Deep models learn biases from datasets, hindering understanding of binding mechanisms.
problem Dataset biases prevent deep models from revealing fragment logic of protein-ligand binding.
method Attribution method to identify and exploit dataset biases in neural networks.
result Deep models can be fooled into learning spurious correlations from biased datasets.
iDeepA predicts RNA-protein binding sites from RNA sequences using a CNN with attention.
problem Predicting RNA-protein binding sites from raw RNA sequences efficiently.
method Attention based convolutional neural network (iDeepA) encoding RNA sequences into one-hot encoding, followed by a CNN with an attention mechanism.
result iDeepA achieves comparable performance to state-of-the-art methods on CLIP-seq data.
Prototype Matching Network (PMN) improves genomic TFBS prediction.
problem Predicting Transcription Factor Binding Sites (TFBSs) with hundreds of TFs as labels.
method Prototype Matching Network (PMN) that learns motif-like features and TF-TF interactions.
result PMN significantly outperforms baselines on a large TFBS dataset.
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.
NeuralMD accelerates protein-ligand binding simulations 1Kx faster.
problem Accurate and efficient simulation of protein-ligand binding dynamics.
method Physics-informed multi-grained group symmetric framework with BindingNet and augmented neural differential equation solver.
result Achieves over 1Kx speedup and up to 15x reduction in reconstruction error compared to standard methods.
Developed accurate empirical potentials for Si:H nanowires using multi-fidelity Gaussian process.
problem Accurate modeling of Si:H nanowires using fast but inaccurate empirical potentials and slow but accurate first-principle calculations.
method Employed multi-fidelity Gaussian process regression to integrate low-fidelity empirical potential data with high-fidelity first-principle calculations.
result Demonstrated the accuracy of developed empirical potentials for Si:H nanowires.
Study on binding numbers of tight contact structures on lens spaces L(n,1).
problem Determining the minimum number of binding components for tight contact structures on lens spaces.
method Using the d3-invariant, restrictions on planar monodromy factorizations, and the Durst-Kegel algorithm. result The binding number of universally tight contact structures on L(n,1) is equal to n. DeepDTA predicts drug-target binding affinities using deep learning.
problem Predicting the continuum of binding strength values between drugs and targets.
method Uses deep learning, specifically CNNs, to model 1D representations of drug and target sequences.
result Deep learning model outperforms state-of-the-art methods in predicting DT binding affinities.
The study shows examples of contact 3-manifold binding sums that fail to preserve certain properties.
problem Examples of contact 3-manifold binding sums that fail to preserve properties like tightness or symplectic fillability.
method Examples and proofs of vanishing Heegaard Floer contact invariant for Stein fillable manifolds.
result Binding sums of contact 3-manifolds do not preserve properties such as tightness or symplectic fillability.
New method shows links can be braided open book bindings.
problem Understanding fibered links and their bindings.
method Mutual arc presentations and braided open books.
result Every fibered link is the binding of a braided open book.
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.
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.
We study an explicit construction of planar open books with four binding components on any three-manifold which is given by integral surgery on three component pure braid closures. This construction is general, indeed any planar open book with four binding components is given this way. Using this construction and resul…
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.
GEFA predicts drug-target affinity using graph neural networks.
problem Accurate prediction of drug-target interactions for rapid drug repurposing.
method GEFA (Graph Early Fusion Affinity) is a novel graph-in-graph neural network with attention mechanism.
result GEFA effectively models drug-target interactions, demonstrating the effectiveness of pre-trained protein embedding and nested graph representation.
Two ML frameworks predict antibody properties using structural data.
problem Predicting antibody properties using sequence and structural data.
method ANTIPASTI and INFUSSE models using graph representations and neural networks.
result ANTIPASTI predicts binding affinity; INFUSSE predicts residue flexibility.
Let T denote a binding component of an open book (Σ,φ) compatible with a closed contact 3-manifold (M,ξ). We describe an explicit open book (Σ′,φ′) compatible with (M,ζ), where ζ is the contact structure obtained from ξ by performing a full Lutz twist along T. Here, (Σ′,φ′) is obtained from $(Σ, …
We introduce the notion of a nested open book, a submanifold equipped with an open book structure compatible with an ambient open book, and describe in detail the special case of a push-off of the binding of an open book. This enables us to explicitly describe a natural open book decomposition of a fibre connected sum …
AKOrN uses synchronized neurons to improve AI tasks.
problem Improving AI performance through better neural representations.
method AKOrN introduces synchronized neurons to replace threshold units.
result AKOrN improves performance across various AI tasks.
Deep learning predicts protein-ligand binding affinity with high accuracy.
problem Predicting protein-ligand binding affinity for drug discovery.
method 3D convolutional neural network trained on CASF and Astex Diverse Set benchmarks.
result Deep learning model outperformed classical scoring functions.
Quantum transport maps network clusters on a circle, revealing complex community structures.
problem Identifying community structures in complex networks.
method Proposes using the Laplace transform of quantum transport to map network nodes onto a circle, forming clusters.
result QTC algorithm effectively clusters network nodes, robust to cluster heterogeneity.
This paper studies a subgroup of the Goeritz group related to Heegaard splittings induced by openbook decompositions.
problem Understanding the subgroup of the Goeritz group associated with Heegaard splittings from openbook decompositions.
method Analyzes the mapping class group of a 3-manifold, focusing on elements that preserve the binding and commute with the monodromy.
result Characterizes the Goeritz group subgroup as a quotient of specific mapping class groups and provides a criterion for certain elements.
New taxonomy reveals different detection limits for various types of fraud.
problem Existing fraud detection treats all fraud as the same, ignoring its diverse forms.
method Introduced an observation-mechanism taxonomy with five fraud classes.
result Separate estimation by fraud class outperforms pooled estimation.
siRF identifies transcription factor binding near enhancers in flies.
problem Identifying functional transcription factor binding near enhancers.
method Signed iterative random forests (siRF) for machine learning.
result Infers regulatory interactions among transcription factors and enhancers.
Computational approaches to drug discovery can reduce the time and cost associated with experimental assays and enable the screening of novel chemotypes. Structure-based drug design methods rely on scoring functions to rank and predict binding affinities and poses. The ever-expanding amount of protein-ligand binding an…
Consider a transverse knot which is the binding of an open book for the ambient contact manifold. In this paper, we show that the transverse invariants defined by Lisca, Ozsvath, Stipsicz, and Szabo (LOSS) are nonvanishing for such transverse knots. This is true regardless of whether or not the ambient contact structur…
We show that if (B,π) is an open book decomposition of a contact 3-manifold (Y,ξ), then the complement of the binding B has no Giroux torsion. We also prove the sutured Heegaard-Floer c-bar invariant of the binding of an open book is non-zero.
We propose a specialized string kernel for small bio-molecules, peptides and pseudo-sequences of binding interfaces. The kernel incorporates physico-chemical properties of amino acids and elegantly generalize eight kernels, such as the Oligo, the Weighted Degree, the Blended Spectrum, and the Radial Basis Function. We …
When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently, externally learned memory models have proven to be effective methods for reasoning ov…
MIMONets speed up neural network inference by processing multiple inputs in parallel.
problem Reducing computational cost in neural network inference for large datasets.
method Proposes MIMONets, which augment neural network architectures with variable binding mechanisms to handle multiple inputs in superposition.
result Achieves significant speedups (2-4x) with minimal accuracy loss, demonstrating adaptability across different architectures.
Paper presents a new model to predict peptide:MHC-II interactions.
problem Predicting peptide interactions with MHC-II for vaccine design and immune response understanding.
method Developed a trans-allelic prediction model using sequence and structural data.
result Model predicts interactions for all three human MHC-II loci and performs comparably to state-of-the-art methods.
NucleusDiff models atomic nuclei interactions to prevent separation violations in drug design.
problem Maintaining minimum pairwise distance between atoms to avoid separation violations in drug design.
method Enforces distance constraint between atomic nuclei and manifolds in a diffusion model.
result Reduces separation violations by up to 100.00% and enhances binding affinity by up to 22.16%.
Parametric insurance offers better risk-sharing in high-risk settings than traditional indemnity insurance.
problem High-risk environments where traditional indemnity insurance is unaffordable or ineffective.
method Comparison of excess-of-loss indemnity insurance and parametric insurance within a mean-variance framework, considering fixed costs and binding budget constraints.
result Parametric insurance yields higher welfare for risk-averse individuals, especially when indemnity insurance is impractical.
Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription factor binding site search as well. However, understanding of the roles of nega…
BIND removes background noise from binary matrices, improving detection accuracy and fairness.
problem Real data often violates the i.i.d assumption for binary matrix entries, leading to inaccurate detection.
method BIND optimizes detection by estimating row- and column-wise mixture distributions and eliminating background noise.
result BIND effectively removes background noise and increases detection accuracy and fairness.
Language models fail to execute simple steps, showing gating and binding errors.
problem Procedural hallucinations in language models, failing to execute simple steps.
method Analyzed long-context binding tasks, identifying gating and binding errors.
result Procedural errors are due to gating and binding failures, with recency bias contributing to the latter.
Deep models generate and optimize DNA sequences for protein binding.
problem Designing DNA sequences with desired properties.
method Three approaches: GAN for synthetic sequences, activation maximization for design, and a combined method.
result Generated DNA sequences have superior properties to those in training data.
The paper optimizes forecasting for risk-adjusted decisions under trading frictions.
problem Optimizing forecasting accuracy for investment decisions in the presence of transaction costs.
method Develops a utility-weighted calibration criterion to minimize decision loss net of costs.
result Utility-weighted calibration reduces decision loss by over 30% and improves Sharpe ratio.
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a drug-like molecule to a given target. These models require expert-level knowled…
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.
DeepRAM evaluates and selects the best deep learning architecture for DNA/RNA binding specificity prediction.
problem Selecting the best deep learning architecture for predicting DNA/RNA binding specificity.
method Systematic exploration of various deep learning architectures using deepRAM, an end-to-end deep learning tool.
result A k-mer embedding convolutional layer and recurrent layer architecture outperforms other methods.
Adaptive anchor methods improve multi-modal learning by balancing intra-modal and inter-modal information.
problem Fixed anchor methods limit multi-modal learning by over-reliance on a single modality and inadequate cross-modal correlation.
method Adaptive anchor methods using centroid-based anchors from all modalities.
result Adaptive anchor methods like CentroBind consistently outperform fixed anchor methods across various datasets.
SILVR generates new molecules fitting protein binding sites.
problem Generating novel small molecule compounds for drug design.
method Selective Iterative Latent Variable Refinement (SILVR) for diffusion-based molecule generation.
result SILVR can generate new molecules similar in shape to original fragments without protein knowledge.
Optimizes ligand binding poses using CNNs and atomic grids.
problem Improving the accuracy of docking predictions for drug discovery.
method Differentiable atomic grid representation, CNN for scoring and optimization.
result Iteratively-trained CNNs outperform single CNNs in optimizing poses.
The study tests a functional-form restriction on risk exposure dynamics using margin debt data.
problem Understanding risk exposure dynamics under capital constraints and slack.
method Testing a regime-conditional functional-form restriction on aggregate risk-exposure dynamics implied by VaR-constrained intermediary models.
result The contraction and growth of exposures under capital constraints and slack are observed and tested.
In this note we define three invariants of contact structures in terms of open books supporting the contact structures. These invariants are the support genus (which is the minimal genus of a page of a supporting open book for the contact structure), the binding number (which is the minimal number of binding components…
An investor with constant relative risk aversion and an infinite planning horizon trades a risky and a safe asset with constant investment opportunities, in the presence of small transaction costs and a binding exogenous portfolio constraint. We explicitly derive the optimal trading policy, its welfare, and implied tra…
In the present paper we describe compatible open books for the fibre connected sum along binding components of open books, as well as for the fibre connected sum along multi-sections of open books. As an application the first description provides simple ways of constructing open books supporting all tight contact struc…