PhyloGFN: Phylogenetic inference with generative flow networks

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods

New Insight into the Anti-liver Fibrosis Effect of Multitargeted Tyrosine Kinase Inhibitors: From Molecular Target to Clinical Trials

Tyrosine kinases (TKs) is a family of tyrosine protein kinases with important functions in the regulation of a broad variety of physiological cell processes. Overactivity of TK disturbs cellular homeostasis and has been linked to the development of certain diseases, including various fibrotic diseases. In regard to liver fibrosis, several TKs, such as vascular endothelial growth factor receptor (VEGFR), platelet-derived growth factor receptor (PDGFR), fibroblast growth factor receptor (FGFR) and epidermal growth factor receptor (EGFR) kinases, have been identified as central mediators in collagen production and potential targets for anti-liver fibrosis therapies. Given the essential role of TKs during liver fibrogenesis, multitargeted inhibitors of aberrant TK activity, including sorafenib, erlotinib, imatinib, sunitinib, nilotinib, brivanib and vatalanib, have been shown to have potential for treating liver fibrosis. Beneficial effects are observed by researchers of this field using these multitargeted TK inhibitors in preclinical animal models and in patients with liver fibrosis. The present review will briefly summarize the anti-liver fibrosis effects of multitargeted TK inhibitors and molecular mechanisms

Recommended high performance telescope system design for the TianQin project

China is planning to construct a new space-borne gravitational-wave (GW) observatory, the TianQin project, in which the spaceborne telescope is an important component in laser interferometry. The telescope is aimed to transmit laser beams between the spacecrafts for the measurement of the displacements between proof-masses in long arms. The telescope should have ultra-small wavefront deviation to minimize noise caused by pointing error, ultra-stable structure to minimize optical path noise caused by temperature jitter, ultra-high stray light suppression ability to eliminate background noise. In this paper, we realize a telescope system design with ultra-stable structure as well as ultra-low wavefront distortion for the space-based GW detection mission. The design requirements demand extreme control of high image quality and extraordinary stray light suppression ability. Based on the primary aberration theory, the initial structure design of the mentioned four-mirror optical system is explored. After optimization, the maximum RMS wavefront error is less than lamda/300 over the full field of view (FOV), which meets the noise budget on the telescope design. The stray light noise caused by the back reflection of the telescope is also analyzed. The noise at the position of optical bench is less than 10-10 of the transmitted power, satisfying the requirements of space gravitational-wave detection. We believe that our design can be a good candidate for TianQin project, and can also be a good guide for the space telescope design in any other similar science project

Towards equilibrium molecular conformation generation with GFlowNets

Sampling diverse, thermodynamically feasible molecular conformations plays a crucial role in predicting properties of a molecule. In this paper we propose to use GFlowNet for sampling conformations of small molecules from the Boltzmann distribution, as determined by the molecule's energy. The proposed approach can be used in combination with energy estimation methods of different fidelity and discovers a diverse set of low-energy conformations for highly flexible drug-like molecules. We demonstrate that GFlowNet can reproduce molecular potential energy surfaces by sampling proportionally to the Boltzmann distribution