AI Networking Cookbook: Practical recipes for AI-assisted network automation and development
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2,394 papers
The results indicate that this fully automated, open-source system holds potential value for improving the efficiency and sustainability of molecular synthesis, and the integration of organic and enzymatic synthesis enhances molecule construction efficiency.
The authors develop mRNABERT, a foundational AI model that designs entire mRNA sequences and demonstrates superior performance across comprehensive benchmarks, which signifies a substantial leap forward in mRNA research and therapeutic development.
Token-Mol is presented, a token-only 3D drug design model that encodes both 2D and 3D structural information, along with molecular properties, into discrete tokens, which introduces a Gaussian cross-entropy loss function tailored for regression tasks, enabling superior performance across multiple downstream applications.
The study of rare events is one of the major challenges in atomistic simulations, and several enhanced sampling methods toward its solution have been proposed. Recently, it has been suggested that the use of the committor, which provides a precise formal description of rare events, could be of use in this context. We have recently followed up on this suggestion and proposed a committor-based method that promotes frequent transitions between the metastable states of the system and allows extensive sampling of the process transition state ensemble. One of the strengths of our approach is being self-consistent and semiautomatic, exploiting a variational criterion to iteratively optimize a neural-network-based parametrization of the committor, which uses a set of physical descriptors as input. Here, we further automate this procedure by combining our previous method with the expressive power of graph neural networks, which can directly process atomic coordinates rather than descriptors. Besides applications on benchmark systems, we highlight the advantages of a graph-based approach in describing the role of solvent molecules in systems, such as ion pair dissociation or ligand binding.
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A comprehensive overview of how enhanced sampling methods are reshaping the field, with a particular focus on the data-driven construction of collective variables, is provided.
RSGPT, a generative model pre-trained on ten billion data points, achieving state-of-the-art performance for synthesis planning, and introduces reinforcement learning to capture the relationships among products, reactants, and templates more accurately.
ERAM aligns pre-trained molecular representations from Protein Language Model with the knowledge of enzyme catalysis by modeling enzymatic reactions as multi-relational data, and demonstrates its potential as a versatile and effective tool for enzyme catalysis research.
Multi-target drugs hold great promise for treating complex diseases, yet existing methodologies predominantly rely on ligand-based approaches, which lack sufficient biological context and are often confined to specific target pairs, resulting in limited generalizability. Here, we introduce LaMGen, a general-purpose multi-target drug design framework powered by large language models (LLMs). Built on MTD2025, a dataset comprising over 600,000 quantum-accurate molecular conformations and 700,000 multi-target associations, LaMGen directly yields energy-favorable conformations with quantum-level accuracy. The framework integrates ESM-C protein embeddings, rotation-aware ligand tokens, and a TriCoupleAttention module to capture multi-level target–ligand interactions. Across independent benchmarks, LaMGen outperforms diffusion-based model across multiple properties, generating molecules in an average of 0.44 s, while preserving high conformational plausibility. Retrospective analyses demonstrate that LaMGen not only can reproduce molecules identical to known actives, but also consistently produces structurally novel candidates with conserved core scaffolds and superior binding affinities. Designing effective multi-target therapeutics remains a major challenge, as existing ligand- or protein-centric methods struggle to generate biologically contextualized, spatially valid 3D molecules, particularly for triple-target systems. This study introduces LaMGen, an LLM-powered framework that leverages large-scale protein-ligand data and rotation-aware molecular encoding to rapidly produce chemically plausible multi-target candidates, achieving strong zero-shot generalization, superior molecular quality, and robust performance across dual- and triple-target design tasks.
Prompting-based (i.e., non-fine-tuning) Text-to-SQL methods, where underlying large language model parameters are not changed for the task, face three problems: (i) relying on coarse-grained schema information that may not reveal the fine-grained relationships needed to distinguish ambiguous columns, (ii) failing to capture recurring SQL-generation failures, and (iii) suffering from omission or hallucination of components in complex questions. This paper develops DexterSQL, a prompting/non-fine-tuning-based Text-to-SQL system that improves SQL generation with three novel components: (i) deep schema explorator that identifies ambiguous columns, analyzes their individual and joint data distributions to uncover their relationships and the distinct role of each, (ii) database-agnostic rule creator that mines mismatches between generated and gold SQL only on the training database and converts them into database-agnostic corrective rules that capture recurring LLM failure patterns; and (iii) multi-path SQL generation that introduces a dependency-tree-based intermediate representation that uses the question's sentence structure to guide its decomposition into an SQL skeleton for final SQL generation. DexterSQL achieves a higher accuracy compared to the state-of-the-art using both open-source/weight and closed-source/weight models. Particularly, DexterSQL shows a high improvement of at least 5.5% using an open-weight model (GPT-OSS-120B) on BIRDDev, with total accuracy 70.4%. DexterSQL also shows better improvement of at least 1.4% using closed-weight models, with total accuracy 72.1% and 72.9% on BIRD-Dev with GPT-4o and GPT-5.2.
The proposed LLM-based multi-agent system automates qualitative data analysis process, creating opportunities for researchers and practitioners, and future improvements focus on enhancing multilingual performance and integrating continuous expert feedback.
This work presents the design and implementation of a governance-aware, multi-tenant AI sandbox for structured experimentation and the generation of reusable evaluation evidence across projects and stakeholder groups.
A Multi-Vocal Literature Review is conducted, combining insights from both academia and industry, including peer-reviewed studies and grey literature to systematically synthesize and analyze existing knowledge on LLM-based multi-agent systems for code generation.
A new method, called CW-Net, translates the reasoning process of an autonomous vehicle’s AI system into understandable concepts that explain its behavior.
With millions of users across the world, Julia has been used to conduct cutting-edge research and to design new drugs, jet engines, heat pumps, and more.
We’re on a journey to advance and democratize artificial intelligence through open source and open science.
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
Algorithms & Theory
New MIT research could lead to better materials for a fossil-fuel-free process for making the chemical that's essential to fertilizer and other products.
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