Capsule Networks classify RAS protein structures with GPU acceleration.
problem Classifying RAS protein structures accurately and interpretably.
method Implemented Capsule Network architecture trained on 2D and 3D structural encodings.
result Capsule Network outperforms traditional CNNs in accuracy and interpretability.
We determine the structure of finitely generated groups which are quasi-isometric to symmetric spaces of noncompact type, allowing Euclidean de Rham factors If X is a symmetric space of noncompact type with no Euclidean de Rham factor, and $\Ga$ is a finitely generated group quasi-isometric to the product $\E^k\times…
It has been proved that there are no real hypersurfaces satisfying RA = 0 in non-flat complex space forms. In this paper we prove that the same is true in the case of CR submanifolds of maximal CR dimension, that is there are no CR submanifolds of maximal CR dimension satisfying RA = 0 in non-flat complex space forms.
This paper deals with naturally reductive pseudo-Riemannian 2-step nilpotent Lie groups $(N, \la \,,\,\ra_N)$, such that $\la \,,\,\ra_N$ is invariant under a left action. The case of nondegenerate center is completely characterized. In fact, whenever $\la \,,\, \ra_N$ restricts to a metric in the center it is proved h…
Consider the principal U(n) bundles over the dual of Grassmann manifolds $U(n)\ra U(n,m)/U(m) \stackrelπ\ra D_{n,m}$. Given a 2-dimensional subspace $\frakm' \subset \frakm $ ⊂u(n,m), assume either $\frakm'$ is induced by $X,Y \in U_{m,n}(\bbc)$ with X∗Y=μIn for some $μ\in \bbr$ or by $X…
The convexity theorem of Atiyah and Guillemin-Sternberg says that any connected compact manifold with Hamiltonian torus action has a moment map whose image is the convex hull of the image of the fixed point set. Sjamaar-Lerman proved that the Marsden-Weinstein reduction of a connected Hamitonian G-manifold is a strat…
A new approach RA improves stochastic optimization by executing multiple steps between subsample updates.
problem Improving the efficiency and effectiveness of stochastic optimization methods.
method Developed Retrospective Approximation (RA) which executes multiple steps between subsample updates using a deterministic solver.
result RA achieves almost sure and L1 consistency under weak conditions and optimizes iteration and oracle complexity. Deep learning framework predicts surface texture parameters and their uncertainties.
problem Predicting surface texture parameters and their uncertainties from multi-instrument datasets.
method Reproducible deep learning framework using multi-instrument dataset, quantile and heteroscedastic heads for uncertainty modeling, and post-hoc conformal calibration.
result High fidelity predictions (R2: Ra 0.9824, Rz 0.9847, RONt 0.9918) and well-modelled uncertainty targets (Ra_uncert 0.9899, Rz_uncert 0.9955).
We prove a generalization of Thom's transversality theorem. It gives conditions under which the jet map $f_*|_Y:Y\subseteq J^r(D,M)\ra J^r(D,N)$ is generically (for $f:M\ra N$) transverse to a submanifold Z⊆Jr(D,N). We apply this to study transversality properties of a restriction of a fixed map $g:M\ra P$ …
Improved RA detection with SNN outperforming baseline by 26.8% EER.
problem Improving RA detection systems' generalizability and discriminability.
method Multi-task learning with Siamese Neural Networks (SNN) and additional reconstruction loss.
result SNN outperforms baseline by 26.8% EER, and further improvement by 13.8% with reconstruction loss.
Paper introduces RAS for robust MTL with contamination.
problem Representation-based multi-task learning struggles with contamination.
method Robust and Adaptive Spectral (RAS) method.
result RAS prevents negative transfer and performs well with up to 80% contamination.
CoarsenRank improves robustness in rank aggregation despite model misspecification.
problem Rank aggregation under model misspecification in real-world scenarios.
method CoarsenRank designs a neighborhood of ideal preferences to handle agnostic noise-corrupted data.
result CoarsenRank achieves robustness against model misspecification within a defined neighborhood.
Develops Heuristic Portfolio Optimization (HPO) as an information-restricted projection of Markowitz/tangency solution
problem Practitioners allocate capital with forecast-light rules like equal weight, inverse volatility, risk parity, HRP, and RA-HRP
method Implies-return principle and fixed-tree cluster-Sharpe recursion
result Formalizes HPO maps, proves defect equals squared inefficiency, and identifies nodewise alphas as policy-gradient coordinates
Nonexistence of quasi-harmonic spheres is necessary for long time existence and convergence of harmonic map heat flows. Let (N,h) be a complete noncompact Riemannian manifolds. Assume the universal covering of (N,h) admits a nonnegative strictly convex function with polynomial growth. Then there is no quasi-harmoni…
The effective representation of proteins is a crucial task that directly affects the performance of many bioinformatics problems. Related proteins usually bind to similar ligands. Chemical characteristics of ligands are known to capture the functional and mechanistic properties of proteins suggesting that a ligand base…
A new framework uses text descriptions to improve protein design.
problem Lack of effective methods to incorporate textual descriptions in protein design.
method ProteinDT framework that combines text and protein structural information.
result ProteinDT significantly improves protein design accuracy and performance.
Efficiently predicts optimal transport plans using sliced potentials.
problem Predicting optimal transport plans across multiple measure pairs efficiently.
method Regression-based and objective-based amortization strategies using sliced optimal transport potentials.
result Efficient and accurate prediction of optimal transport plans for various tasks.
Deep learning models optimize protein sequences.
problem Optimizing protein properties through sequence design.
method Deep generative models guided by machine learning.
result Improved protein sequence generation from prior knowledge.
Mathematical pipeline identifies structural homology of knotted proteins.
problem Quantification and classification of protein structures, especially knotted proteins, require noise-free and complete data.
method Developed a geometric framework using persistent homology to analyze protein structures.
result Persistent homology accurately represents structural homology of knotted proteins and identifies geometric features of protein entanglement.
Feature selection predicts immune state changes in RA mouse model.
problem Predicting the immune state change after RA immunotherapy.
method Feature selection algorithms applied to mouse CIA model data.
result Selected features predict both T cell markers and treatment efficacy.
In this paper, we give a complete criterion for a discrete faithful representation $ρ:F_n \ra \pslc$ to be primitive stable. This will answer Minsky's conjectures about geometric conditions on $\H^3/ρ(F_n)$ regarding the primitive stability of ρ.
ProGen models protein sequences for synthetic biology.
problem Generating proteins without structural annotations.
method Trained a 1.2B-parameter language model on 280M protein sequences.
result ProGen generates proteins with fine-grained control and accuracy.
Paper proposes MLPCD for protein community detection in large PPI networks.
problem Identifying reliable protein communities from large-scale PPI networks.
method Integrates Gene Expression Data and uses Multi-source Learning with cloud computing.
result Demonstrates superior performance compared to existing methods.
New 3D protein analysis methods improve accuracy.
problem Lack of suitable learning algorithms for protein data.
method Intrinsic-Extrinsic Convolution and Pooling for 3D protein structures.
result Outperforms state-of-the-art methods on protein analysis tasks.
New method detects and compares folding pathways of knotted proteins.
problem Understanding the function of knots in protein folding.
method Topological analysis of protein knotoid distributions and entanglement.
result Reveals unique folding pathway for shallow knotted Carbonic Anhydrases.
Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stability are necessary to facilitate efficient protein design. However, accuracy of predic…
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.
PANDA predicts protein binding affinity changes from sequences, outperforming existing methods.
problem Accurately predicting changes in protein binding affinity due to mutations.
method Sequence-based machine learning approach using protein sequence information.
result PANDA achieves higher Pearson correlation coefficients than existing methods.
A new model explains protein interactions via electron delocalization.
problem Understanding how protein interactions affect each other.
method Quantized discrete differential geometry of n-simplices.
result Allosteric regulation follows from the model of interactions.
EBM predicts protein conformations at atomic scale using crystallized data.
problem Predicting the conformation of a side chain from its context within a protein structure.
method Energy-based model trained on crystallized protein data, evaluating performance on rotamer recovery task.
result EBM achieves performance close to state-of-the-art methods, including Rosetta energy function.
Knot theory applied to proteins, distinguishing folded linear chains.
problem Classifying proteins as unknots when intra-chain interactions are ignored.
method Developing knot theory for folded linear molecular chains, considering self-bonding, and using Gauss codes and quandles.
result Extended knot theory to distinguish topologies of proteins with intra-chain bonds.
Experimental determination of protein function is resource-consuming. As an alternative, computational prediction of protein function has received attention. In this context, protein structural classification (PSC) can help, by allowing for determining structural classes of currently unclassified proteins based on thei…
Mathematician summarizes protein geometry and mutation effects.
problem Understanding how proteins mutate and their structure-function relationship.
method Mathematical analysis of protein structures and functions, focusing on hydrogen bonds and secondary structure.
result Protein secondary structure regulates mutation by stabilizing or destabilizing regions.
Machine learning predicts protein structures and simulates dynamics.
problem Understanding and predicting protein folding and dynamics.
method Machine learning techniques for structure prediction and simulation.
result Machine learning enhances protein simulation and structure prediction.
A new method predicts protein functions using variable-length sequences.
problem Computational methods for protein function prediction are slow and inaccurate for long sequences.
method Two feature sets: single fixed-sized segments and multi-sized segments, using bi-directional LSTM. Combined with MLDA features.
result Significant improvement in accuracy for long protein sequences.
EGR refines and assesses protein complex structures.
problem Improving the accuracy of protein complex 3D structures for drug discovery.
method E(3)-equivariant graph neural network (GNN) for multi-task refinement and assessment.
result EGR achieves state-of-the-art performance in refining and assessing protein complexes.
We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be stored and manipulated as triples of permutations, and these methods are therefore a…
ProteinNet provides a standardized data set for protein structure prediction.
problem Lack of standardized data sets for protein structure prediction.
method Created high-quality sequence alignments, multiple data splits, and validation sets.
result Facilitates fair assessment of machine learning models for protein structure.
Two proteins are homologous if they have a common evolutionary origin, and the binary classification problem is to identify proteins in a candidate set that are homologous to a particular native protein. The feature (explanatory) variables available for classification are various measures of similarity of proteins. The…
Flexible Kernels for Protein Property Prediction
problem Predicting protein properties from sparse experimental data
method Sequence kernels using evolutionary substitution matrices and local linearity
result Data-efficient models of protein property landscapes
New method maps protein sequences to embeddings encoding structural information.
problem Inferring structural properties from amino acid sequences when structures are unknown.
method Representation learning using bidirectional LSTM models with structural similarity and residue contact maps.
result Trained embeddings improve structural similarity prediction and transfer to other tasks.
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.
A new diffusion model generates novel protein backbones without relying on pretrained networks.
problem Generating novel protein backbones without relying on pretrained networks.
method Developed a SE(3) invariant diffusion model on multiple frames, called FrameDiff.
result Generated designable protein monomers up to 500 amino acids without pretrained networks.
DeepProteomics uses neural networks to classify protein families efficiently.
problem Lack of functional annotation for many protein sequences in databases.
method Used RNN, LSTM, GRU, and deep neural network models on a dataset of 40,433 proteins.
result Achieved maximum 78% accuracy in classifying protein families.
Let A be a finite-dimensional local commutative algebra over R, dimRA=n. In this work we consider compact manifolds over A, and prove that the real part of an A-differentiable function is constant. Also we find estimates for the dimensions of some spaces of 1-form.
ProtTrans models predict protein features without evolutionary info.
problem Predicting protein features from amino acid sequences.
method Self-supervised deep learning on large protein datasets.
result ProtT5 embeddings outperform state-of-the-art for per-residue predictions.
WideDTA predicts drug-target binding affinity using text-based information.
problem Predicting drug-target binding affinity is a major challenge in drug discovery.
method WideDTA uses chemical and biological textual sequence information, including protein sequence, ligand SMILES, protein domains and motifs, and maximum common substructure words.
result WideDTA outperformed DeepDTA on the KIBA dataset, indicating the word-based sequence representation is a promising alternative.
PLUS pre-trains protein sequences with structural info, improving performance.
problem Lack of labeled protein sequences for training models.
method PLUS combines masked language modeling with same-family prediction for pre-training.
result PLUS-RNN outperforms other models in protein biology tasks.