Application of Transformers in Cheminformatics.

By accelerating time-consuming processes with high efficiency, computing has become an essential part of many modern chemical pipelines. Machine learning is a class of computing methods that can discover patterns within chemical data and utilize this knowledge for a wide variety of downstream tasks, such as property prediction or substance generation. The complex and diverse chemical space requires complex machine learning architectures with great learning power.

Agriculture models for restoring degraded land to enhance CO biosequestration and carbon credits in the Vindhyan region of India.

The study's objective was to evaluate the status of converted degraded land into productive agricultural models by improving the physicochemical properties of the soil, soil organic matter (SOM), soil organic carbon (SOC) fractions (active and passive), and microbial biomass carbon (MBC), while also generating carbon (C) credit for additional farmers' income. Six models were analyzed, namely: (1) Arjun forest-based agroecosystems (AFBAE); (2) Lemon grass-based agroecosystems (LGBAE); (3) Legume-cereal-moong-based agroecosystems (LCMBAE); (4) Bael-black mustard-based agroecosystems (BMBAE); (5) Guava-wheat-based agroecosystems (GWBAE), and (6) Custard apple -lentil -based agroecosystems (CALBAE). These models were replicated three times in a randomized block design (RBD).

Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43 Aggregation.

Abnormal cytosolic aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) is observed in multiple diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and Alzheimer's disease. Previous studies have shown that TDP-43 located at the C-terminal of TDP-43 can form higher-order oligomers and fibrils. Of particular interest are the hexamers that adopt a cylindrin structure that has been strongly correlated to neurotoxicity.

Computationally Designed Small Molecules Disassemble Both Soluble Oligomers and Protofibrils of Amyloid β-Protein Responsible for Alzheimer's Disease.

Alzheimer's disease (AD) is one of the world's most pressing health crises. AD is an incurable disease affecting more than 6.5 million Americans, predominantly the elderly, and in its later stages, leads to memory loss, dementia, and death.

Predictive models for human-AI nexus in group decision making.

Machine learning (ML) and artificial intelligence (AI) have had a profound impact on our lives. Domains like health and learning are naturally helped by human-AI interactions and decision making. In these areas, as ML algorithms prove their value in making important decisions, humans add their distinctive expertise and judgment on social and interpersonal issues that need to be considered in tandem with algorithmic inputs of information.

Modulating ALS-Related Amyloidogenic TDP-43 Oligomeric Aggregates with Computationally Derived Therapeutic Molecules.

TDP-43 aggregates are a salient feature of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and a variety of other neurodegenerative diseases, including Alzheimer's disease (AD). With an anticipated growth in the most susceptible demographic, projections predict neurodegenerative diseases will potentially affect 15 million people in the United States by 2050. Currently, there are no cures for ALS, FTD, or AD.

Structural balance emerges and explains performance in risky decision-making.

Polarization affects many forms of social organization. A key issue focuses on which affective relationships are prone to change and how their change relates to performance. In this study, we analyze a financial institutional over a two-year period that employed 66 day traders, focusing on links between changes in affective relations and trading performance.

Dynamics of collective performance in collaboration networks.

Today, many complex tasks are assigned to teams, rather than individuals. One reason for teaming up is expansion of the skill coverage of each individual to the joint team skill set. However, numerous empirical studies of human groups suggest that the performance of equally skilled teams can widely differ.

Inhibiting and Remodeling Toxic Amyloid-Beta Oligomer Formation Using a Computationally Designed Drug Molecule That Targets Alzheimer's Disease.

Alzheimer's disease (AD) is rapidly reaching epidemic status among a burgeoning aging population. Much evidence suggests the toxicity of this amyloid disease is most influenced by the formation of soluble oligomeric forms of amyloid β-protein, particularly the 42-residue alloform (Aβ42). Developing potential therapeutics in a directed, streamlined approach to treating this disease is necessary.

Spatial coherence of oriented white matter microstructure: Applications to white matter regions associated with genetic similarity.

We present a method to discover differences between populations with respect to the spatial coherence of their oriented white matter microstructure in arbitrarily shaped white matter regions. This method is applied to diffusion MRI scans of a subset of the Human Connectome Project dataset: 57 pairs of monozygotic and 52 pairs of dizygotic twins. After controlling for morphological similarity between twins, we identify 3.

Learning about learning: Mining human brain sub-network biomarkers from fMRI data.

Modeling the brain as a functional network can reveal the relationship between distributed neurophysiological processes and functional interactions between brain structures. Existing literature on functional brain networks focuses mainly on a battery of network properties in "resting state" employing, for example, modularity, clustering, or path length among regions. In contrast, we seek to uncover functionally connected subnetworks that predict or correlate with cohort differences and are conserved within the subjects within a cohort.

Discovery of LRRK2 inhibitors using sequential in silico joint pharmacophore space (JPS) and ensemble docking.

Joint pharmacophore space (JPS), ensemble docking and sequential JPS-ensemble docking were used to select three panels of compounds (10 per panel) for evaluation as LRRK2 inhibitors. These computational methods identified four LRRK2 inhibitors with IC50 values <12μM. The sequential JPS-ensemble docking predicted the majority of active hits.

Base motif recognition and design of DNA templates for fluorescent silver clusters by machine learning.

Discriminative base motifs within DNA templates for fluorescent silver clusters are identified using methods that combine large experimental data sets with machine learning tools for pattern recognition. Combining the discovery of certain multibase motifs important for determining fluorescence brightness with a generative algorithm, the probability of selecting DNA templates that stabilize fluorescent silver clusters is increased by a factor of >3.

A latent parameter node-centric model for spatial networks.

Spatial networks, in which nodes and edges are embedded in space, play a vital role in the study of complex systems. For example, many social networks attach geo-location information to each user, allowing the study of not only topological interactions between users, but spatial interactions as well. The defining property of spatial networks is that edge distances are associated with a cost, which may subtly influence the topology of the network.

Quantifying spatial relationships from whole retinal images.

Motivation: Microscopy advances have enabled the acquisition of large-scale biological images that capture whole tissues in situ. This in turn has fostered the study of spatial relationships between cells and various biological structures, which has proved enormously beneficial toward understanding organ and organism function. However, the unique nature of biological images and tissues precludes the application of many existing spatial mining and quantification methods necessary to make inferences about the data.

Probabilistic Substructure Mining From Small-Molecule Screens.

Identifying the overrepresented substructures from a set of molecules with similar activity is a common task in chemical informatics. Existing substructure miners are deterministic, requiring the activity of all mined molecules to be known with high confidence. In contrast, we introduce pGraphSig, a probabilistic structure miner, which effectively mines structures from noisy data, where many molecules are labeled with their probability of being active.

Novel method for pharmacophore analysis by examining the joint pharmacophore space.

We propose a novel method for pharmacophore analysis by examining the Joint Pharmacophore Space of chemical compounds, targets, and chemical/biological properties. The proposed approach is a notable deviation from existing techniques that analyze compounds on a target-by-target basis, aimed at extracting and optimizing a specific pharmacophore. The underlying geometry of the pharmacophores is responsible for binding between compounds and targets as well as properties of compounds such as Blood Brain Barrier permeability.

Using stochastic causal trees to augment Bayesian networks for modeling eQTL datasets.

Background: The combination of genotypic and genome-wide expression data arising from segregating populations offers an unprecedented opportunity to model and dissect complex phenotypes. The immense potential offered by these data derives from the fact that genotypic variation is the sole source of perturbation and can therefore be used to reconcile changes in gene expression programs with the parental genotypes. To date, several methodologies have been developed for modeling eQTL data.

Molecular function prediction using neighborhood features.

The recent advent of high-throughput methods has generated large amounts of gene interaction data. This has allowed the construction of genomewide networks. A significant number of genes in such networks remain uncharacterized and predicting the molecular function of these genes remains a major challenge.

Accurate and scalable techniques for the complex/pathway membership problem in protein networks.

A protein network shows physical interactions as well as functional associations. An important usage of such networks is to discover unknown members of partially known complexes and pathways. A number of methods exist for such analyses, and they can be divided into two main categories based on their treatment of highly connected proteins.

Bisque: a platform for bioimage analysis and management.

Motivation: Advances in the field of microscopy have brought about the need for better image management and analysis solutions. Novel imaging techniques have created vast stores of images and metadata that are difficult to organize, search, process and analyze. These tasks are further complicated by conflicting and proprietary image and metadata formats, that impede analyzing and sharing of images and any associated data.

Mining statistically significant molecular substructures for efficient molecular classification.

The increased availability of large repositories of chemical compounds has created new challenges in designing efficient molecular querying and mining systems. Molecular classification is an important problem in drug development where libraries of chemical compounds are screened and molecules with the highest probability of success against a given target are selected. We have developed a technique called GraphSig to mine significantly over-represented molecular substructures in a given class of molecules.

RRW: repeated random walks on genome-scale protein networks for local cluster discovery.

Background: We propose an efficient and biologically sensitive algorithm based on repeated random walks (RRW) for discovering functional modules, e.g., complexes and pathways, within large-scale protein networks.

Predicting genetic interactions with random walks on biological networks.

Background: Several studies have demonstrated that synthetic lethal genetic interactions between gene mutations provide an indication of functional redundancy between molecular complexes and pathways. These observations help explain the finding that organisms are able to tolerate single gene deletions for a large majority of genes. For example, system-wide gene knockout/knockdown studies in S.