms existing methods in building prediction intervals.
FPPI selectively uses predictions to improve inference efficiency.
problem Improving statistical inference with limited labeled data and heterogeneous prediction quality.
method Filtered Prediction-Powered Inference (FPPI) framework.
result FPPI achieves strictly improved asymptotic efficiency compared to existing methods.
COP improves online conformal prediction by incorporating data patterns, leading to tighter prediction sets.
problem Overly conservative prediction sets in online conformal prediction methods when data distribution shifts.
method Conformal Optimistic Prediction (COP) incorporating estimated cumulative distribution function of non-conformity scores.
result COP produces tighter prediction sets with valid coverage guarantees, outperforming other methods.
Proposes a model to update industrial data predictions based on temporal changes.
problem Improving prediction accuracy in industrial data analytics by addressing changing conditions over time.
method Integrates similarity and loss functions to estimate and update prediction models adaptively.
result The data renewal model enhances prediction accuracy by identifying and updating model changes.
Unified framework for estimating random forest prediction errors.
problem Estimating prediction errors for random forests.
method Novel estimator of conditional prediction error distribution function.
result Proposed estimators enable competitive prediction intervals.
Predicts food ingredient amounts from images.
problem Predicting relative amounts of ingredients from food images.
method Proposes two deep learning models for sparse and dense predictions, with semi-automatic data pre-processing.
result Encouraging experimental results on a recipe dataset.
This paper studies trade-offs in private prediction methods.
problem Leakage of training data information in machine learning predictions.
method Private training and private prediction methods with trade-offs.
result Private training methods outperform private prediction methods in various settings.
Conformal prediction helps quantify uncertainty but its use by humans is unclear.
problem Uncertainty quantification in predictions for human decision making.
method Decision theoretic framework for evaluating predictive uncertainty.
result Conformal prediction sets and human decision making goals are in tension.
New tree splitting criteria improve probabilistic predictions.
problem Improving tree-based nonparametric predictive distributions.
method Using proper scoring rules for tree splitting criteria.
result Trees with new splitting criteria produce better predictive distributions.
Prediction is arguably one of the most basic functions of an intelligent system. In general, the problem of predicting events in the future or between two waypoints is exceedingly difficult. However, most phenomena naturally pass through relatively predictable bottlenecks---while we cannot predict the precise trajector…
New method improves predictive systems with better theoretical guarantees.
problem Constructing predictive systems with out-of-sample calibration guarantees.
method Residual Distribution Predictive Systems (RDPs) that nest conformal predictive systems and offer flexibility.
result Empirically, RDPs perform competitively with conformal predictive systems and can be implemented with various regression methods.
Paper introduces PCP for efficient, reliable predictive inference.
problem Developing reliable predictive inference methods for target variables.
method Probabilistic conformal prediction using conditional random samples.
result PCP provides sharper predictive sets compared to existing methods.
A framework for private prediction sets using conformal prediction and differential privacy.
problem Jointly addressing reliability and privacy in machine learning predictions.
method Split conformal prediction with privatized quantile subroutine.
result Private prediction sets can be generated from privately-trained models.
Variational Prediction simplifies Bayesian inference without test time costs.
problem Bayesian inference's computational costs and posterior predictive distribution marginalization.
method Variational Prediction learns a variational approximation to the posterior predictive distribution using a variational bound.
result Directly learns a variational approximation to the posterior predictive distribution without test time marginalization costs.