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Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
Numerical optimization for the inverse design of photonic structures is a tool which is providing increasingly convincing results -- even though the wave nature of problems in photonics makes them particularly complex. In the meantime, the…
The discovery of therapeutic molecules is fundamentally a multi-objective optimization problem. One formulation of the problem is to identify molecules that simultaneously exhibit strong binding affinity for a target protein, minimal…
The goal of most materials discovery is to discover materials that are superior to those currently known. Fundamentally, this is close to extrapolation, which is a weak point for most machine learning models that learn the probability…
The measurable properties of the artifacts or objects in the computer, management, or finance disciplines are extrinsic, not inherent -- dependent on their problem definitions and solution instantiations. Only after the instantiation can…
Recent advancements in structure-based drug design (SBDD) have significantly enhanced the efficiency and precision of drug discovery by generating molecules tailored to bind specific protein pockets. Despite these technological strides,…
Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various…
Despite its fundamental importance and widespread use for assessing reaction success in organic chemistry, deducing chemical structures from nuclear magnetic resonance (NMR) measurements has remained largely manual and time consuming. To…
Indentation test is used with growing popularity for the characterization of various materials on different scales. Developed methods are combining the test with computer simulation and inverse analyses to assess material parameters…
System design tools are often only available as input-output blackboxes: for a given design as input they compute an output representing system behavior. Blackboxes are intended to be run in the forward direction. This paper presents a new…
Recent advances in quantum computers are demonstrating the ability to solve problems at a scale beyond brute force classical simulation. As such, a widespread interest in quantum algorithms has developed in many areas, with optimization…
Existing benchmarks for computational materials discovery primarily evaluate static predictive tasks or isolated computational sub-tasks. While valuable, these evaluations neglect the inherently iterative and adaptive nature of scientific…
Academic tabular benchmarks often contain small sets of curated features. In contrast, data scientists typically collect as many features as possible into their datasets, and even engineer new features from existing ones. To prevent…
Virtual cell (VC) models aim to predict cellular responses to any perturbations in silico and have emerged as a promising approach for drug discovery and precision medicine. Yet, a clear gap still remains: while models routinely reported…
Inverse design in science and engineering involves determining optimal design parameters that achieve desired performance outcomes, a process often hindered by the complexity and high dimensionality of design spaces, leading to significant…
We present a benchmark to facilitate simulated manipulation; an attempt to overcome the obstacles of physical benchmarks through the distribution of a real world, ground truth dataset. Users are given various simulated manipulation tasks…
Efficiently retrieving an enormous chemical library to design targeted molecules is crucial for accelerating drug discovery, organic chemistry, and optoelectronic materials. Despite the emergence of generative models to produce novel…
The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
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.…