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Sequence-specific RNA-binding proteins (RBPs) play central roles in splicing decisions. Here, we describe a modular splicing architecture that leverages in vitro-derived RNA affinity models for 79 human RBPs and the annotated human genome to produce improved models of RBP binding and activity. Binding and activity are modeled by separate Motif and Aggregator components that can be mixed and matched, enforcing sparsity to improve interpretability. Training a new Adjusted Motif (AM) architecture on the splicing task not only yields better splicing predictions but also improves prediction of RBP-binding sites in vivo and of splicing activity, assessed using independent data.

 

We present a new general-purpose synthesis technique for generating programs from input-output examples. Our method, called metric program synthesis, relaxes the observational equivalence idea (used widely in bottom-up enumerative synthesis) into a weaker notion of observational similarity, with the goal of reducing the search space that the synthesizer needs to explore. Our method clusters programs into equivalence classes based on an expert-provided distance metric and constructs a version space that compactly represents “approximately correct” programs. Then, given a “close enough” program sampled from this version space, our approach uses a distance-guided repair algorithm to find a program that exactly matches the given input-output examples. We have implemented our proposed metric program synthesis technique in a tool called SyMetric and evaluate it in three different domains considered in prior work. Our evaluation shows that SyMetric outperforms other domain-agnostic synthesizers that use observational equivalence and that it achieves results competitive with domain-specific synthesizers that are either designed for or trained on those domains.

 

We present a new algorithm that synthesizes functional reactive programs from observation data. The key novelty is to iterate between a functional synthesis step, which attempts to generate a transition function over observed states, and an automata synthesis step, which adds any additional latent state necessary to fully account for the observations. We develop a functional reactive DSL called Autumn that can express a rich variety of causal dynamics in time-varying, Atari-style grid worlds, and apply our method to synthesize Autumn programs from data. We evaluate our algorithm on a benchmark suite of 30 Autumn programs as well as a third-party corpus of grid-world-style video games. We find that our algorithm synthesizes 27 out of 30 programs in our benchmark suite and 21 out of 27 programs from the third-party corpus, including several programs describing complex latent state transformations, and from input traces containing hundreds of observations. We expect that our approach will provide a template for how to integrate functional and automata synthesis in other induction domains. 

Abstract Automated, data-driven construction and evaluation of scientific models and theories is a long-standing challenge in artificial intelligence. We present a framework for algorithmically synthesizing models of a basic part of human language: morpho-phonology, the system that builds word forms from sounds. We integrate Bayesian inference with program synthesis and representations inspired by linguistic theory and cognitive models of learning and discovery. Across 70 datasets from 58 diverse languages, our system synthesizes human-interpretable models for core aspects of each language’s morpho-phonology, sometimes approaching models posited by human linguists. Joint inference across all 70 data sets automatically synthesizes a meta-model encoding interpretable cross-language typological tendencies. Finally, the same algorithm captures few-shot learning dynamics, acquiring new morphophonological rules from just one or a few examples. These results suggest routes to more powerful machine-enabled discovery of interpretable models in linguistics and other scientific domains. 

This paper introduces corpus-guided top-down synthesis as a mechanism for synthesizing library functions that capture common functionality from a corpus of programs in a domain specific language (DSL). The algorithm builds abstractions directly from initial DSL primitives, using syntactic pattern matching of intermediate abstractions to intelligently prune the search space and guide the algorithm towards abstractions that maximally capture shared structures in the corpus. We present an implementation of the approach in a tool called Stitch and evaluate it against the state-of-the-art deductive library learning algorithm from DreamCoder. Our evaluation shows that Stitch is 3-4 orders of magnitude faster and uses 2 orders of magnitude less memory while maintaining comparable or better library quality (as measured by compressivity). We also demonstrate Stitch’s scalability on corpora containing hundreds of complex programs that are intractable with prior deductive approaches and show empirically that it is robust to terminating the search procedure early—further allowing it to scale to challenging datasets by means of early stopping. 

Many problem domains, including program synthesis and rewrite-based optimization, require searching astronomically large spaces of programs. Existing approaches often rely on building specialized data structures—version-space algebras, finite tree automata, or e-graphs—to compactly represent such spaces. At their core, all these data structures exploit independence of subterms; as a result, they cannot efficiently represent more complex program spaces, where the choices of subterms are entangled. We introduce equality-constrained tree automata (ECTAs), a new data structure, designed to compactly represent large spaces of programs with entangled subterms. We present efficient algorithms for extracting programs from ECTAs, implemented in a performant Haskell library, ecta. Using the ecta library, we construct Hectare, a type-driven program synthesizer for Haskell. Hectare significantly outperforms a state-of-the-art synthesizer Hoogle+—providing an average speedup of 8×—despite its implementation being an order of magnitude smaller. 

We present a system for inductive program synthesis called DreamCoder, which inputs a corpus of synthesis problems each specified by one or a few examples, and automatically derives a library of program components and a neural search policy that can be used to efficiently solve other similar synthesis problems. The library and search policy bootstrap each other iteratively through a variant of "wake-sleep" approximate Bayesian learning. A new refactoring algorithm based on E-graph matching identifies common sub-components across synthesized programs, building a progressively deepening library of abstractions capturing the structure of the input domain. We evaluate on eight domains including classic program synthesis areas and AI tasks such as planning, inverse graphics, and equation discovery. We show that jointly learning the library and neural search policy leads to solving more problems, and solving them more quickly.