Computational synthesis planning approaches have achieved recent success in organic chemistry, where tabulated synthesis procedures are readily available for supervised learning. The syntheses of inorganic materials, however, exist primarily as natural language narratives contained within scientific journal articles. This synthesis information must first be extracted from the text in order to enable analogous synthesis planning methods for inorganic materials. In this work, we present a system for automatically extracting structured representations of synthesis procedures from the texts of materials science journal articles that describe explicit, experimental syntheses of inorganic compounds. We define the structured representation as a set of linked events made up of extracted scientific entities and evaluate two unsupervised approaches for extracting these structures on expert-annotated articles: a strong heuristic baseline and a generative model of procedural text. We also evaluate a variety of supervised models for extracting scientific entities. Our results provide insight into the nature of the data and directions for further work in this exciting new area of research.
While significant strides have been made in computational synthesis planning via the prediction of synthetic action graphs in organic chemistry, these approaches have relied significantly on datasets comprised of historical chemical reactions. Despite efforts to standardize the reporting of chemical and materials science data @cite_3 , materials synthesis routes continue to reside in non-standard form. Several past studies have applied a variety of text extraction techniques to materials science literature using regular expressions, lexicon matches, or human-driven data labelling to extract synthesis information @cite_18 @cite_0 @cite_11 @cite_15 @cite_9 , but such approaches are inherently difficult to scale across sub-domains of materials science since new rules and lexicons must be created by domain experts for different types of materials or synthesis techniques. Accordingly, have previously developed automatic methods for extracting aspects of inorganic synthesis routes from natural language text to step in the direction of building comprehensive databases of the syntheses of inorganic materials @cite_26 @cite_27 .
@cite_18 @cite_26 @cite_9 @cite_3 @cite_0 @cite_27 @cite_15 @cite_11
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ConspectusComputer-aided synthesis planning (CASP) is focused on the goal of accelerating the process by which chemists decide how to synthesize small molecule compounds. The ideal CASP program would take a molecular structure as input and output a sorted list of detailed reaction schemes that each connect that target to purchasable starting materials via a series of chemically feasible reaction steps. Early work in this field relied on expert-crafted reaction rules and heuristics to describe possible retrosynthetic disconnections and selectivity rules but suffered from incompleteness, infeasible suggestions, and human bias. With the relatively recent availability of large reaction corpora (such as the United States Patent and Trademark Office (USPTO), Reaxys, and SciFinder databases), consisting of millions of tabulated reaction examples, it is now possible to construct and validate purely data-driven approaches to synthesis planning. As a result, synthesis planning has been opened to machine learning te... The synthesis of complex organic compounds is largely a manual process that is often incompletely documented. To address these shortcomings, we developed an abstraction that maps commonly reported methodological instructions into discrete steps amenable to automation. These unit operations were implemented in a modular robotic platform using a chemical programming language which formalizes and controls the assembly of the molecules. We validated the concept by directing the automated system to synthesize three pharmaceutical compounds, Nytol, rufinamide, and sildenafil, without any human intervention. Yields and purities of products and intermediates were comparable to or better than those achieved manually. The syntheses are captured as digital code that can be published, versioned, and transferred flexibly between platforms with no modification, thereby greatly enhancing reproducibility and reliable access to complex molecules. There is an intuitive analogy of an organic chemist's understanding of a compound and a language speaker's understanding of a word. Based on this analogy, it is possible to introduce the basic concepts and analyze potential impacts of linguistic analysis to the world of organic chemistry. In this work, we cast the reaction prediction task as a translation problem by introducing a template-free sequence-to-sequence model, trained end-to-end and fully data-driven. We propose a tokenization, which is arbitrarily extensible with reaction information. Using an attention-based model borrowed from human language translation, we improve the state-of-the-art solutions in reaction prediction on the top-1 accuracy by achieving 80.3 without relying on auxiliary knowledge, such as reaction templates or explicit atomic features. Also, a top-1 accuracy of 65.4 is reached on a larger and noisier dataset. This paper describes a novel technique for the synthesis of imperative programs. Automated program synthesis has the potential to make programming and the design of systems easier by allowing programs to be specified at a higher-level than executable code. In our approach, which we call proof-theoretic synthesis, the user provides an input-output functional specification, a description of the atomic operations in the programming language, and a specification of the synthesized program's looping structure, allowed stack space, and bound on usage of certain operations. Our technique synthesizes a program, if there exists one, that meets the input-output specification and uses only the given resources. The insight behind our approach is to interpret program synthesis as generalized program verification, which allows us to bring verification tools and techniques to program synthesis. Our synthesis algorithm works by creating a program with unknown statements, guards, inductive invariants, and ranking functions. It then generates constraints that relate the unknowns and enforces three kinds of requirements: partial correctness, loop termination, and well-formedness conditions on program guards. We formalize the requirements that program verification tools must meet to solve these constraint and use tools from prior work as our synthesizers. We demonstrate the feasibility of the proposed approach by synthesizing programs in three different domains: arithmetic, sorting, and dynamic programming. Using verification tools that we previously built in the VS3 project we are able to synthesize programs for complicated arithmetic algorithms including Strassen's matrix multiplication and Bresenham's line drawing; several sorting algorithms; and several dynamic programming algorithms. For these programs, the median time for synthesis is 14 seconds, and the ratio of synthesis to verification time ranges between 1x to 92x (with an median of 7x), illustrating the potential of the approach.