A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Paper introduces a graph-based approach for retrosynthesis prediction.
The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on graph-to-graph translation methods for molecular optimization. In particular, we realize …
METRO predicts reactions using minimal templates, reducing computational overhead and achieving state-of-the-art results.
This paper uses MIL and MHCNN-RNN to predict precursors to aviation safety events.
New method identifies precursors of financial crises in market correlation structures.
In this paper mechanisms of reversion - momentum transition are considered. Two basic nonlinear mechanisms are highlighted: a slow and fast bifurcation. A slow bifurcation leads to the equilibrium evolution, preceded by stability loss delay of a control parameter. A single order parameter is introduced by Markovian cha…
Paper proposes a method to design molecules with specific properties.
Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees that the molecules can actually be synthesized in practice. We propose a new molecu…
Although machine learning has been successfully used to propose novel molecules that satisfy desired properties, it is still challenging to explore a large chemical space efficiently. In this paper, we present a conditional molecular design method that facilitates generating new molecules with desired properties. The p…
A new model designs molecules with desired properties.
In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language process…
SILVR generates new molecules fitting protein binding sites.
GCDM generates valid large 3D molecules and optimizes existing molecules.
Modof-pipe optimizes molecules by modifying a single site, outperforming state-of-the-art methods.
This article demonstrates the possibility of constructing indicators of critical and crisis phenomena in the volatile market of cryptocurrency. For this purpose, the methods of the theory of complex systems such as recurrent analysis of dynamic systems and the calculation of permutation entropy are used. It is shown th…
Improved RL model for fragment-based molecule generation.
CORE optimizes molecules by copying or generating substructures, improving accuracy.
A new method improves molecule generation accuracy and efficiency.
Generative model learns to create molecules with multiple properties using interpretable substructures.
A new deep model generates molecules by fragments, improving validity and uniqueness.
We present a framework, which we call Molecule Deep -Networks (MolDQN), for molecule optimization by combining domain knowledge of chemistry and state-of-the-art reinforcement learning techniques (double -learning and randomized value functions). We directly define modifications on molecules, thereby ensuring 100…
In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which can be of medical and biological importance. Graphs are are useful in this prob…
Generative neural network designs novel 3D molecules with specified properties.
Equivariant diffusion model generates 3D molecules efficiently.
Searching new molecules in areas like drug discovery often starts from the core structures of candidate molecules to optimize the properties of interest. The way as such has called for a strategy of designing molecules retaining a particular scaffold as a substructure. On this account, our present work proposes a scaff…
We obtain multirelative connectivity statements about spaces of Poincare embeddings, as precursors to analogous statements about spaces of smooth embeddings. The latter are the key to convergence results in the functor calculus approach to spaces of embeddings.
Recent methods for generating novel molecules use graph representations of molecules and employ various forms of graph convolutional neural networks for inference. However, training requires solving an expensive graph isomorphism problem, which previous approaches do not address or solve only approximately. In this wor…
Bayesian optimization improves molecule design by addressing three pitfalls.
The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally matter engineering -- generally denoted as inverse design -- was based massively on…
Designing a new drug is a lengthy and expensive process. As the space of potential molecules is very large (10^23-10^60), a common technique during drug discovery is to start from a molecule which already has some of the desired properties. An interdisciplinary team of scientists generates hypothesis about the required…
New model generates larger molecules more effectively.
Graph neural network predicts protonation energies of oxygen atoms in bio-oil molecules.
AI and HPC help screen millions of molecules for SARS-CoV-2 treatments.
A new graph model HMG and neural network HMGNN improve molecule property predictions.
Molecular optimization aims to discover novel molecules with desirable properties. Two fundamental challenges are: (i) it is not trivial to generate valid molecules in a controllable way due to hard chemical constraints such as the valency conditions, and (ii) it is often costly to evaluate a property of a novel molecu…
CogMol designs novel drug-like molecules for SARS-CoV-2 targets.
A set of molecular descriptors whose length is independent of molecular size is developed for machine learning models that target thermodynamic and electronic properties of molecules. These features are evaluated by monitoring performance of kernel ridge regression models on well-studied data sets of small organic mole…
VecMol generates 3D molecules as continuous vector fields, overcoming modality and geometry constraints.
Recent studies illustrate how machine learning (ML) can be used to bypass a core challenge of molecular modeling: the tradeoff between accuracy and computational cost. Here, we assess multiple ML approaches for predicting the atomization energy of organic molecules. Our resulting models learn the difference between low…
The new wave of successful generative models in machine learning has increased the interest in deep learning driven de novo drug design. However, assessing the performance of such generative models is notoriously difficult. Metrics that are typically used to assess the performance of such generative models are the perc…
We study precursors to the global market crash that occurred on all main stock exchanges throughout the world in October 2008 about three weeks after the bankruptcy of Lehman Brothers Holdings Inc. on 15 September. We examine the collective behavior of stock returns and analyze the market mode, which is a market-wide c…
Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that molecules interact with each other, both in terms of steric complementarity, as well …
The study of the critical dynamics in complex systems is always interesting yet challenging. Here, we choose financial market as an example of a complex system, and do a comparative analyses of two stock markets - the S&P 500 (USA) and Nikkei 225 (JPN). Our analyses are based on the evolution of crosscorrelation struct…
MAT uses attention mechanism for molecule property prediction.
Method scales up ML science by measuring multiple molecules at once.
Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on either 1-D or 2-D representations of typically small, drug-like molecules. Howev…
MoleculeSTM learns from molecule structures and texts for better drug design.
We present a machine learning algorithm for the prediction of molecule properties inspired by ideas from density functional theory. Using Gaussian-type orbital functions, we create surrogate electronic densities of the molecule from which we compute invariant "solid harmonic scattering coefficients" that account for di…