arXiv research

Given two open books with equal pages we show the existence of an exact symplectic cobordism whose negative end equals the disjoint union of the contact manifolds associated to the given open books, and whose positive end induces the contact manifold associated to the open book with the same page and concatenated monod…

The paper refines the three-page index for links, proving a new bound and characterizing specific links.

Geometrization theorem, fibered case: Every three-manifold that fibers over the circle admits a geometric decomposition. Double limit theorem: for any sequence of quasi-Fuchsian groups whose controlling pair of conformal structures tends toward a pair of projectively measured laminations that bind the surface, there is…

This abstract reviews recent methods for predicting protein-ligand binding affinity.

RNA-binding proteins (RBPs) play crucial roles in many biological processes, e.g. gene regulation. Computational identification of RBP binding sites on RNAs are urgently needed. In particular, RBPs bind to RNAs by recognizing sequence motifs. Thus, fast locating those motifs on RNA sequences is crucial and time-efficie…

Improved linear upper bound for ribbonlength of knots.

The study shows examples of contact 3-manifold binding sums that fail to preserve certain properties.

New method shows links can be braided open book bindings.

PANDA predicts protein binding affinity changes from sequences, outperforming existing methods.

The identification of novel drug-target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where the goal is to determine whether a DT pair interacts or not. However, protein-l…

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…

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, …

One of the fundamental tasks in understanding genomics is the problem of predicting Transcription Factor Binding Sites (TFBSs). With more than hundreds of Transcription Factors (TFs) as labels, genomic-sequence based TFBS prediction is a challenging multi-label classification task. There are two major biological mechan…

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 …

Motivation: Prediction of the interaction affinity between proteins and compounds is a major challenge in the drug discovery process. WideDTA is a deep-learning based prediction model that employs chemical and biological textual sequence information to predict binding affinity. Results: WideDTA uses four text-based inf…

NeuralMD accelerates protein-ligand binding simulations 1Kx faster.

Deep neural networks have achieved state of the art accuracy at classifying molecules with respect to whether they bind to specific protein targets. A key breakthrough would occur if these models could reveal the fragment pharmacophores that are causally involved in binding. Extracting chemical details of binding from …

This paper studies a subgroup of the Goeritz group related to Heegaard splittings induced by openbook decompositions.

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 for a taut foliation F with one-sided branching of an atoroidal 3-manifold M, one can construct a pair of genuine laminations with solid torus complementary regions which bind every leaf of F in a geodesic lamination. These laminations come from a universal circle, a refinement of the universal circles pro…

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 …

Major histocompatibility complex class two (MHC-II) molecules are trans-membrane proteins and key components of the cellular immune system. Upon recognition of foreign peptides expressed on the MHC-II binding groove, helper T cells mount an immune response against invading pathogens. Therefore, mechanistic identificati…

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…

NucleusDiff models atomic nuclei interactions to prevent separation violations in drug design.

Parametric insurance offers better risk-sharing in high-risk settings than traditional indemnity insurance.

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.

Language models fail to execute simple steps, showing gating and binding errors.

Standard ChIP-seq peak calling pipelines seek to differentiate biochemically reproducible signals of individual genomic elements from background noise. However, reproducibility alone does not imply functional regulation (e.g., enhancer activation, alternative splicing). Here we present a general-purpose, interpretable …

We present a simple, modular graph-based convolutional neural network that takes structural information from protein-ligand complexes as input to generate models for activity and binding mode prediction. Complex structures are generated by a standard docking procedure and fed into a dual-graph architecture that include…

Quantum time evolution exhibits rich physics, attributable to the interplay between the density and phase of a wave function. However, unlike classical heat diffusion, the wave nature of quantum mechanics has not yet been extensively explored in modern data analysis. We propose that the Laplace transform of quantum tra…

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…

We study R-covered foliations of 3-manifolds from the point of view of their transverse geometry. For an R-covered foliation in an atoroidal 3-manifold M, we show that M-tilde can be partially compactified by a canonical cylinder S^1_univ x R on which pi_1(M) acts by elements of Homeo(S^1) x Homeo(R), where the S^1 fac…

A new model explains protein interactions via electron delocalization.

Adaptive anchor methods improve multi-modal learning by balancing intra-modal and inter-modal information.

SILVR generates new molecules fitting protein binding sites.

We unify recent neural approaches to one-shot learning with older ideas of associative memory in a model for metalearning. Our model learns jointly to represent data and to bind class labels to representations in a single shot. It builds representations via slow weights, learned across tasks through SGD, while fast wei…

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…

Given a closed binding curve $γ$ of a surface $Σ$, any equivalence class of marked complete hyperbolic structure can be decomposed into polygons(possibly with a puncture) with sides being hyperbolic geodesic segments. When $Σ$ is a one-holed torus and $γ= A^3 B^2$, we show that any equivalence class of marked complete …

Active learning speeds up antibody affinity prediction.

By recent results of Baker--Etnyre--Van Horn-Morris, a rational open book decomposition defines a compatible contact structure. We show that the Heegaard Floer contact invariant of such a contact structure can be computed in terms of the knot Floer homology of its (rationally null-homologous) binding. We then use this …

Developed accurate empirical potentials for Si:H nanowires using multi-fidelity Gaussian process.

Suppose $(B,π)$ is an open book supporting $(Y,ξ)$, where the binding $B$ is possibly disconnected, and $K$ is a braid about this open book. Then $B\cup K$ is naturally a transverse link in $(Y,ξ)$. We prove that the transverse link invariant in knot Floer homology, \[\widehat{t}(B\cup K)\in \widehat{HFK}(-Y,B\cup K),\…

CogMol designs novel drug-like molecules for SARS-CoV-2 targets.