arXiv subjects

Srinivasan Parthiban

Publications and source records attributed to Srinivasan Parthiban.

3 recordsLinked to original sources

arXiv2024

HeCiX: Integrating Knowledge Graphs and Large Language Models for Biomedical Research

Despite advancements in drug development strategies, 90% of clinical trials fail. This suggests overlooked aspects in target validation and drug optimization. In order to address this, we introduce HeCiX-KG, Hetionet-Clinicaltrials neXus Knowledge Graph, a novel fusion of data from ClinicalTrials.gov and Hetionet in a single knowledge graph. HeCiX-KG combines data on previously conducted clinical trials from ClinicalTrials.gov, and domain expertise on diseases and genes from Hetionet. This offers a thorough resource for clinical researchers. Further, we introduce HeCiX, a system that uses LangChain to integrate HeCiX-KG with GPT-4, and increase its usability. HeCiX shows high performance during evaluation against a range of clinically relevant issues, proving this model to be promising for enhancing the effectiveness of clinical research. Thus, this approach provides a more holistic view of clinical trials and existing biological data.

cs.CL↗

arXiv2001

The heats of formation of the haloacetylenes XCCY [X, Y = H, F, Cl]: basis set limit ab initio results and thermochemical analysis

The heats of formation of haloacetylenes are evaluated using the recent W1 and W2 ab initio computational thermochemistry methods. These calculations involve CCSD and CCSD(T) coupled cluster methods, basis sets of up to spdfgh quality, extrapolations to the one-particle basis set limit, and contributions of inner-shell correlation, scalar relativistic effects, and (where relevant) first-order spin-orbit coupling. The heats of formation determined using W2 theory are: \hof(HCCH) = 54.48 kcal/mol, \hof(HCCF) = 25.15 kcal/mol, \hof(FCCF) = 1.38 kcal/mol, \hof(HCCCl) = 54.83 kcal/mol, \hof(ClCCCl) = 56.21 kcal/mol, and \hof(FCCCl) = 28.47 kcal/mol. Enthalpies of hydrogenation and destabilization energies relative to acetylene were obtained at the W1 level of theory. So doing we find the following destabilization order for acetylenes: FCCF $>$ ClCCF $>$ HCCF $>$ ClCCCl $>$ HCCCl $>$ HCCH. By a combination of W1 theory and isodesmic reactions, we show that the generally accepted heat of formation of 1,2-dichloroethane should be revised to -31.8$\pm$0.6 kcal/mol, in excellent agreement with a very recent critically evaluated review. The performance of compound thermochemistry schemes such as G2, G3, G3X and CBS-QB3 theories has been analyzed.

physics.chem-ph↗

arXiv2000

Benchmark {\em ab initio} energy profiles for the gas-phase S$_N$2 reactions Y$^-$ + CH$_3$X $\to$ CH$_3$Y + X$^-$ (X,Y = F,Cl,Br). Validation of hybrid DFT methods

The energetics of the gas-phase S$_N$2 reactions Y$^-$ + CH$_3$X $\longrightarrow$ CH$_3$Y + X$^-$ (where X,Y = F, Cl, Br), were studied using (variants on) the recent W1 and W2 {\em ab initio} computational thermochemistry methods. Our computed benchmark data (including cases for which experimental data are unavailable altogether) are used to assess the quality of a number of semiempirical compound thermochemistry schemes such as G2 theory, G3 theory, and CBS-QB3, as well as a variety of density functional theory methods. Upon applying some modifications to the level of theory used for the reference geometry (adding diffuse functions, replacing B3LYP by the very recently proposed mPW1K functional), the compound methods appear to perform well. Only the 'half-and-half' functionals BH&HLYP and mPWH&HPW91, and the empirical mPW1K functional, consistently find all required stationary points; the other functionals fail to find a transition state in the F/Br case. BH&HLYP and mPWH&HPW91 somewhat overcorrect for the tendency of B3LYP (and, to a lesser extent, mPW1PW91) to underestimate barrier heights. The Becke97 and Becke97-1 functionals perform similarly to B3LYP for the problem under study, while the HCTH and HCTH-120 functionals both appear to underestimate central barriers. HCTH underestimates complexation energies; this problem is resolved in HCTH-120. mPW1K appears to exhibit the best performance of the functionals considered, although its energetics are still inferior to the compound thermochemistry methods.

physics.chem-ph↗