Applications of modular co-design for <i>de novo</i> 3D molecule generation

Traditional computational approaches to design chemical species are limited by the need to compute properties for a vast number of candidates, e.g., by discriminative modeling. Therefore, inverse design methods aim to start from the desired property and optimize a corresponding chemical structure. From a machine learning viewpoint, the inverse design problem can be addressed through so-called generative modeling. Mathematically, discriminative models are defined by learning the probability distribution function of properties given the molecular or material structure. In contrast, a generative model seeks to exploit the joint probability of a chemical species with target characteristics. The overarching idea of generative modeling is to implement a system that produces novel compounds that are expected to have a desired set of chemical features, effectively sidestepping issues found in the forward design process. In this contribution, we overview and critically analyze popular generative algorithms like generative adversarial networks, variational autoencoders, flow, and diffusion models. We highlight key differences between each of the models, provide insights into recent success stories, and discuss outstanding challenges for realizing generative modeling discovered solutions in chemical applications.

There has been a recent focus within Alzheimer's Disease (AD) research on potential CSF biomarkers as diagnostic tools. PET imaging and CSF biomarkers have been used to determine the amyloid status of individuals when characterising AD. While these measures have largely correlated with each other, it is also suggested that there could be patients who can have discordant results. However, it is still unclear what proportion of AD subjects demonstrate the discordance. Additionally, whether these changes are associated with different pathological and clinical characteristics of the patients. Here, we investigated the discordance between CSF A&#x3b2;42:40 and amyloid status and evaluated whether there are any significant changes in their levels of tau aggregation. 313 participants' data were selected from the ADNI database. The cutoff for A&#x3b2;42:40 was then calculated using the Youden Index resulting from receiver operating characteristic (ROC) curve. The formula used was J&#xa0;=&#xa0;maxc Se (c) + Sp (c) - 1, resulting in a maximum cutoff of J&#xa0;=&#xa0;0.057 for A&#x3b2;42:40. This cutoff produced a discordance rate of 10.5%, with n&#xa0;=&#xa0;33 of 313 patients being discordant. We then performed t-tests to investigate the potential clinical differences between concordant and discordant patients. Independent samples t-tests indicated that levels of pTau181 and total Tau significantly differed between the concordant and discordant groups. pTau181 was significantly lower in the discordant group (t(71.2)=-3.166, p&#xa0;=&#xa0;.002), as was Tau (t(53.9)=-2.046, p&#xa0;=&#xa0;.046). Further data is found in Figure 1. Demonstration of different levels of tau deposition in the discordant groups implies there may be other pathological processes influencing neurodegeneration in these subjects. A discordance of 10% between CSF amyloid and PET amyloid implies that we should evaluate these subjects in greater detail before enrolling them in intervention studies. References 1. Hansson, O. et al. (2019). https://doi.org/10.1186/s13195-019-0485-0 2. Pyun, JM. et al. (2024) https://doi.org/10.1038/s41398-024-02766-6.

Revisiting GEOM drugs: corrected metrics and novel energy-based structural benchmark enable rigorous evaluation of 3D molecule generative models.