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Cancer drug response prediction (DRP) models present a promising approach towards precision oncology, tailoring treatments to individual patient profiles. While deep learning (DL) methods have shown great potential in this area, models that can be successfully translated into clinical practice and shed light on the molecular mechanisms underlying treatment response will likely emerge from collaborative research efforts. This highlights the need for reusable and adaptable models that can be improved and tested by the wider scientific community. In this study, we present a scoring system for assessing the reusability of prediction DRP models, and apply it to 17 peer-reviewed DL-based DRP models. As part of the IMPROVE (Innovative Methodologies and New Data for Predictive Oncology Model Evaluation) project, which aims to develop methods for systematic evaluation and comparison DL models across scientific domains, we analyzed these 17 DRP models focusing on three key categories: software environment, code modularity, and data availability and preprocessing. While not the primary focus, we also attempted to reproduce key performance metrics to verify model behavior and adaptability. Our assessment of 17 DRP models reveals both strengths and shortcomings in model reusability. To promote rigorous practices and open-source sharing, we offer recommendations for developing and sharing prediction models. Following these recommendations can address many of the issues identified in this study, improving model reusability without adding significant burdens on researchers. This work offers the first comprehensive assessment of reusability and reproducibility across diverse DRP models, providing insights into current model sharing practices and promoting standards within the DRP and broader AI-enabled scientific research community., Comment: 12 pages, 2 figures

An ideal $I$ of a commutative ring $R$ is said to be of linear type when its Rees algebra and symmetric algebra exhibit isomorphism. In this paper, we investigate the conjecture put forth by Jayanthan, Kumar, and Sarkar (2021) that if $G$ is a tree or a unicyclic graph, then the binomial edge ideal of $G$ is of linear type. Our investigation validates this conjecture for trees. However, our study reveals that not all unicyclic graphs adhere to this conjecture., Comment: 14 pages, removed Theorem 5.1, comments are welcome

Large language models (LLMs) have shown remarkable potential in various domains, but they often lack the ability to access and reason over domain-specific knowledge and tools. In this paper, we introduced CACTUS (Chemistry Agent Connecting Tool-Usage to Science), an LLM-based agent that integrates cheminformatics tools to enable advanced reasoning and problem-solving in chemistry and molecular discovery. We evaluate the performance of CACTUS using a diverse set of open-source LLMs, including Gemma-7b, Falcon-7b, MPT-7b, Llama2-7b, and Mistral-7b, on a benchmark of thousands of chemistry questions. Our results demonstrate that CACTUS significantly outperforms baseline LLMs, with the Gemma-7b and Mistral-7b models achieving the highest accuracy regardless of the prompting strategy used. Moreover, we explore the impact of domain-specific prompting and hardware configurations on model performance, highlighting the importance of prompt engineering and the potential for deploying smaller models on consumer-grade hardware without significant loss in accuracy. By combining the cognitive capabilities of open-source LLMs with domain-specific tools, CACTUS can assist researchers in tasks such as molecular property prediction, similarity searching, and drug-likeness assessment. Furthermore, CACTUS represents a significant milestone in the field of cheminformatics, offering an adaptable tool for researchers engaged in chemistry and molecular discovery. By integrating the strengths of open-source LLMs with domain-specific tools, CACTUS has the potential to accelerate scientific advancement and unlock new frontiers in the exploration of novel, effective, and safe therapeutic candidates, catalysts, and materials. Moreover, CACTUS's ability to integrate with automated experimentation platforms and make data-driven decisions in real time opens up new possibilities for autonomous discovery.

An almost complete intersection ideal can be seen as a $d$-sequence ideal with the minimal number of generators being one more than its height. In this paper, we give exact formulas for the regularity of powers of graded almost complete intersection ideals. We also present the minimal bigraded free resolutions of Rees algebras associated with linear type ideals having one generator more than their grade and study the properties of Cohen-Macaualyness, Koszulness associated to their diagonals., Comment: Comments and suggestions are welcome

Strongly-correlated transition-metal oxides are widely known for their various exotic phenomena. This is exemplified by rare-earth nickelates such as LaNiO$_{3}$, which possess intimate interconnections between their electronic, spin, and lattice degrees of freedom. Their properties can be further enhanced by pairing them in hybrid heterostructures, which can lead to hidden phases and emergent phenomena. An important example is the LaNiO$_{3}$/LaTiO$_{3}$ superlattice, where an interlayer electron transfer has been observed from LaTiO$_{3}$ into LaNiO$_{3}$ leading to a high-spin state. However, macroscopic emergence of magnetic order associated with this high-spin state has so far not been observed. Here, by using muon spin rotation, x-ray absorption, and resonant inelastic x-ray scattering, we present direct evidence of an emergent antiferromagnetic order with high magnon energy and exchange interactions at the LaNiO$_{3}$/LaTiO$_{3}$ interface. As the magnetism is purely interfacial, a single LaNiO$_{3}$/LaTiO$_{3}$ interface can essentially behave as an atomically thin strongly-correlated quasi-two-dimensional antiferromagnet, potentially allowing its technological utilisation in advanced spintronic devices. Furthermore, its strong quasi-two-dimensional magnetic correlations, orbitally-polarized planar ligand holes, and layered superlattice design make its electronic, magnetic, and lattice configurations resemble the precursor states of superconducting cuprates and nickelates, but with an $S \rightarrow 1$ spin state instead., Comment: 41 pages, 14 figures