Nada Amin

David Brandfonbrener, Simon Henniger, Sibi Raja et al.

Large Language Models (LLMs) can generate useful code, but often the code they generate cannot be trusted to be sound. In this paper, we present VerMCTS, an approach to begin to resolve this issue by generating verified programs in Dafny and Coq. VerMCTS uses a logical verifier in concert with an LLM to guide a modified Monte Carlo Tree Search (MCTS). This approach leverages the verifier to gain intermediate feedback inside the search algorithm by checking partial programs at each step to estimate an upper bound on the value function. To measure the performance of VerMCTS, we develop a new suite of multi-step verified programming problems in Dafny and Coq. In terms of pass@T, a new metric which computes the pass rate given a budget of T tokens sampled from the LLM, VerMCTS leads to more than a 30% absolute increase in average pass@5000 across the suite over repeated sampling from the base language model. Our code and benchmarks are available at https://github.com/namin/llm-verified-with-monte-carlo-tree-search .

Gabriel Poesia, Chloe Loughridge, Nada Amin

Formal verification has the potential to drastically reduce software bugs, but its high additional cost has hindered large-scale adoption. While Dafny presents a promise to significantly reduce the effort to write verified programs, users are often required to provide logical annotations to aid the verifier. Here, we explore using a combination of Large Language Models and search to build dafny-annotator: a tool that adds logical annotations to a Dafny method until the verifier can prove it correct. On a test set from the DafnyBench collection of programs, greedy search guided by LLaMa 3.1 8B successfully annotates only 15.7% of the methods. Since this data-driven approach is hindered by the lack of large-scale training data, we propose a method for open-ended synthesis of new Dafny programs in a flexible pipeline where LLMs formulate high-level ideas, implement them, and incrementally propose changes to existing programs, which Dafny validates. This gives us a synthetic dataset, DafnySynth, which we use to augment DafnyBench for training. Fine-tuning on both datasets boosts LLaMa 8B's success rate to 50.6% -- significantly better than the base model, or training on either dataset alone. Our results suggest a path towards capable AI assistants for languages that don't yet have large-scale human-generated examples. In turn, such assistants might reduce friction for users and ultimately drive adoption.

Joey Velez-Ginorio, Nada Amin, Konrad Kording et al.

We don't program neural networks directly. Instead, we rely on an indirect style where learning algorithms, like gradient descent, determine a neural network's function by learning from data. This indirect style is often a virtue; it empowers us to solve problems that were previously impossible. But it lacks discrete structure. We can't compile most algorithms into a neural network -- even if these algorithms could help the network learn. This limitation occurs because discrete algorithms are not obviously differentiable, making them incompatible with the gradient-based learning algorithms that determine a neural network's function. To address this, we introduce $\textsf{Cajal}$: a typed, higher-order and linear programming language intended to be a minimal vehicle for exploring a direct style of programming neural networks. We prove $\textsf{Cajal}$ programs compile to linear neurons, allowing discrete algorithms to be expressed in a differentiable form compatible with gradient-based learning. With our implementation of $\textsf{Cajal}$, we conduct several experiments where we link these linear neurons against other neural networks to determine part of their function prior to learning. Linking with these neurons allows networks to learn faster, with greater data-efficiency, and in a way that's easier to debug. A key lesson is that linear programming languages provide a path towards directly programming neural networks, enabling a rich interplay between learning and the discrete structures of ordinary programming.

Joey Velez-Ginorio, Nada Amin, Konrad Kording et al.

Discrete structures are currently second-class in differentiable programming. Since functions over discrete structures lack overt derivatives, differentiable programs do not differentiate through them and limit where they can be used. For example, when programming a neural network, conditionals and iteration cannot be used everywhere; they can break the derivatives necessary for gradient-based learning to work. This limits the class of differentiable algorithms we can directly express, imposing restraints on how we build neural networks and differentiable programs more generally. However, these restraints are not fundamental. Recent work shows conditionals can be first-class, by compiling them into differentiable form as linear neurons. Similarly, this work shows iteration can be first-class -- by compiling to linear recurrent neurons. We present a minimal typed, higher-order and linear programming language with iteration called $\textsf{Cajal}\scriptstyle(\mathbb{\multimap}, \mathbb{2}, \mathbb{N})$. We prove its programs compile correctly to recurrent neurons, allowing discrete algorithms to be expressed in a differentiable form compatible with gradient-based learning. With our implementation, we conduct two experiments where we link these recurrent neurons against a neural network solving an iterative image transformation task. This determines part of its function prior to learning. As a result, the network learns faster and with greater data-efficiency relative to a neural network programmed without first-class iteration. A key lesson is that recurrent neurons enable a rich interplay between learning and the discrete structures of ordinary programming.

Chloe Loughridge, Qinyi Sun, Seth Ahrenbach et al.

We introduce DafnyBench, the largest benchmark of its kind for training and evaluating machine learning systems for formal software verification. We test the ability of LLMs such as GPT-4 and Claude 3 to auto-generate enough hints for the Dafny formal verification engine to successfully verify over 750 programs with about 53,000 lines of code. The best model and prompting scheme achieved 68% success rate, and we quantify how this rate improves when retrying with error message feedback and how it deteriorates with the amount of required code and hints. We hope that DafnyBench will enable rapid improvements from this baseline as LLMs and verification techniques grow in quality.

Ayush Noori, Iñaki Arango, William E. Byrd et al.

The strict selectivity of the blood-brain barrier (BBB) represents one of the most formidable challenges to successful central nervous system (CNS) drug delivery. Computational methods to generate BBB permeable drugs in silico may be valuable tools in the CNS drug design pipeline. However, in real-world applications, BBB penetration alone is insufficient; rather, after transiting the BBB, molecules must bind to a specific target or receptor in the brain and must also be safe and non-toxic. To discover small molecules that concurrently satisfy these constraints, we use multi-objective generative AI to synthesize drug-like BBB-permeable small molecules. Specifically, we computationally synthesize molecules with predicted binding affinity against dopamine receptor D2, the primary target for many clinically effective antipsychotic drugs. After training several graph neural network-based property predictors, we adapt SyntheMol (Swanson et al., 2024), a recently developed Monte Carlo Tree Search-based algorithm for antibiotic design, to perform a multi-objective guided traversal over an easily synthesizable molecular space. We design a library of 26,581 novel and diverse small molecules containing hits with high predicted BBB permeability and favorable predicted safety and toxicity profiles, and that could readily be synthesized for experimental validation in the wet lab. We also validate top scoring molecules with molecular docking simulation against the D2 receptor and demonstrate predicted binding affinity on par with risperidone, a clinically prescribed D2-targeting antipsychotic. In the future, the SyntheMol-based computational approach described here may enable the discovery of novel neurotherapeutics for currently intractable disorders of the CNS.