Daily Papers

Recent work by (Richardson and Kuhn, 2017a,b; Richardson et al., 2018) looks at semantic parser induction and question answering in the domain of source code libraries and APIs. In this brief note, we formalize the representations being learned in these studies and introduce a simple domain specific language and a systematic translation from this language to first-order logic. By recasting the target representations in terms of classical logic, we aim to broaden the applicability of existing code datasets for investigating more complex natural language understanding and reasoning problems in the software domain.

Large Language Models (LLMs) are increasingly used by software engineers for code generation. However, limitations of LLMs such as irrelevant or incorrect code have highlighted the need for prompt programming (or prompt engineering) where engineers apply specific prompt techniques (e.g., chain-of-thought or input-output examples) to improve the generated code. Despite this, the impact of different prompt techniques -- and their combinations -- on code generation remains underexplored. In this study, we introduce CodePromptEval, a dataset of 7072 prompts designed to evaluate five prompt techniques (few-shot, persona, chain-of-thought, function signature, list of packages) and their effect on the correctness, similarity, and quality of complete functions generated by three LLMs (GPT-4o, Llama3, and Mistral). Our findings show that while certain prompt techniques significantly influence the generated code, combining multiple techniques does not necessarily improve the outcome. Additionally, we observed a trade-off between correctness and quality when using prompt techniques. Our dataset and replication package enable future research on improving LLM-generated code and evaluating new prompt techniques.

Repository-level code generation has attracted growing attention in recent years. Unlike function-level code generation, it requires the model to understand the entire repository, reasoning over complex dependencies across functions, classes, and modules. However, existing approaches such as retrieval-augmented generation (RAG) or context-based function selection often fall short: they primarily rely on surface-level similarity and struggle to capture the rich dependencies that govern repository-level semantics. In this paper, we introduce InlineCoder, a novel framework for repository-level code generation. InlineCoder enhances the understanding of repository context by inlining the unfinished function into its call graph, thereby reframing the challenging repository understanding as an easier function-level coding task. Given a function signature, InlineCoder first generates a draft completion, termed an anchor, which approximates downstream dependencies and enables perplexity-based confidence estimation. This anchor drives a bidirectional inlining process: (i) Upstream Inlining, which embeds the anchor into its callers to capture diverse usage scenarios; and (ii) Downstream Retrieval, which integrates the anchor's callees into the prompt to provide precise dependency context. The enriched context, combining draft completion with upstream and downstream perspectives, equips the LLM with a comprehensive repository view.

With the rapidly increasing capabilities and adoption of code agents for AI-assisted coding, safety concerns, such as generating or executing risky code, have become significant barriers to the real-world deployment of these agents. To provide comprehensive and practical evaluations on the safety of code agents, we propose RedCode, a benchmark for risky code execution and generation: (1) RedCode-Exec provides challenging prompts that could lead to risky code execution, aiming to evaluate code agents' ability to recognize and handle unsafe code. We provide a total of 4,050 risky test cases in Python and Bash tasks with diverse input formats including code snippets and natural text. They covers 25 types of critical vulnerabilities spanning 8 domains (e.g., websites, file systems). We provide Docker environments and design corresponding evaluation metrics to assess their execution results. (2) RedCode-Gen provides 160 prompts with function signatures and docstrings as input to assess whether code agents will follow instructions to generate harmful code or software. Our empirical findings, derived from evaluating three agent frameworks based on 19 LLMs, provide insights into code agents' vulnerabilities. For instance, evaluations on RedCode-Exec show that agents are more likely to reject executing risky operations on the operating system, but are less likely to reject executing technically buggy code, indicating high risks. Risky operations described in natural text lead to a lower rejection rate than those in code format. Additionally, evaluations on RedCode-Gen show that more capable base models and agents with stronger overall coding abilities, such as GPT4, tend to produce more sophisticated and effective harmful software. Our findings highlight the need for stringent safety evaluations for diverse code agents. Our dataset and code are available at https://github.com/AI-secure/RedCode.

Large language models (LLMs) have exhibited the ability to effectively utilize external tools to address user queries. However, their performance may be limited in complex, multi-turn interactions involving users and multiple tools. To address this, we propose Magnet, a principled framework for synthesizing high-quality training trajectories to enhance the function calling capability of large language model agents in multi-turn conversations with humans. The framework is based on automatic and iterative translations from a function signature path to a sequence of queries and executable function calls. We model the complicated function interactions in multi-turn cases with graph and design novel node operations to build reliable signature paths. Motivated by context distillation, when guiding the generation of positive and negative trajectories using a teacher model, we provide reference function call sequences as positive hints in context and contrastive, incorrect function calls as negative hints. Experiments show that training with the positive trajectories with supervised fine-tuning and preference optimization against negative trajectories, our 14B model, Magnet-14B-mDPO, obtains 68.01 on BFCL-v3 and 73.30 on ToolQuery, surpassing the performance of the teacher model Gemini-1.5-pro-002 by a large margin in function calling.

This paper presents the second ChatGPT4PCG competition at the 2024 IEEE Conference on Games. In this edition of the competition, we follow the first edition, but make several improvements and changes. We introduce a new evaluation metric along with allowing a more flexible format for participants' submissions and making several improvements to the evaluation pipeline. Continuing from the first edition, we aim to foster and explore the realm of prompt engineering (PE) for procedural content generation (PCG). While the first competition saw success, it was hindered by various limitations; we aim to mitigate these limitations in this edition. We introduce diversity as a new metric to discourage submissions aimed at producing repetitive structures. Furthermore, we allow submission of a Python program instead of a prompt text file for greater flexibility in implementing advanced PE approaches, which may require control flow, including conditions and iterations. We also make several improvements to the evaluation pipeline with a better classifier for similarity evaluation and better-performing function signatures. We thoroughly evaluate the effectiveness of the new metric and the improved classifier. Additionally, we perform an ablation study to select a function signature to instruct ChatGPT for level generation. Finally, we provide implementation examples of various PE techniques in Python and evaluate their preliminary performance. We hope this competition serves as a resource and platform for learning about PE and PCG in general.

Understanding and reasoning over diagrams is a fundamental aspect of human intelligence. While Large Multimodal Models (LMMs) have demonstrated impressive capabilities across various tasks, existing benchmarks lack comprehensive evaluation of their diagram interpretation and reasoning abilities, particularly in coding contexts. We present HumanEval-V, a rigorous benchmark of human-annotated coding tasks that spans six task types and evaluates diverse visual reasoning capabilities. Each task features carefully crafted diagrams paired with function signatures and test cases, employing novel code generation tasks to thoroughly assess models' diagram comprehension. Through extensive experiments with 22 LMMs, we find that even top-performing models achieve modest success rates, with Claude 3.5 Sonnet reaching only 36.8% pass@1, highlighting substantial room for improvement. Our analysis reveals that current LMMs struggle with spatial transformations, topological relationships, and dynamic patterns that humans find intuitive. These findings provide valuable insights for advancing LMMs' visual reasoning abilities. We have open-sourced our code and benchmark at https://github.com/HumanEval-V/HumanEval-V-Benchmark.

We introduce a graph-aware autoencoder ensemble framework, with associated formalisms and tooling, designed to facilitate deep learning for scholarship in the humanities. By composing sub-architectures to produce a model isomorphic to a humanistic domain we maintain interpretability while providing function signatures for each sub-architectural choice, allowing both traditional and computational researchers to collaborate without disrupting established practices. We illustrate a practical application of our approach to a historical study of the American post-Atlantic slave trade, and make several specific technical contributions: a novel hybrid graph-convolutional autoencoder mechanism, batching policies for common graph topologies, and masking techniques for particular use-cases. The effectiveness of the framework for broadening participation of diverse domains is demonstrated by a growing suite of two dozen studies, both collaborations with humanists and established tasks from machine learning literature, spanning a variety of fields and data modalities. We make performance comparisons of several different architectural choices and conclude with an ambitious list of imminent next steps for this research.

In recent years, the application of large language models (LLMs) to code-related tasks has gained significant attention. However, existing evaluation benchmarks often focus on limited scenarios, such as code generation or completion, which do not reflect the diverse challenges developers face in real-world contexts. To address this, we introduce ComplexCodeEval, a benchmark designed to assess LCMs in various development tasks, including code generation, completion, API recommendation, and test case generation. It includes 3,897 Java samples and 7,184 Python samples from high-star GitHub repositories, each annotated with function signatures, docstrings, and API references to simulate real development environments. Our experiments across ten LCMs reveal that context improves performance and that data leakage can lead to overestimation, highlighting the need for more accurate evaluations.

Motivated by the paradigm of reservoir computing, we consider randomly initialized controlled ResNets defined as Euler-discretizations of neural controlled differential equations (Neural CDEs), a unified architecture which enconpasses both RNNs and ResNets. We show that in the infinite-width-depth limit and under proper scaling, these architectures converge weakly to Gaussian processes indexed on some spaces of continuous paths and with kernels satisfying certain partial differential equations (PDEs) varying according to the choice of activation function, extending the results of Hayou (2022); Hayou & Yang (2023) to the controlled and homogeneous case. In the special, homogeneous, case where the activation is the identity, we show that the equation reduces to a linear PDE and the limiting kernel agrees with the signature kernel of Salvi et al. (2021a). We name this new family of limiting kernels neural signature kernels. Finally, we show that in the infinite-depth regime, finite-width controlled ResNets converge in distribution to Neural CDEs with random vector fields which, depending on whether the weights are shared across layers, are either time-independent and Gaussian or behave like a matrix-valued Brownian motion.

Galaxy clusters selected based on overdensities of galaxies in photometric surveys provide the largest cluster samples. Yet modeling the selection function of such samples is complicated by non-cluster members projected along the line of sight (projection effects) and the potential detection of unvirialized objects (contamination). We empirically constrain the magnitude of these effects by cross-matching galaxy clusters selected in the Dark Energy survey data with the \rdmpr, algorithm with significant detections in three South Pole Telescope surveys (SZ, pol-ECS, pol-500d). For matched clusters, we augment the \rdmpr,catalog by the SPT detection significance. For unmatched objects we use the SPT detection threshold as an upper limit on the SZe signature. Using a Bayesian population model applied to the collected multi-wavelength data, we explore various physically motivated models to describe the relationship between observed richness and halo mass. Our analysis reveals the limitations of a simple lognormal scatter model in describing the data. We rule out significant contamination by unvirialized objects at the high-richness end of the sample. While dedicated simulations offer a well-fitting calibration of projection effects, our findings suggest the presence of redshift-dependent trends that these simulations may not have captured. Our findings highlight that modeling the selection function of optically detected clusters remains a complicated challenge, requiring a combination of simulation and data-driven approaches.

Searches for stochastic gravitational-wave backgrounds using pulsar timing arrays look for correlations in the timing residuals induced by the background across the pulsars in the array. The correlation signature of an isotropic, unpolarized gravitational-wave background predicted by general relativity follows the so-called Hellings and Downs curve, which is a relatively simple function of the angle between a pair of Earth-pulsar baselines. In this paper, we give a pedagogical discussion of the Hellings and Downs curve for pulsar timing arrays, considering simpler analogous scenarios involving sound and electromagnetic waves. We calculate Hellings-and-Downs-type functions for these two scenarios and develop a framework suitable for doing more general correlation calculations.

Large language models (LLMs) fine-tuned by reinforcement learning from human feedback (RLHF) are becoming more widely deployed. We coin the term Implicit Reward Model (IRM) to refer to the changes that occur to an LLM during RLHF that result in high-reward generations. We interpret IRMs, and measure their divergence from the RLHF reward model used in the fine-tuning process that induced them. By fitting a linear function to an LLM's IRM, a reward model with the same type signature as the RLHF reward model is constructed, allowing for direct comparison. Additionally, we validate our construction of the IRM through cross-comparison with classifications of features generated by an LLM based on their relevance to the RLHF reward model. Better comprehending IRMs can help minimize discrepencies between LLM behavior and training objectives, which we believe to be an essential component of the safety and alignment of LLMs.

We introduce a mathematically rigorous framework based on rough path theory to model stochastic spiking neural networks (SSNNs) as stochastic differential equations with event discontinuities (Event SDEs) and driven by c\`adl\`ag rough paths. Our formalism is general enough to allow for potential jumps to be present both in the solution trajectories as well as in the driving noise. We then identify a set of sufficient conditions ensuring the existence of pathwise gradients of solution trajectories and event times with respect to the network's parameters and show how these gradients satisfy a recursive relation. Furthermore, we introduce a general-purpose loss function defined by means of a new class of signature kernels indexed on c\`adl\`ag rough paths and use it to train SSNNs as generative models. We provide an end-to-end autodifferentiable solver for Event SDEs and make its implementation available as part of the diffrax library. Our framework is, to our knowledge, the first enabling gradient-based training of SSNNs with noise affecting both the spike timing and the network's dynamics.

Unit tests play a key role in ensuring the correctness of software. However, manually creating unit tests is a laborious task, motivating the need for automation. Large Language Models (LLMs) have recently been applied to this problem, utilizing additional training or few-shot learning on examples of existing tests. This paper presents a large-scale empirical evaluation on the effectiveness of LLMs for automated unit test generation without additional training or manual effort, providing the LLM with the signature and implementation of the function under test, along with usage examples extracted from documentation. We also attempt to repair failed generated tests by re-prompting the model with the failing test and error message. We implement our approach in TestPilot, a test generation tool for JavaScript that automatically generates unit tests for all API functions in an npm package. We evaluate TestPilot using OpenAI's gpt3.5-turbo LLM on 25 npm packages with a total of 1,684 API functions. The generated tests achieve a median statement coverage of 70.2% and branch coverage of 52.8%, significantly improving on Nessie, a recent feedback-directed JavaScript test generation technique, which achieves only 51.3% statement coverage and 25.6% branch coverage. We also find that 92.8% of TestPilot's generated tests have no more than 50% similarity with existing tests (as measured by normalized edit distance), with none of them being exact copies. Finally, we run TestPilot with two additional LLMs, OpenAI's older code-cushman-002 LLM and the open LLM StarCoder. Overall, we observed similar results with the former (68.2% median statement coverage), and somewhat worse results with the latter (54.0% median statement coverage), suggesting that the effectiveness of the approach is influenced by the size and training set of the LLM, but does not fundamentally depend on the specific model.

We extend JAX with the capability to automatically differentiate higher-order functions (functionals and operators). By representing functions as a generalization of arrays, we seamlessly use JAX's existing primitive system to implement higher-order functions. We present a set of primitive operators that serve as foundational building blocks for constructing several key types of functionals. For every introduced primitive operator, we derive and implement both linearization and transposition rules, aligning with JAX's internal protocols for forward and reverse mode automatic differentiation. This enhancement allows for functional differentiation in the same syntax traditionally use for functions. The resulting functional gradients are themselves functions ready to be invoked in python. We showcase this tool's efficacy and simplicity through applications where functional derivatives are indispensable. The source code of this work is released at https://github.com/sail-sg/autofd .

Despite recent progress made by large language models in code generation, they still struggle with programs that meet complex requirements. Recent work utilizes plan-and-solve decomposition to decrease the complexity and leverage self-tests to refine the generated program. Yet, planning deep-inside requirements in advance can be challenging, and the tests need to be accurate to accomplish self-improvement. To this end, we propose FunCoder, a code generation framework incorporating the divide-and-conquer strategy with functional consensus. Specifically, FunCoder recursively branches off sub-functions as smaller goals during code generation, represented by a tree hierarchy. These sub-functions are then composited to attain more complex objectives. Additionally, we designate functions via a consensus formed by identifying similarities in program behavior, mitigating error propagation. FunCoder outperforms state-of-the-art methods by +9.8% on average in HumanEval, MBPP, xCodeEval and MATH with GPT-3.5 and GPT-4. Moreover, our method demonstrates superiority on smaller models: With FunCoder, StableCode-3b surpasses GPT-3.5 by +18.6% and achieves 97.7% of GPT-4's performance on HumanEval. Further analysis reveals that our proposed dynamic function decomposition is capable of handling complex requirements, and the functional consensus prevails over self-testing in correctness evaluation.

Signature synthesis is a computation technique that generates artificial specimens which can support decision making in automatic signature verification. A lot of work has been dedicated to this subject, which centres on synthesizing dynamic and static two-dimensional handwriting on canvas. This paper proposes a framework to generate synthetic 3D on-air signatures exploiting the lognormality principle, which mimics the complex neuromotor control processes at play as the fingertip moves. Addressing the usual cases involving the development of artificial individuals and duplicated samples, this paper contributes to the synthesis of: (1) the trajectory and velocity of entirely 3D new signatures; (2) kinematic information when only the 3D trajectory of the signature is known, and (3) duplicate samples of 3D real signatures. Validation was conducted by generating synthetic 3D signature databases mimicking real ones and showing that automatic signature verifications of genuine and skilled forgeries report performances similar to those of real and synthetic databases. We also observed that training 3D automatic signature verifiers with duplicates can reduce errors. We further demonstrated that our proposal is also valid for synthesizing 3D air writing and gestures. Finally, a perception test confirmed the human likeness of the generated specimens. The databases generated are publicly available, only for research purposes, at .

We study the problem of designing models for machine learning tasks defined on sets. In contrast to traditional approach of operating on fixed dimensional vectors, we consider objective functions defined on sets that are invariant to permutations. Such problems are widespread, ranging from estimation of population statistics poczos13aistats, to anomaly detection in piezometer data of embankment dams Jung15Exploration, to cosmology Ntampaka16Dynamical,Ravanbakhsh16ICML1. Our main theorem characterizes the permutation invariant functions and provides a family of functions to which any permutation invariant objective function must belong. This family of functions has a special structure which enables us to design a deep network architecture that can operate on sets and which can be deployed on a variety of scenarios including both unsupervised and supervised learning tasks. We also derive the necessary and sufficient conditions for permutation equivariance in deep models. We demonstrate the applicability of our method on population statistic estimation, point cloud classification, set expansion, and outlier detection.

Predicting vulnerable source code helps to focus attention on those parts of the code that need to be examined with more scrutiny. Recent work proposed the use of function names as semantic cues that can be learned by a deep neural network (DNN) to aid in the hunt for vulnerability of functions. Combining identifier splitting, which splits each function name into its constituent words, with a novel frequency-based algorithm, we explore the extent to which the words that make up a function's name can predict potentially vulnerable functions. In contrast to *lightweight* predictions by a DNN that considers only function names, avoiding the use of a DNN provides *featherweight* predictions. The underlying idea is that function names that contain certain "dangerous" words are more likely to accompany vulnerable functions. Of course, this assumes that the frequency-based algorithm can be properly tuned to focus on truly dangerous words. Because it is more transparent than a DNN, the frequency-based algorithm enables us to investigate the inner workings of the DNN. If successful, this investigation into what the DNN does and does not learn will help us train more effective future models. We empirically evaluate our approach on a heterogeneous dataset containing over 73000 functions labeled vulnerable, and over 950000 functions labeled benign. Our analysis shows that words alone account for a significant portion of the DNN's classification ability. We also find that words are of greatest value in the datasets with a more homogeneous vocabulary. Thus, when working within the scope of a given project, where the vocabulary is unavoidably homogeneous, our approach provides a cheaper, potentially complementary, technique to aid in the hunt for source-code vulnerabilities. Finally, this approach has the advantage that it is viable with orders of magnitude less training data.

We address the problem of learning the dynamics of an unknown non-parametric system linking a target and a feature time series. The feature time series is measured on a sparse and irregular grid, while we have access to only a few points of the target time series. Once learned, we can use these dynamics to predict values of the target from the previous values of the feature time series. We frame this task as learning the solution map of a controlled differential equation (CDE). By leveraging the rich theory of signatures, we are able to cast this non-linear problem as a high-dimensional linear regression. We provide an oracle bound on the prediction error which exhibits explicit dependencies on the individual-specific sampling schemes. Our theoretical results are illustrated by simulations which show that our method outperforms existing algorithms for recovering the full time series while being computationally cheap. We conclude by demonstrating its potential on real-world epidemiological data.

The field of Automatic Machine Learning (AutoML) has recently attained impressive results, including the discovery of state-of-the-art machine learning solutions, such as neural image classifiers. This is often done by applying an evolutionary search method, which samples multiple candidate solutions from a large space and evaluates the quality of each candidate through a long training process. As a result, the search tends to be slow. In this paper, we show that large efficiency gains can be obtained by employing a fast unified functional hash, especially through the functional equivalence caching technique, which we also present. The central idea is to detect by hashing when the search method produces equivalent candidates, which occurs very frequently, and this way avoid their costly re-evaluation. Our hash is "functional" in that it identifies equivalent candidates even if they were represented or coded differently, and it is "unified" in that the same algorithm can hash arbitrary representations; e.g. compute graphs, imperative code, or lambda functions. As evidence, we show dramatic improvements on multiple AutoML domains, including neural architecture search and algorithm discovery. Finally, we consider the effect of hash collisions, evaluation noise, and search distribution through empirical analysis. Altogether, we hope this paper may serve as a guide to hashing techniques in AutoML.

Large language models (LLMs) have recently shown tremendous promise in serving as the backbone to agentic systems, as demonstrated by their performance in multi-faceted, challenging benchmarks like SWE-Bench and Agent-Bench. However, to realize the true potential of LLMs as autonomous agents, they must learn to identify, call, and interact with external tools and application program interfaces (APIs) to complete complex tasks. These tasks together are termed function calling. Endowing LLMs with function calling abilities leads to a myriad of advantages, such as access to current and domain-specific information in databases and knowledge sources, and the ability to outsource tasks that can be reliably performed by tools, e.g., a Python interpreter or calculator. While there has been significant progress in function calling with LLMs, there is still a dearth of open models that perform on par with proprietary LLMs like GPT, Claude, and Gemini. Therefore, in this work, we introduce the GRANITE-20B-FUNCTIONCALLING model under an Apache 2.0 license. The model is trained using a multi-task training approach on seven fundamental tasks encompassed in function calling, those being Nested Function Calling, Function Chaining, Parallel Functions, Function Name Detection, Parameter-Value Pair Detection, Next-Best Function, and Response Generation. We present a comprehensive evaluation on multiple out-of-domain datasets comparing GRANITE-20B-FUNCTIONCALLING to more than 15 other best proprietary and open models. GRANITE-20B-FUNCTIONCALLING provides the best performance among all open models on the Berkeley Function Calling Leaderboard and fourth overall. As a result of the diverse tasks and datasets used for training our model, we show that GRANITE-20B-FUNCTIONCALLING has better generalizability on multiple tasks in seven different evaluation datasets.

In this work we take a Category Theoretic perspective on the relationship between probabilistic modeling and function approximation. We begin by defining two extensions of function composition to stochastic process subordination: one based on the co-Kleisli category under the comonad (Omega x -) and one based on the parameterization of a category with a Lawvere theory. We show how these extensions relate to the category Stoch and other Markov Categories. Next, we apply the Para construction to extend stochastic processes to parameterized statistical models and we define a way to compose the likelihood functions of these models. We conclude with a demonstration of how the Maximum Likelihood Estimation procedure defines an identity-on-objects functor from the category of statistical models to the category of Learners. Code to accompany this paper can be found at https://github.com/dshieble/Categorical_Stochastic_Processes_and_Likelihood

We examine the connections between deterministic, complete, and general global optimisation of continuous functions and a general concept of regression from the perspective of constructive type theory via the concept of 'searchability'. We see how the property of convergence of global optimisation is a straightforward consequence of searchability. The abstract setting allows us to generalise searchability and continuity to higher-order functions, so that we can formulate novel convergence criteria for regression, derived from the convergence of global optimisation. All the theory and the motivating examples are fully formalised in the proof assistant Agda.

Auxiliary function is a helpful component to improve language model's code generation ability. However, a systematic exploration of how they affect has yet to be done. In this work, we comprehensively evaluate the ability to utilize auxiliary functions encoded in recent code-pretrained language models. First, we construct a human-crafted evaluation set, called HumanExtension, which contains examples of two functions where one function assists the other. With HumanExtension, we design several experiments to examine their ability in a multifaceted way. Our evaluation processes enable a comprehensive understanding of including auxiliary functions in the prompt in terms of effectiveness and robustness. An additional implementation style analysis captures the models' various implementation patterns when they access the auxiliary function. Through this analysis, we discover the models' promising ability to utilize auxiliary functions including their self-improving behavior by implementing the two functions step-by-step. However, our analysis also reveals the model's underutilized behavior to call the auxiliary function, suggesting the future direction to enhance their implementation by eliciting the auxiliary function call ability encoded in the models. We release our code and dataset to facilitate this research direction.

Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can accelerate this process by learning a scoring function with a functional form that allows for more rapid optimization. Specifically, we define the scoring function to be the cross-correlation of multi-channel ligand and protein scalar fields parameterized by equivariant graph neural networks, enabling rapid optimization over rigid-body degrees of freedom with fast Fourier transforms. The runtime of our approach can be amortized at several levels of abstraction, and is particularly favorable for virtual screening settings with a common binding pocket. We benchmark our scoring functions on two simplified docking-related tasks: decoy pose scoring and rigid conformer docking. Our method attains similar but faster performance on crystal structures compared to the widely-used Vina and Gnina scoring functions, and is more robust on computationally predicted structures. Code is available at https://github.com/bjing2016/scalar-fields.

Function calling is a core capability of large language models, essential for AI agents. Existing benchmarks such as the Berkeley Function Calling Leaderboard (BFCL), tau^2-Bench (arXiv:2506.07982), and ACEBench (arXiv:2501.12851) evaluate argument correctness but do not test adherence to format instructions embedded in parameter descriptions, such as enclosing values in double quotes or using ISO date formats. We introduce IFEval-FC, a benchmark inspired by IFEval (arXiv:2311.07911) that assesses precise instruction following in function calling. IFEval-FC encodes verifiable formats directly within JSON schema descriptions, for example specifying that a value must not contain punctuation. It includes 750 test cases, each consisting of a function with an embedded format for one of its input parameters and a corresponding user query. Evaluation is fully algorithmic, ensuring objectivity, reproducibility, and scalability. Our results show that even state-of-the-art proprietary models, including GPT-5 and Claude 4.1 Opus, frequently fail to follow basic formatting rules, highlighting a practical limitation for real-world agent systems. The complete codebase and data are publicly available at https://github.com/Skripkon/IFEval-FC.

Program synthesis is challenging largely because of the difficulty of search in a large space of programs. Human programmers routinely tackle the task of writing complex programs by writing sub-programs and then analyzing their intermediate results to compose them in appropriate ways. Motivated by this intuition, we present a new synthesis approach that leverages learning to guide a bottom-up search over programs. In particular, we train a model to prioritize compositions of intermediate values during search conditioned on a given set of input-output examples. This is a powerful combination because of several emergent properties. First, in bottom-up search, intermediate programs can be executed, providing semantic information to the neural network. Second, given the concrete values from those executions, we can exploit rich features based on recent work on property signatures. Finally, bottom-up search allows the system substantial flexibility in what order to generate the solution, allowing the synthesizer to build up a program from multiple smaller sub-programs. Overall, our empirical evaluation finds that the combination of learning and bottom-up search is remarkably effective, even with simple supervised learning approaches. We demonstrate the effectiveness of our technique on two datasets, one from the SyGuS competition and one of our own creation.

Neural networks have proven to be a highly effective tool for solving complex problems in many areas of life. Recently, their importance and practical usability have further been reinforced with the advent of deep learning. One of the important conditions for the success of neural networks is the choice of an appropriate activation function introducing non-linearity into the model. Many types of these functions have been proposed in the literature in the past, but there is no single comprehensive source containing their exhaustive overview. The absence of this overview, even in our experience, leads to redundancy and the unintentional rediscovery of already existing activation functions. To bridge this gap, our paper presents an extensive survey involving 400 activation functions, which is several times larger in scale than previous surveys. Our comprehensive compilation also references these surveys; however, its main goal is to provide the most comprehensive overview and systematization of previously published activation functions with links to their original sources. The secondary aim is to update the current understanding of this family of functions.

Large language models have demonstrated impressive value in performing as autonomous agents when equipped with external tools and API calls. Nonetheless, effectively harnessing their potential for executing complex tasks crucially relies on enhancements in their function calling capabilities. This paper identifies a critical gap in existing function calling models, where performance varies significantly across benchmarks, often due to being misled by specific naming conventions. To address such an issue, we introduce Hammer, a novel family of foundation models specifically engineered for on-device function calling. Hammer employs an augmented dataset that enhances models' sensitivity to irrelevant functions and incorporates function masking techniques to minimize misleading. Our empirical evaluations reveal that Hammer not only outperforms larger models but also demonstrates robust generalization across diverse benchmarks, achieving sota results. Our open source contributions include a specialized dataset for irrelevance detection, a tuning framework for enhanced generalization, and the Hammer models, establishing a new standard for function calling performance.

Watermark has been widely deployed by industry to detect AI-generated images. A recent watermarking framework called Stable Signature (proposed by Meta) roots watermark into the parameters of a diffusion model's decoder such that its generated images are inherently watermarked. Stable Signature makes it possible to watermark images generated by open-source diffusion models and was claimed to be robust against removal attacks. In this work, we propose a new attack to remove the watermark from a diffusion model by fine-tuning it. Our results show that our attack can effectively remove the watermark from a diffusion model such that its generated images are non-watermarked, while maintaining the visual quality of the generated images. Our results highlight that Stable Signature is not as stable as previously thought.

We present a set-theoretic, proof-irrelevant model for Calculus of Constructions (CC) with predicative induction and judgmental equality in Zermelo-Fraenkel set theory with an axiom for countably many inaccessible cardinals. We use Aczel's trace encoding which is universally defined for any function type, regardless of being impredicative. Direct and concrete interpretations of simultaneous induction and mutually recursive functions are also provided by extending Dybjer's interpretations on the basis of Aczel's rule sets. Our model can be regarded as a higher-order generalization of the truth-table methods. We provide a relatively simple consistency proof of type theory, which can be used as the basis for a theorem prover.

Functional data play a pivotal role across science and engineering, yet their infinite-dimensional nature makes representation learning challenging. Conventional statistical models depend on pre-chosen basis expansions or kernels, limiting the flexibility of data-driven discovery, while many deep-learning pipelines treat functions as fixed-grid vectors, ignoring inherent continuity. In this paper, we introduce Functional Attention with a Mixture-of-Experts (FAME), an end-to-end, fully data-driven framework for function-on-function regression. FAME forms continuous attention by coupling a bidirectional neural controlled differential equation with MoE-driven vector fields to capture intra-functional continuity, and further fuses change to inter-functional dependencies via multi-head cross attention. Extensive experiments on synthetic and real-world functional-regression benchmarks show that FAME achieves state-of-the-art accuracy, strong robustness to arbitrarily sampled discrete observations of functions.

Diffusion models have made compelling progress on facilitating high-throughput daily production. Nevertheless, the appealing customized requirements are remain suffered from instance-level finetuning for authentic fidelity. Prior zero-shot customization works achieve the semantic consistence through the condensed injection of identity features, while addressing detailed low-level signatures through complex model configurations and subject-specific fabrications, which significantly break the statistical coherence within the overall system and limit the applicability across various scenarios. To facilitate the generic signature concentration with rectified efficiency, we present AnyLogo, a zero-shot region customizer with remarkable detail consistency, building upon the symbiotic diffusion system with eliminated cumbersome designs. Streamlined as vanilla image generation, we discern that the rigorous signature extraction and creative content generation are promisingly compatible and can be systematically recycled within a single denoising model. In place of the external configurations, the gemini status of the denoising model promote the reinforced subject transmission efficiency and disentangled semantic-signature space with continuous signature decoration. Moreover, the sparse recycling paradigm is adopted to prevent the duplicated risk with compressed transmission quota for diversified signature stimulation. Extensive experiments on constructed logo-level benchmarks demonstrate the effectiveness and practicability of our methods.

Publicly available source-code libraries are continuously growing and changing. This makes it impossible for models of code to keep current with all available APIs by simply training these models on existing code repositories. Thus, existing models inherently cannot generalize to using unseen functions and libraries, because these would never appear in the training data. In contrast, when human programmers use functions and libraries for the first time, they frequently refer to textual resources such as code manuals and documentation, to explore and understand the available functionality. Inspired by this observation, we introduce DocPrompting: a natural-language-to-code generation approach that explicitly leverages documentation by (1) retrieving the relevant documentation pieces given an NL intent, and (2) generating code based on the NL intent and the retrieved documentation. DocPrompting is general: it can be applied to any programming language and is agnostic to the underlying neural model. We demonstrate that DocPrompting consistently improves NL-to-code models: DocPrompting improves strong base models such as CodeT5 by 2.85% in pass@1 (52% relative gain) and 4.39% in pass@10 (30% relative gain) in execution-based evaluation on the popular Python CoNaLa benchmark; on a new Bash dataset tldr, DocPrompting improves CodeT5 and GPT-Neo1.3B by up to absolute 6.9% exact match.

There is a long history, as well as a recent explosion of interest, in statistical and generative modeling approaches based on score functions -- derivatives of the log-likelihood of a distribution. In seminal works, Hyv\"arinen proposed vanilla score matching as a way to learn distributions from data by computing an estimate of the score function of the underlying ground truth, and established connections between this method and established techniques like Contrastive Divergence and Pseudolikelihood estimation. It is by now well-known that vanilla score matching has significant difficulties learning multimodal distributions. Although there are various ways to overcome this difficulty, the following question has remained unanswered -- is there a natural way to sample multimodal distributions using just the vanilla score? Inspired by a long line of related experimental works, we prove that the Langevin diffusion with early stopping, initialized at the empirical distribution, and run on a score function estimated from data successfully generates natural multimodal distributions (mixtures of log-concave distributions).

As a vital stage of automated rule checking (ARC), rule interpretation of regulatory texts requires considerable effort. However, interpreting regulatory clauses with implicit properties or complex computational logic is still challenging due to the lack of domain knowledge and limited expressibility of conventional logic representations. Thus, LLM-FuncMapper, an approach to identifying predefined functions needed to interpret various regulatory clauses based on the large language model (LLM), is proposed. First, by systematically analysis of building codes, a series of atomic functions are defined to capture shared computational logics of implicit properties and complex constraints, creating a database of common blocks for interpreting regulatory clauses. Then, a prompt template with the chain of thought is developed and further enhanced with a classification-based tuning strategy, to enable common LLMs for effective function identification. Finally, the proposed approach is validated with statistical analysis, experiments, and proof of concept. Statistical analysis reveals a long-tail distribution and high expressibility of the developed function database, with which almost 100% of computer-processible clauses can be interpreted and represented as computer-executable codes. Experiments show that LLM-FuncMapper achieve promising results in identifying relevant predefined functions for rule interpretation. Further proof of concept in automated rule interpretation also demonstrates the possibility of LLM-FuncMapper in interpreting complex regulatory clauses. To the best of our knowledge, this study is the first attempt to introduce LLM for understanding and interpreting complex regulatory clauses, which may shed light on further adoption of LLM in the construction domain.

Set function learning has emerged as a crucial area in machine learning, addressing the challenge of modeling functions that take sets as inputs. Unlike traditional machine learning that involves fixed-size input vectors where the order of features matters, set function learning demands methods that are invariant to permutations of the input set, presenting a unique and complex problem. This survey provides a comprehensive overview of the current development in set function learning, covering foundational theories, key methodologies, and diverse applications. We categorize and discuss existing approaches, focusing on deep learning approaches, such as DeepSets and Set Transformer based methods, as well as other notable alternative methods beyond deep learning, offering a complete view of current models. We also introduce various applications and relevant datasets, such as point cloud processing and multi-label classification, highlighting the significant progress achieved by set function learning methods in these domains. Finally, we conclude by summarizing the current state of set function learning approaches and identifying promising future research directions, aiming to guide and inspire further advancements in this promising field.

Normalization layers and activation functions are fundamental components in deep networks and typically co-locate with each other. Here we propose to design them using an automated approach. Instead of designing them separately, we unify them into a single tensor-to-tensor computation graph, and evolve its structure starting from basic mathematical functions. Examples of such mathematical functions are addition, multiplication and statistical moments. The use of low-level mathematical functions, in contrast to the use of high-level modules in mainstream NAS, leads to a highly sparse and large search space which can be challenging for search methods. To address the challenge, we develop efficient rejection protocols to quickly filter out candidate layers that do not work well. We also use multi-objective evolution to optimize each layer's performance across many architectures to prevent overfitting. Our method leads to the discovery of EvoNorms, a set of new normalization-activation layers with novel, and sometimes surprising structures that go beyond existing design patterns. For example, some EvoNorms do not assume that normalization and activation functions must be applied sequentially, nor need to center the feature maps, nor require explicit activation functions. Our experiments show that EvoNorms work well on image classification models including ResNets, MobileNets and EfficientNets but also transfer well to Mask R-CNN with FPN/SpineNet for instance segmentation and to BigGAN for image synthesis, outperforming BatchNorm and GroupNorm based layers in many cases.

CONTEXT The R programming language has a huge and active community, especially in the area of statistical computing. Its interpreted nature allows for several interesting constructs, like the manipulation of functions at run-time, that hinder the static analysis of R programs. At the same time, there is a lack of existing research regarding how these features, or even the R language as a whole are used in practice. OBJECTIVE In this paper, we conduct a large-scale, static analysis of more than 50 million lines of real-world R programs and packages to identify their characteristics and the features that are actually used. Moreover, we compare the similarities and differences between the scripts of R users and the implementations of package authors. We provide insights for static analysis tools like the lintr package as well as potential interpreter optimizations and uncover areas for future research. METHOD We analyze 4230 R scripts submitted alongside publications and the sources of 19450 CRAN packages for over 350000 R files, collecting and summarizing quantitative information for features of interest. RESULTS We find a high frequency of name-based indexing operations, assignments, and loops, but a low frequency for most of R's reflective functions. Furthermore, we find neither testing functions nor many calls to R's foreign function interface (FFI) in the publication submissions. CONCLUSION R scripts and package sources differ, for example, in their size, the way they include other packages, and their usage of R's reflective capabilities. We provide features that are used frequently and should be prioritized by static analysis tools, like operator assignments, function calls, and certain reflective functions like load.

Labeling neural network submodules with human-legible descriptions is useful for many downstream tasks: such descriptions can surface failures, guide interventions, and perhaps even explain important model behaviors. To date, most mechanistic descriptions of trained networks have involved small models, narrowly delimited phenomena, and large amounts of human labor. Labeling all human-interpretable sub-computations in models of increasing size and complexity will almost certainly require tools that can generate and validate descriptions automatically. Recently, techniques that use learned models in-the-loop for labeling have begun to gain traction, but methods for evaluating their efficacy are limited and ad-hoc. How should we validate and compare open-ended labeling tools? This paper introduces FIND (Function INterpretation and Description), a benchmark suite for evaluating the building blocks of automated interpretability methods. FIND contains functions that resemble components of trained neural networks, and accompanying descriptions of the kind we seek to generate. The functions are procedurally constructed across textual and numeric domains, and involve a range of real-world complexities, including noise, composition, approximation, and bias. We evaluate new and existing methods that use language models (LMs) to produce code-based and language descriptions of function behavior. We find that an off-the-shelf LM augmented with only black-box access to functions can sometimes infer their structure, acting as a scientist by forming hypotheses, proposing experiments, and updating descriptions in light of new data. However, LM-based descriptions tend to capture global function behavior and miss local corruptions. These results show that FIND will be useful for characterizing the performance of more sophisticated interpretability methods before they are applied to real-world models.

In 2011, einsum was introduced to NumPy as a practical and convenient notation for tensor expressions in machine learning, quantum circuit simulation, and other fields. It has since been implemented in additional Python frameworks such as PyTorch and TensorFlow, as well as in other programming languages such as Julia. Despite its practical success, the einsum notation still lacks a solid theoretical basis, and is not unified across the different frameworks, limiting opportunities for formal reasoning and systematic optimization. In this work, we discuss the terminology of tensor expressions and provide a formal definition of the einsum language. Based on this definition, we formalize and prove important equivalence rules for tensor expressions and highlight their relevance in practical applications.

A comparative analysis of the special shapes (patterns, profiles) of the eclipses applied for the phenomenological modeling of the light curves of eclipsing binary stars is conducted. Families of functions are considered, generalizing local approximations (Andronov, 2010, 2012) and the functions theoretically unlimited in a width, based on a Gaussian (Mikulasek, 2015). For an analysis, the light curve of the star V0882 Car = 2MASS J11080308 - 6145589 of the classic Algol - subtype (\beta Persei) is used. By analyzing dozens of modified functions with additional parameters, it was chosen the 14 best ones according to the criterion of the least sum of squares of deviations. The best are the functions with an additional parameter, describing profiles, which are limited in phase.

We present a unified representation of the most popular neural network activation functions. Adopting Mittag-Leffler functions of fractional calculus, we propose a flexible and compact functional form that is able to interpolate between various activation functions and mitigate common problems in training neural networks such as vanishing and exploding gradients. The presented gated representation extends the scope of fixed-shape activation functions to their adaptive counterparts whose shape can be learnt from the training data. The derivatives of the proposed functional form can also be expressed in terms of Mittag-Leffler functions making it a suitable candidate for gradient-based backpropagation algorithms. By training multiple neural networks of different complexities on various datasets with different sizes, we demonstrate that adopting a unified gated representation of activation functions offers a promising and affordable alternative to individual built-in implementations of activation functions in conventional machine learning frameworks.

Biometric authentication systems that make use of signature verification methods often render optimum performance only under limited and restricted conditions. Such methods utilize several training samples so as to achieve high accuracy. Moreover, several constraints are imposed on the end-user so that the system may work optimally, and as expected. For example, the user is made to sign within a small box, in order to limit their signature to a predefined set of dimensions, thus eliminating scaling. Moreover, the angular rotation with respect to the referenced signature that will be inadvertently introduced as human error, hampers performance of biometric signature verification systems. To eliminate this, traditionally, a user is asked to sign exactly on top of a reference line. In this paper, we propose a robust system that optimizes the signature obtained from the user for a large range of variation in Rotation-Scaling-Translation (RST) and resolves these error parameters in the user signature according to the reference signature stored in the database.

While large language models (LLMs) appear to be increasingly capable of solving compositional tasks, it is an open question whether they do so using compositional mechanisms. In this work, we investigate how feedforward LLMs solve two-hop factual recall tasks, which can be expressed compositionally as g(f(x)). We first confirm that modern LLMs continue to suffer from the "compositionality gap": i.e. their ability to compute both z = f(x) and y = g(z) does not entail their ability to compute the composition y = g(f(x)). Then, using logit lens on their residual stream activations, we identify two processing mechanisms, one which solves tasks compositionally, computing f(x) along the way to computing g(f(x)), and one which solves them directly, without any detectable signature of the intermediate variable f(x). Finally, we find that which mechanism is employed appears to be related to the embedding space geometry, with the idiomatic mechanism being dominant in cases where there exists a linear mapping from x to g(f(x)) in the embedding spaces. We fully release our data and code at: https://github.com/apoorvkh/composing-functions .

Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at https://github.com/gersteinlab/biocoder.

We present CRUXEval (Code Reasoning, Understanding, and eXecution Evaluation), a benchmark consisting of 800 Python functions (3-13 lines). Each function comes with an input-output pair, leading to two natural tasks: input prediction and output prediction. First, we propose a generic recipe for generating our execution benchmark which can be used to create future variation of the benchmark. Second, we evaluate twenty code models on our benchmark and discover that many recent high-scoring models on HumanEval do not show the same improvements on our benchmark. Third, we show that simple CoT and fine-tuning schemes can improve performance on our benchmark but remain far from solving it. The best setup, GPT-4 with chain of thought (CoT), achieves a pass@1 of 75% and 81% on input and output prediction, respectively. In contrast, Code Llama 34B achieves a pass@1 of 50% and 46% on input and output prediction, highlighting the gap between open and closed source models. As no model is close to acing CRUXEval, we provide examples of consistent GPT-4 failures on simple programs as a lens into its code reasoning capabilities and areas for improvement.

Real-valued functions on geometric data -- such as node attributes on a graph -- can be optimized using descriptors from persistent homology, allowing the user to incorporate topological terms in the loss function. When optimizing a single real-valued function (the one-parameter setting), there is a canonical choice of descriptor for persistent homology: the barcode. The operation mapping a real-valued function to its barcode is differentiable almost everywhere, and the convergence of gradient descent for losses using barcodes is relatively well understood. When optimizing a vector-valued function (the multiparameter setting), there is no unique choice of descriptor for multiparameter persistent homology, and many distinct descriptors have been proposed. This calls for the development of a general framework for differentiability and optimization that applies to a wide range of multiparameter homological descriptors. In this article, we develop such a framework and show that it encompasses well-known descriptors of different flavors, such as signed barcodes and the multiparameter persistence landscape. We complement the theory with numerical experiments supporting the idea that optimizing multiparameter homological descriptors can lead to improved performances compared to optimizing one-parameter descriptors, even when using the simplest and most efficiently computable multiparameter descriptors.

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

We introduce Functional Diffusion Processes (FDPs), which generalize score-based diffusion models to infinite-dimensional function spaces. FDPs require a new mathematical framework to describe the forward and backward dynamics, and several extensions to derive practical training objectives. These include infinite-dimensional versions of Girsanov theorem, in order to be able to compute an ELBO, and of the sampling theorem, in order to guarantee that functional evaluations in a countable set of points are equivalent to infinite-dimensional functions. We use FDPs to build a new breed of generative models in function spaces, which do not require specialized network architectures, and that can work with any kind of continuous data. Our results on real data show that FDPs achieve high-quality image generation, using a simple MLP architecture with orders of magnitude fewer parameters than existing diffusion models.

We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lov\'asz' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.

Fine-tuning pre-trained language models (PLMs), e.g., SciBERT, generally requires large numbers of annotated data to achieve state-of-the-art performance on a range of NLP tasks in the scientific domain. However, obtaining the fine-tune data for scientific NLP task is still challenging and expensive. Inspired by recent advancement in prompt learning, in this paper, we propose the Mix Prompt Tuning (MPT), which is a semi-supervised method to alleviate the dependence on annotated data and improve the performance of multi-granularity academic function recognition tasks with a small number of labeled examples. Specifically, the proposed method provides multi-perspective representations by combining manual prompt templates with automatically learned continuous prompt templates to help the given academic function recognition task take full advantage of knowledge in PLMs. Based on these prompt templates and the fine-tuned PLM, a large number of pseudo labels are assigned to the unlabeled examples. Finally, we fine-tune the PLM using the pseudo training set. We evaluate our method on three academic function recognition tasks of different granularity including the citation function, the abstract sentence function, and the keyword function, with datasets from computer science domain and biomedical domain. Extensive experiments demonstrate the effectiveness of our method and statistically significant improvements against strong baselines. In particular, it achieves an average increase of 5% in Macro-F1 score compared with fine-tuning, and 6% in Macro-F1 score compared with other semi-supervised method under low-resource settings. In addition, MPT is a general method that can be easily applied to other low-resource scientific classification tasks.

We study the code generation behavior of instruction-tuned models built on top of code pre-trained language models when they could access an auxiliary function to implement a function. We design several ways to provide auxiliary functions to the models by adding them to the query or providing a response prefix to incorporate the ability to utilize auxiliary functions with the instruction-following capability. Our experimental results show the effectiveness of combining the base models' auxiliary function utilization ability with the instruction following ability. In particular, the performance of adopting our approaches with the open-sourced language models surpasses that of the recent powerful proprietary language models, i.e., gpt-4o.

A supervised learning algorithm searches over a set of functions A to B parametrised by a space P to find the best approximation to some ideal function fcolon A to B. It does this by taking examples (a,f(a)) in Atimes B, and updating the parameter according to some rule. We define a category where these update rules may be composed, and show that gradient descent---with respect to a fixed step size and an error function satisfying a certain property---defines a monoidal functor from a category of parametrised functions to this category of update rules. This provides a structural perspective on backpropagation, as well as a broad generalisation of neural networks.

We introduce DafnyCOMP, a benchmark for evaluating large language models (LLMs) on compositional specification generation in Dafny. Unlike prior benchmarks that focus on single-function tasks, DafnyCOMP targets programs composed of multiple interacting functions with data dependencies, requiring reasoning across component boundaries. The benchmark consists of 300 automatically synthesized multi-function programs. We evaluate several state-of-the-art LLM families and find that, while they perform well on single-function verification, their performance drops sharply on compositional tasks. Analysis reveals systematic failures in cross-functional reasoning, including fragile specifications, misalignment between implementations and proofs, and unstable reasoning. DafnyCOMP thus provides a diagnostic tool for measuring progress toward reliable, verifiable, and compositional code generation with LLMs.

Traditional approaches to semantic parsing (SP) work by training individual models for each available parallel dataset of text-meaning pairs. In this paper, we explore the idea of polyglot semantic translation, or learning semantic parsing models that are trained on multiple datasets and natural languages. In particular, we focus on translating text to code signature representations using the software component datasets of Richardson and Kuhn (2017a,b). The advantage of such models is that they can be used for parsing a wide variety of input natural languages and output programming languages, or mixed input languages, using a single unified model. To facilitate modeling of this type, we develop a novel graph-based decoding framework that achieves state-of-the-art performance on the above datasets, and apply this method to two other benchmark SP tasks.

We present a modular semantic account of Bayesian inference algorithms for probabilistic programming languages, as used in data science and machine learning. Sophisticated inference algorithms are often explained in terms of composition of smaller parts. However, neither their theoretical justification nor their implementation reflects this modularity. We show how to conceptualise and analyse such inference algorithms as manipulating intermediate representations of probabilistic programs using higher-order functions and inductive types, and their denotational semantics. Semantic accounts of continuous distributions use measurable spaces. However, our use of higher-order functions presents a substantial technical difficulty: it is impossible to define a measurable space structure over the collection of measurable functions between arbitrary measurable spaces that is compatible with standard operations on those functions, such as function application. We overcome this difficulty using quasi-Borel spaces, a recently proposed mathematical structure that supports both function spaces and continuous distributions. We define a class of semantic structures for representing probabilistic programs, and semantic validity criteria for transformations of these representations in terms of distribution preservation. We develop a collection of building blocks for composing representations. We use these building blocks to validate common inference algorithms such as Sequential Monte Carlo and Markov Chain Monte Carlo. To emphasize the connection between the semantic manipulation and its traditional measure theoretic origins, we use Kock's synthetic measure theory. We demonstrate its usefulness by proving a quasi-Borel counterpart to the Metropolis-Hastings-Green theorem.

We introduce the Formally Verified Automated Programming Progress Standards, or FVAPPS, a benchmark of 4715 samples for writing programs and proving their correctness, the largest formal verification benchmark, including 1083 curated and quality controlled samples. Previously, APPS provided a benchmark and dataset for programming puzzles to be completed in Python and checked against unit tests, of the kind seen in technical assessments in the software engineering industry. Building upon recent approaches for benchmarks in interactive theorem proving, we generalize the unit tests to Lean 4 theorems given without proof (i.e., using Lean's "sorry" keyword). On the 406 theorems of 100 randomly selected samples, Sonnet correctly proves 30% and Gemini correctly proves 18%. We challenge the machine learning and program synthesis communities to solve both each general purpose programming problem and its associated correctness specifications. The benchmark is available at https://huggingface.co/datasets/quinn-dougherty/fvapps.

The parameter space for any fixed architecture of feedforward ReLU neural networks serves as a proxy during training for the associated class of functions - but how faithful is this representation? It is known that many different parameter settings can determine the same function. Moreover, the degree of this redundancy is inhomogeneous: for some networks, the only symmetries are permutation of neurons in a layer and positive scaling of parameters at a neuron, while other networks admit additional hidden symmetries. In this work, we prove that, for any network architecture where no layer is narrower than the input, there exist parameter settings with no hidden symmetries. We also describe a number of mechanisms through which hidden symmetries can arise, and empirically approximate the functional dimension of different network architectures at initialization. These experiments indicate that the probability that a network has no hidden symmetries decreases towards 0 as depth increases, while increasing towards 1 as width and input dimension increase.

Proof-oriented programs mix computational content with proofs of program correctness. However, the human effort involved in programming and proving is still substantial, despite the use of Satisfiability Modulo Theories (SMT) solvers to automate proofs in languages such as F*. Seeking to spur research on using AI to automate the construction of proof-oriented programs, we curate a dataset of 600K lines of open-source F* programs and proofs, including software used in production systems ranging from Windows and Linux, to Python and Firefox. Our dataset includes around 32K top-level F* definitions, each representing a type-directed program and proof synthesis problem -- producing a definition given a formal specification expressed as an F* type. We provide a program-fragment checker that queries F* to check the correctness of candidate solutions. We believe this is the largest corpus of SMT-assisted program proofs coupled with a reproducible program-fragment checker. Grounded in this dataset, we investigate the use of AI to synthesize programs and their proofs in F*, with promising results. Our main finding in that the performance of fine-tuned smaller language models (such as Phi-2 or StarCoder) compare favorably with large language models (such as GPT-4), at a much lower computational cost. We also identify various type-based retrieval augmentation techniques and find that they boost performance significantly. With detailed error analysis and case studies, we identify potential strengths and weaknesses of models and techniques and suggest directions for future improvements.

Verifiable delay functions have found a lot of applications in blockchain technology in recent times. Continuous verifiable delay functions are an improvement over the basic notion of VDFs with recursive capabilities. We are proposing the application of VDF for constructing more space time-efficient provers and simulators required for the iterative non-interactive zero-knowledge systems.

The goal of decompilation is to convert compiled low-level code (e.g., assembly code) back into high-level programming languages, enabling analysis in scenarios where source code is unavailable. This task supports various reverse engineering applications, such as vulnerability identification, malware analysis, and legacy software migration. The end-to-end decompile method based on large langauge models (LLMs) reduces reliance on additional tools and minimizes manual intervention due to its inherent properties. However, previous end-to-end methods often lose critical information necessary for reconstructing control flow structures and variables when processing binary files, making it challenging to accurately recover the program's logic. To address these issues, we propose the ReF Decompile method, which incorporates the following innovations: (1) The Relabelling strategy replaces jump target addresses with labels, preserving control flow clarity. (2) The Function Call strategy infers variable types and retrieves missing variable information from binary files. Experimental results on the Humaneval-Decompile Benchmark demonstrate that ReF Decompile surpasses comparable baselines and achieves state-of-the-art (SOTA) performance of 61.43%.

We propose a new class of generative diffusion models, called functional diffusion. In contrast to previous work, functional diffusion works on samples that are represented by functions with a continuous domain. Functional diffusion can be seen as an extension of classical diffusion models to an infinite-dimensional domain. Functional diffusion is very versatile as images, videos, audio, 3D shapes, deformations, \etc, can be handled by the same framework with minimal changes. In addition, functional diffusion is especially suited for irregular data or data defined in non-standard domains. In our work, we derive the necessary foundations for functional diffusion and propose a first implementation based on the transformer architecture. We show generative results on complicated signed distance functions and deformation functions defined on 3D surfaces.

Code generation models based on the pre-training and fine-tuning paradigm have been increasingly attempted by both academia and industry, resulting in well-known industrial models such as Codex, CodeGen, and PanGu-Coder. To evaluate the effectiveness of these models, multiple existing benchmarks are proposed, including only cases of generating a standalone function, i.e., a function that may invoke or access only built-in functions and standard libraries. However, non-standalone functions, which typically are not included in the existing benchmarks, constitute more than 70% of the functions in popular open-source projects, and evaluating models' effectiveness on standalone functions cannot reflect these models' effectiveness on pragmatic code generation scenarios. To help bridge the preceding gap, in this paper, we propose a benchmark named CoderEval, consisting of 230 Python and 230 Java code generation tasks carefully curated from popular real-world open-source projects and a self-contained execution platform to automatically assess the functional correctness of generated code. CoderEval supports code generation tasks from six levels of context dependency, where context refers to code elements such as types, APIs, variables, and consts defined outside the function under generation but within the dependent third-party libraries, current class, file, or project. CoderEval can be used to evaluate the effectiveness of models in generating code beyond only standalone functions. By evaluating three code generation models on CoderEval, we find that the effectiveness of these models in generating standalone functions is substantially higher than that in generating non-standalone functions. Our analysis highlights the current progress and pinpoints future directions to further improve a model's effectiveness by leveraging contextual information for pragmatic code generation.

Automatic Differentiation (AD) has become a dominant technique in ML. AD frameworks have first been implemented for imperative languages using tapes. Meanwhile, functional implementations of AD have been developed, often based on dual numbers, which are close to the formal specification of differentiation and hence easier to prove correct. But these papers have focussed on correctness not efficiency. Recently, it was shown how an approach using dual numbers could be made efficient through the right optimizations. Optimizations are highly dependent on order, as one optimization can enable another. It can therefore be useful to have fine-grained control over the scheduling of optimizations. One method expresses compiler optimizations as rewrite rules, whose application can be combined and controlled using strategy languages. Previous work describes the use of term rewriting and strategies to generate high-performance code in a compiler for a functional language. In this work, we implement dual numbers AD in a functional array programming language using rewrite rules and strategy combinators for optimization. We aim to combine the elegance of differentiation using dual numbers with a succinct expression of the optimization schedule using a strategy language. We give preliminary evidence suggesting the viability of the approach on a micro-benchmark.

Lion (Evolved Sign Momentum), a new optimizer discovered through program search, has shown promising results in training large AI models. It performs comparably or favorably to AdamW but with greater memory efficiency. As we can expect from the results of a random search program, Lion incorporates elements from several existing algorithms, including signed momentum, decoupled weight decay, Polak, and Nesterov momentum, but does not fit into any existing category of theoretically grounded optimizers. Thus, even though Lion appears to perform well as a general-purpose optimizer for a wide range of tasks, its theoretical basis remains uncertain. This lack of theoretical clarity limits opportunities to further enhance and expand Lion's efficacy. This work aims to demystify Lion. Based on both continuous-time and discrete-time analysis, we demonstrate that Lion is a theoretically novel and principled approach for minimizing a general loss function f(x) while enforcing a bound constraint |x|_infty leq 1/lambda. Lion achieves this through the incorporation of decoupled weight decay, where lambda represents the weight decay coefficient. Our analysis is made possible by the development of a new Lyapunov function for the Lion updates. It applies to a broader family of Lion-kappa algorithms, where the sign(cdot) operator in Lion is replaced by the subgradient of a convex function kappa, leading to the solution of a general composite optimization problem of min_x f(x) + kappa^*(x). Our findings provide valuable insights into the dynamics of Lion and pave the way for further improvements and extensions of Lion-related algorithms.

Ongoing efforts that span over decades show a rise of AI methods for accelerating scientific discovery, yet accelerating discovery in mathematics remains a persistent challenge for AI. Specifically, AI methods were not effective in creation of formulas for mathematical constants because each such formula must be correct for infinite digits of precision, with "near-true" formulas providing no insight toward the correct ones. Consequently, formula discovery lacks a clear distance metric needed to guide automated discovery in this realm. In this work, we propose a systematic methodology for categorization, characterization, and pattern identification of such formulas. The key to our methodology is introducing metrics based on the convergence dynamics of the formulas, rather than on the numerical value of the formula. These metrics enable the first automated clustering of mathematical formulas. We demonstrate this methodology on Polynomial Continued Fraction formulas, which are ubiquitous in their intrinsic connections to mathematical constants, and generalize many mathematical functions and structures. We test our methodology on a set of 1,768,900 such formulas, identifying many known formulas for mathematical constants, and discover previously unknown formulas for pi, ln(2), Gauss', and Lemniscate's constants. The uncovered patterns enable a direct generalization of individual formulas to infinite families, unveiling rich mathematical structures. This success paves the way towards a generative model that creates formulas fulfilling specified mathematical properties, accelerating the rate of discovery of useful formulas.

In this paper, we describe Function Assistant, a lightweight Python-based toolkit for querying and exploring source code repositories using natural language. The toolkit is designed to help end-users of a target API quickly find information about functions through high-level natural language queries and descriptions. For a given text query and background API, the tool finds candidate functions by performing a translation from the text to known representations in the API using the semantic parsing approach of Richardson and Kuhn (2017). Translations are automatically learned from example text-code pairs in example APIs. The toolkit includes features for building translation pipelines and query engines for arbitrary source code projects. To explore this last feature, we perform new experiments on 27 well-known Python projects hosted on Github.

Existing evaluation benchmarks of language models of code (code LMs) focus almost exclusively on whether the LMs can generate functionally-correct code. In real-world software engineering, developers think beyond functional correctness. They have requirements on "how" a functionality should be implemented to meet overall system design objectives like efficiency, security, and maintainability. They would also trust the code LMs more if the LMs demonstrate robust understanding of requirements and code semantics. We propose a new benchmark NoFunEval to evaluate code LMs on non-functional requirements and simple classification instances for both functional and non-functional requirements. We propose a prompting method, Coding Concepts (CoCo), as a way for a developer to communicate the domain knowledge to the LMs. We conduct an extensive evaluation of twenty-two code LMs. Our finding is that they generally falter when tested on our benchmark, hinting at fundamental blindspots in their training setups. Surprisingly, even the classification accuracy on functional-correctness instances derived from the popular HumanEval benchmark is low, calling in question the depth of their comprehension and the source of their success in generating functionally-correct code in the first place. We will release our benchmark and evaluation scripts publicly at https://aka.ms/NoFunEval.

We introduce a new type of programming challenge called programming puzzles, as an objective and comprehensive evaluation of program synthesis, and release an open-source dataset of Python Programming Puzzles (P3). Each puzzle is defined by a short Python program f, and the goal is to find an input which makes f return True. The puzzles are objective in that each one is specified entirely by the source code of its verifier f, so evaluating f is all that is needed to test a candidate solution. They do not require an answer key or input/output examples, nor do they depend on natural language understanding. The dataset is comprehensive in that it spans problems of a range of difficulties and domains, ranging from trivial string manipulation problems, to classic programming puzzles (e.g., Tower of Hanoi), to interview/competitive-programming problems (e.g., dynamic programming), to longstanding open problems in algorithms and mathematics (e.g., factoring). We develop baseline enumerative program synthesis, GPT-3 and Codex solvers that are capable of solving puzzles -- even without access to any reference solutions -- by learning from their own past solutions. Codex performs best, solving up to 18% of 397 test problems with a single try and 80% of the problems with 1,000 tries per problem. In a small user study, we find a positive correlation between puzzle-solving performance and coding experience, and between the puzzle difficulty for humans and AI solvers. Therefore, further improvements on P3 could have a significant impact on many program synthesis areas.

Decompilation aims to recover the source code form of a binary executable. It has many security applications such as malware analysis, vulnerability detection and code hardening. A prominent challenge in decompilation is to recover variable names. We propose a novel technique that leverages the strengths of generative models while mitigating model biases and potential hallucinations. We build a prototype, GenNm, from pre-trained generative models CodeGemma-2B and CodeLlama-7B. We finetune GenNm on decompiled functions, and mitigate model biases by incorporating symbol preference to the training pipeline. GenNm includes names from callers and callees while querying a function, providing rich contextual information within the model's input token limitation. It further leverages program analysis to validate the consistency of names produced by the generative model. Our results show that GenNm improves the state-of-the-art name recovery accuracy by 8.6 and 11.4 percentage points on two commonly used datasets, and improves the state-of-the-art from 8.5% to 22.8% in the most challenging setup where ground-truth variable names are not seen in the training dataset.

We introduce the use of rectified linear units (ReLU) as the classification function in a deep neural network (DNN). Conventionally, ReLU is used as an activation function in DNNs, with Softmax function as their classification function. However, there have been several studies on using a classification function other than Softmax, and this study is an addition to those. We accomplish this by taking the activation of the penultimate layer h_{n - 1} in a neural network, then multiply it by weight parameters theta to get the raw scores o_{i}. Afterwards, we threshold the raw scores o_{i} by 0, i.e. f(o) = max(0, o_{i}), where f(o) is the ReLU function. We provide class predictions y through argmax function, i.e. argmax f(x).

It is often very challenging to manually design reward functions for complex, real-world tasks. To solve this, one can instead use reward learning to infer a reward function from data. However, there are often multiple reward functions that fit the data equally well, even in the infinite-data limit. This means that the reward function is only partially identifiable. In this work, we formally characterise the partial identifiability of the reward function given several popular reward learning data sources, including expert demonstrations and trajectory comparisons. We also analyse the impact of this partial identifiability for several downstream tasks, such as policy optimisation. We unify our results in a framework for comparing data sources and downstream tasks by their invariances, with implications for the design and selection of data sources for reward learning.

When trying to gain better visibility into a machine learning model in order to understand and mitigate the associated risks, a potentially valuable source of evidence is: which training examples most contribute to a given behavior? Influence functions aim to answer a counterfactual: how would the model's parameters (and hence its outputs) change if a given sequence were added to the training set? While influence functions have produced insights for small models, they are difficult to scale to large language models (LLMs) due to the difficulty of computing an inverse-Hessian-vector product (IHVP). We use the Eigenvalue-corrected Kronecker-Factored Approximate Curvature (EK-FAC) approximation to scale influence functions up to LLMs with up to 52 billion parameters. In our experiments, EK-FAC achieves similar accuracy to traditional influence function estimators despite the IHVP computation being orders of magnitude faster. We investigate two algorithmic techniques to reduce the cost of computing gradients of candidate training sequences: TF-IDF filtering and query batching. We use influence functions to investigate the generalization patterns of LLMs, including the sparsity of the influence patterns, increasing abstraction with scale, math and programming abilities, cross-lingual generalization, and role-playing behavior. Despite many apparently sophisticated forms of generalization, we identify a surprising limitation: influences decay to near-zero when the order of key phrases is flipped. Overall, influence functions give us a powerful new tool for studying the generalization properties of LLMs.

Deep functional maps have recently emerged as a powerful tool for solving non-rigid shape correspondence tasks. Methods that use this approach combine the power and flexibility of the functional map framework, with data-driven learning for improved accuracy and generality. However, most existing methods in this area restrict the learning aspect only to the feature functions and still rely on axiomatic modeling for formulating the training loss or for functional map regularization inside the networks. This limits both the accuracy and the applicability of the resulting approaches only to scenarios where assumptions of the axiomatic models hold. In this work, we show, for the first time, that both in-network regularization and functional map training can be replaced with data-driven methods. For this, we first train a generative model of functional maps in the spectral domain using score-based generative modeling, built from a large collection of high-quality maps. We then exploit the resulting model to promote the structural properties of ground truth functional maps on new shape collections. Remarkably, we demonstrate that the learned models are category-agnostic, and can fully replace commonly used strategies such as enforcing Laplacian commutativity or orthogonality of functional maps. Our key technical contribution is a novel distillation strategy from diffusion models in the spectral domain. Experiments demonstrate that our learned regularization leads to better results than axiomatic approaches for zero-shot non-rigid shape matching. Our code is available at: https://github.com/daidedou/diffumatch/

Machine learning as a discipline has seen an incredible surge of interest in recent years due in large part to a perfect storm of new theory, superior tooling, renewed interest in its capabilities. We present in this paper a framework named Flux that shows how further refinement of the core ideas of machine learning, built upon the foundation of the Julia programming language, can yield an environment that is simple, easily modifiable, and performant. We detail the fundamental principles of Flux as a framework for differentiable programming, give examples of models that are implemented within Flux to display many of the language and framework-level features that contribute to its ease of use and high productivity, display internal compiler techniques used to enable the acceleration and performance that lies at the heart of Flux, and finally give an overview of the larger ecosystem that Flux fits inside of.

Solutions of nonlinear functional equations are generally not expressed as a finite number of combinations and compositions of elementary and known special functions. One of the approaches to study them is, firstly, to find formal solutions (that is, series whose terms are described and ordered in some way but which do not converge apriori) and, secondly, to study the convergence or summability of these formal solutions (the existence and uniqueness of actual solutions with the given asymptotic expansion in a certain domain). In this paper we deal only with the convergence of formal functional series having the form of an infinite sum of power functions with (complex, in general) power exponents and satisfying analytical functional equations of the following three types: a differential, q-difference or Mahler equation.

Pretrained code language models have enabled great progress towards program synthesis. However, common approaches only consider in-file local context and thus miss information and constraints imposed by other parts of the codebase and its external dependencies. Existing code completion benchmarks also lack such context. To resolve these restrictions we curate a new dataset of permissively licensed Python packages that includes full projects and their dependencies and provide tools to extract non-local information with the help of program analyzers. We then focus on the task of function call argument completion which requires predicting the arguments to function calls. We show that existing code completion models do not yield good results on our completion task. To better solve this task, we query a program analyzer for information relevant to a given function call, and consider ways to provide the analyzer results to different code completion models during inference and training. Our experiments show that providing access to the function implementation and function usages greatly improves the argument completion performance. Our ablation study provides further insights on how different types of information available from the program analyzer and different ways of incorporating the information affect the model performance.

While multitask representation learning has become a popular approach in reinforcement learning (RL) to boost the sample efficiency, the theoretical understanding of why and how it works is still limited. Most previous analytical works could only assume that the representation function is already known to the agent or from linear function class, since analyzing general function class representation encounters non-trivial technical obstacles such as generalization guarantee, formulation of confidence bound in abstract function space, etc. However, linear-case analysis heavily relies on the particularity of linear function class, while real-world practice usually adopts general non-linear representation functions like neural networks. This significantly reduces its applicability. In this work, we extend the analysis to general function class representations. Specifically, we consider an agent playing M contextual bandits (or MDPs) concurrently and extracting a shared representation function phi from a specific function class Phi using our proposed Generalized Functional Upper Confidence Bound algorithm (GFUCB). We theoretically validate the benefit of multitask representation learning within general function class for bandits and linear MDP for the first time. Lastly, we conduct experiments to demonstrate the effectiveness of our algorithm with neural net representation.

We introduce a new functional space U designed to contain all classical arithmetic functions (Mobius, von Mangoldt, Euler phi, divisor functions, Dirichlet characters, etc.). The norm of U combines a Hilbert-type component, based on square summability of Dirichlet coefficients for every s > 1, with a Banach component controlling logarithmic averages of partial sums. We prove that U is a complete Banach space which embeds continuously all standard Hilbert spaces of Dirichlet series and allows natural actions of Dirichlet convolution and shift operators. This framework provides a unified analytic setting for classical and modern problems in multiplicative number theory.

Background: The C and C++ languages hold significant importance in Software Engineering research because of their widespread use in practice. Numerous studies have utilized Machine Learning (ML) and Deep Learning (DL) techniques to detect software vulnerabilities (SVs) in the source code written in these languages. However, the application of these techniques in function-level SV assessment has been largely unexplored. SV assessment is increasingly crucial as it provides detailed information on the exploitability, impacts, and severity of security defects, thereby aiding in their prioritization and remediation. Aims: We conduct the first empirical study to investigate and compare the performance of ML and DL models, many of which have been used for SV detection, for function-level SV assessment in C/C++. Method: Using 9,993 vulnerable C/C++ functions, we evaluated the performance of six multi-class ML models and five multi-class DL models for the SV assessment at the function level based on the Common Vulnerability Scoring System (CVSS). We further explore multi-task learning, which can leverage common vulnerable code to predict all SV assessment outputs simultaneously in a single model, and compare the effectiveness and efficiency of this model type with those of the original multi-class models. Results: We show that ML has matching or even better performance compared to the multi-class DL models for function-level SV assessment with significantly less training time. Employing multi-task learning allows the DL models to perform significantly better, with an average of 8-22% increase in Matthews Correlation Coefficient (MCC). Conclusions: We distill the practices of using data-driven techniques for function-level SV assessment in C/C++, including the use of multi-task DL to balance efficiency and effectiveness. This can establish a strong foundation for future work in this area.

A wide range of scientific problems, such as those described by continuous-time dynamical systems and partial differential equations (PDEs), are naturally formulated on function spaces. While function spaces are typically infinite-dimensional, deep learning has predominantly advanced through applications in computer vision and natural language processing that focus on mappings between finite-dimensional spaces. Such fundamental disparities in the nature of the data have limited neural networks from achieving a comparable level of success in scientific applications as seen in other fields. Neural operators are a principled way to generalize neural networks to mappings between function spaces, offering a pathway to replicate deep learning's transformative impact on scientific problems. For instance, neural operators can learn solution operators for entire classes of PDEs, e.g., physical systems with different boundary conditions, coefficient functions, and geometries. A key factor in deep learning's success has been the careful engineering of neural architectures through extensive empirical testing. Translating these neural architectures into neural operators allows operator learning to enjoy these same empirical optimizations. However, prior neural operator architectures have often been introduced as standalone models, not directly derived as extensions of existing neural network architectures. In this paper, we identify and distill the key principles for constructing practical implementations of mappings between infinite-dimensional function spaces. Using these principles, we propose a recipe for converting several popular neural architectures into neural operators with minimal modifications. This paper aims to guide practitioners through this process and details the steps to make neural operators work in practice. Our code can be found at https://github.com/neuraloperator/NNs-to-NOs

We consider minimizing functions for which it is expensive to compute the (possibly stochastic) gradient. Such functions are prevalent in reinforcement learning, imitation learning and adversarial training. Our target optimization framework uses the (expensive) gradient computation to construct surrogate functions in a target space (e.g. the logits output by a linear model for classification) that can be minimized efficiently. This allows for multiple parameter updates to the model, amortizing the cost of gradient computation. In the full-batch setting, we prove that our surrogate is a global upper-bound on the loss, and can be (locally) minimized using a black-box optimization algorithm. We prove that the resulting majorization-minimization algorithm ensures convergence to a stationary point of the loss. Next, we instantiate our framework in the stochastic setting and propose the SSO algorithm, which can be viewed as projected stochastic gradient descent in the target space. This connection enables us to prove theoretical guarantees for SSO when minimizing convex functions. Our framework allows the use of standard stochastic optimization algorithms to construct surrogates which can be minimized by any deterministic optimization method. To evaluate our framework, we consider a suite of supervised learning and imitation learning problems. Our experiments indicate the benefits of target optimization and the effectiveness of SSO.

Automated software engineering has been greatly empowered by the recent advances in Large Language Models (LLMs) for programming. While current benchmarks have shown that LLMs can perform various software engineering tasks like human developers, the majority of their evaluations are limited to short and self-contained algorithmic tasks. Solving challenging and practical programming tasks requires the capability of utilizing diverse function calls as tools to efficiently implement functionalities like data analysis and web development. In addition, using multiple tools to solve a task needs compositional reasoning by accurately understanding complex instructions. Fulfilling both of these characteristics can pose a great challenge for LLMs. To assess how well LLMs can solve challenging and practical programming tasks, we introduce Bench, a benchmark that challenges LLMs to invoke multiple function calls as tools from 139 libraries and 7 domains for 1,140 fine-grained programming tasks. To evaluate LLMs rigorously, each programming task encompasses 5.6 test cases with an average branch coverage of 99%. In addition, we propose a natural-language-oriented variant of Bench, Benchi, that automatically transforms the original docstrings into short instructions only with essential information. Our extensive evaluation of 60 LLMs shows that LLMs are not yet capable of following complex instructions to use function calls precisely, with scores up to 60%, significantly lower than the human performance of 97%. The results underscore the need for further advancements in this area.

Which functions can be used as activations in deep neural networks? This article explores families of functions based on orthonormal bases, including the Hermite polynomial basis and the Fourier trigonometric basis, as well as a basis resulting from the tropicalization of a polynomial basis. Our study shows that, through simple variance-preserving initialization and without additional clamping mechanisms, these activations can successfully be used to train deep models, such as GPT-2 for next-token prediction on OpenWebText and ConvNeXt for image classification on ImageNet. Our work addresses the issue of exploding and vanishing activations and gradients, particularly prevalent with polynomial activations, and opens the door for improving the efficiency of large-scale learning tasks. Furthermore, our approach provides insight into the structure of neural networks, revealing that networks with polynomial activations can be interpreted as multivariate polynomial mappings. Finally, using Hermite interpolation, we show that our activations can closely approximate classical ones in pre-trained models by matching both the function and its derivative, making them especially useful for fine-tuning tasks. These activations are available in the torchortho library, which can be accessed via: https://github.com/K-H-Ismail/torchortho.

Scientists often infer abstract procedures from specific instances of problems and use the abstractions to generate new, related instances. For example, programs encoding the formal rules and properties of a system have been useful in fields ranging from RL (procedural environments) to physics (simulation engines). These programs can be seen as functions which execute to different outputs based on their parameterizations (e.g., gridworld configuration or initial physical conditions). We introduce the term EFA (Executable Functional Abstraction) to denote such programs for math problems. EFA-like constructs have been shown to be useful for math reasoning as problem generators for stress-testing models. However, prior work has been limited to abstractions for grade-school math (whose simple rules are easy to encode in programs), while generating EFAs for advanced math has thus far required human engineering. We explore the automatic construction of EFAs for advanced math problems. We operationalize the task of automatically constructing EFAs as a program synthesis task, and develop EFAGen, which conditions an LLM on a seed math problem and its step-by-step solution to generate candidate EFA programs that are faithful to the generalized problem and solution class underlying the seed problem. Furthermore, we formalize properties any valid EFA must possess in terms of executable unit tests, and show how the tests can be used as verifiable rewards to train LLMs to become better writers of EFAs. We demonstrate that EFAs constructed by EFAGen behave rationally by remaining faithful to seed problems, produce learnable problem variations, and that EFAGen can infer EFAs across multiple diverse sources of competition-level math problems. Finally, we show downstream uses of model-written EFAs e.g. finding problem variations that are harder or easier for a learner to solve, as well as data generation.

Understanding the internal representations learned by neural networks is a cornerstone challenge in the science of machine learning. While there have been significant recent strides in some cases towards understanding how neural networks implement specific target functions, this paper explores a complementary question -- why do networks arrive at particular computational strategies? Our inquiry focuses on the algebraic learning tasks of modular addition, sparse parities, and finite group operations. Our primary theoretical findings analytically characterize the features learned by stylized neural networks for these algebraic tasks. Notably, our main technique demonstrates how the principle of margin maximization alone can be used to fully specify the features learned by the network. Specifically, we prove that the trained networks utilize Fourier features to perform modular addition and employ features corresponding to irreducible group-theoretic representations to perform compositions in general groups, aligning closely with the empirical observations of Nanda et al. and Chughtai et al. More generally, we hope our techniques can help to foster a deeper understanding of why neural networks adopt specific computational strategies.

Natural Language to Code Generation has made significant progress in recent years with the advent of Large Language Models(LLMs). While generation for general-purpose languages like C, C++, and Python has improved significantly, LLMs struggle with custom function names in Domain Specific Languages or DSLs. This leads to higher hallucination rates and syntax errors, specially for DSLs having a high number of custom function names. Additionally, constant updates to function names add to the challenge as LLMs need to stay up-to-date. In this paper, we present optimizations for using Retrieval Augmented Generation (or RAG) with LLMs for DSL generation along with an ablation study comparing these strategies. We generated a train as well as test dataset with a DSL to represent automation tasks across roughly 700 APIs in public domain. We used the training dataset to fine-tune a Codex model for this DSL. Our results showed that the fine-tuned model scored the best on code similarity metric. With our RAG optimizations, we achieved parity for similarity metric. The compilation rate, however, showed that both the models still got the syntax wrong many times, with RAG-based method being 2 pts better. Conversely, hallucination rate for RAG model lagged by 1 pt for API names and by 2 pts for API parameter keys. We conclude that an optimized RAG model can match the quality of fine-tuned models and offer advantages for new, unseen APIs.

Expanding on neural operators, we propose a novel framework for stochastic process learning across arbitrary domains. In particular, we develop operator flow matching (OFM) for learning stochastic process priors on function spaces. OFM provides the probability density of the values of any collection of points and enables mathematically tractable functional regression at new points with mean and density estimation. Our method outperforms state-of-the-art models in stochastic process learning, functional regression, and prior learning.

We study the problem of learning hierarchical polynomials over the standard Gaussian distribution with three-layer neural networks. We specifically consider target functions of the form h = g circ p where p : R^d rightarrow R is a degree k polynomial and g: R rightarrow R is a degree q polynomial. This function class generalizes the single-index model, which corresponds to k=1, and is a natural class of functions possessing an underlying hierarchical structure. Our main result shows that for a large subclass of degree k polynomials p, a three-layer neural network trained via layerwise gradient descent on the square loss learns the target h up to vanishing test error in mathcal{O}(d^k) samples and polynomial time. This is a strict improvement over kernel methods, which require widetilde Theta(d^{kq}) samples, as well as existing guarantees for two-layer networks, which require the target function to be low-rank. Our result also generalizes prior works on three-layer neural networks, which were restricted to the case of p being a quadratic. When p is indeed a quadratic, we achieve the information-theoretically optimal sample complexity mathcal{O}(d^2), which is an improvement over prior work~nichani2023provable requiring a sample size of widetildeTheta(d^4). Our proof proceeds by showing that during the initial stage of training the network performs feature learning to recover the feature p with mathcal{O}(d^k) samples. This work demonstrates the ability of three-layer neural networks to learn complex features and as a result, learn a broad class of hierarchical functions.

In this paper, we present a general framework for the derivation of interesting finite combinatorial sums starting with certain classes of polynomial identities. The sums that can be derived involve products of binomial coefficients and also harmonic numbers and squared harmonic numbers. We apply the framework to discuss combinatorial sums associated with some prominent polynomial identities from the recent past.

Source code is rarely written in isolation. It depends significantly on the programmatic context, such as the class that the code would reside in. To study this phenomenon, we introduce the task of generating class member functions given English documentation and the programmatic context provided by the rest of the class. This task is challenging because the desired code can vary greatly depending on the functionality the class provides (e.g., a sort function may or may not be available when we are asked to "return the smallest element" in a particular member variable list). We introduce CONCODE, a new large dataset with over 100,000 examples consisting of Java classes from online code repositories, and develop a new encoder-decoder architecture that models the interaction between the method documentation and the class environment. We also present a detailed error analysis suggesting that there is significant room for future work on this task.

Research on offline signature verification has explored a large variety of methods on multiple signature datasets, which are collected under controlled conditions. However, these datasets may not fully reflect the characteristics of the signatures in some practical use cases. Real-world signatures extracted from the formal documents may contain different types of occlusions, for example, stamps, company seals, ruling lines, and signature boxes. Moreover, they may have very high intra-class variations, where even genuine signatures resemble forgeries. In this paper, we address a real-world writer independent offline signature verification problem, in which, a bank's customers' transaction request documents that contain their occluded signatures are compared with their clean reference signatures. Our proposed method consists of two main components, a stamp cleaning method based on CycleGAN and signature representation based on CNNs. We extensively evaluate different verification setups, fine-tuning strategies, and signature representation approaches to have a thorough analysis of the problem. Moreover, we conduct a human evaluation to show the challenging nature of the problem. We run experiments both on our custom dataset, as well as on the publicly available Tobacco-800 dataset. The experimental results validate the difficulty of offline signature verification on real-world documents. However, by employing the stamp cleaning process, we improve the signature verification performance significantly.

We discuss methods for modeling eclipsing binary stars using the "physical", "simplified" and "phenomenological" models. There are few realizations of the "physical" Wilson-Devinney (1971) code and its improvements, e.g. Binary Maker, Phoebe. A parameter search using the Monte-Carlo method was realized by Zola et al. (2010), which is efficient in expense of too many evaluations of the test function. We compare existing algorithms of minimization of multi-parametric functions and propose to use a "combined" algorithm, depending on if the Hessian matrix is positively determined. To study methods, a simply fast-computed function resembling the "complete" test function for the physical model. Also we adopt a simplified model of an eclipsing binary at a circular orbit assuming spherical components with an uniform brightness distribution. This model resembles more advanced models in a sense of correlated parameter estimates due to a similar topology of the test function. Such a model may be applied to detached Algol-type systems, where the tidal distortion of components is negligible.

We propose Hyper-Dimensional Function Encoding (HDFE). Given samples of a continuous object (e.g. a function), HDFE produces an explicit vector representation of the given object, invariant to the sample distribution and density. Sample distribution and density invariance enables HDFE to consistently encode continuous objects regardless of their sampling, and therefore allows neural networks to receive continuous objects as inputs for machine learning tasks, such as classification and regression. Besides, HDFE does not require any training and is proved to map the object into an organized embedding space, which facilitates the training of the downstream tasks. In addition, the encoding is decodable, which enables neural networks to regress continuous objects by regressing their encodings. Therefore, HDFE serves as an interface for processing continuous objects. We apply HDFE to function-to-function mapping, where vanilla HDFE achieves competitive performance as the state-of-the-art algorithm. We apply HDFE to point cloud surface normal estimation, where a simple replacement from PointNet to HDFE leads to immediate 12% and 15% error reductions in two benchmarks. In addition, by integrating HDFE into the PointNet-based SOTA network, we improve the SOTA baseline by 2.5% and 1.7% in the same benchmarks.

We consider the task of mapping pseudocode to long programs that are functionally correct. Given test cases as a mechanism to validate programs, we search over the space of possible translations of the pseudocode to find a program that passes the validation. However, without proper credit assignment to localize the sources of program failures, it is difficult to guide search toward more promising programs. We propose to perform credit assignment based on signals from compilation errors, which constitute 88.7% of program failures. Concretely, we treat the translation of each pseudocode line as a discrete portion of the program, and whenever a synthesized program fails to compile, an error localization method tries to identify the portion of the program responsible for the failure. We then focus search over alternative translations of the pseudocode for those portions. For evaluation, we collected the SPoC dataset (Search-based Pseudocode to Code) containing 18,356 programs with human-authored pseudocode and test cases. Under a budget of 100 program compilations, performing search improves the synthesis success rate over using the top-one translation of the pseudocode from 25.6% to 44.7%.

The behavior of neural networks still remains opaque, and a recently widely noted phenomenon is that networks often achieve similar performance when initialized with different random parameters. This phenomenon has attracted significant attention in measuring the similarity between features learned by distinct networks. However, feature similarity could be vague in describing the same feature since equivalent features hardly exist. In this paper, we expand the concept of equivalent feature and provide the definition of what we call functionally equivalent features. These features produce equivalent output under certain transformations. Using this definition, we aim to derive a more intrinsic metric for the so-called feature complexity regarding the redundancy of features learned by a neural network at each layer. We offer a formal interpretation of our approach through the lens of category theory, a well-developed area in mathematics. To quantify the feature complexity, we further propose an efficient algorithm named Iterative Feature Merging. Our experimental results validate our ideas and theories from various perspectives. We empirically demonstrate that the functionally equivalence widely exists among different features learned by the same neural network and we could reduce the number of parameters of the network without affecting the performance.The IFM shows great potential as a data-agnostic model prune method. We have also drawn several interesting empirical findings regarding the defined feature complexity.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

The remarkable capability of large language models (LLMs) in generating high-quality code has drawn increasing attention in the software testing community. However, existing code LLMs often demonstrate unsatisfactory capabilities in generating accurate and complete tests since they were trained on code snippets collected without differentiating between code for testing purposes and other code. In this paper, we present a large-scale dataset UniTSyn, which is capable of enhancing the prowess of LLMs for Unit Test Synthesis. Associating tests with the tested functions is crucial for LLMs to infer the expected behavior and the logic paths to be verified. By leveraging Language Server Protocol, UniTSyn achieves the challenging goal of collecting focal-test pairs without per-project execution setups or per-language heuristics that tend to be fragile and difficult to scale. It contains 2.7 million focal-test pairs across five mainstream programming languages, making it possible to be utilized for enhancing the test generation ability of LLMs. The details of UniTSyn can be found in Table 1. Our experiments demonstrate that, by building an autoregressive model based on UniTSyn, we can achieve significant benefits in learning and understanding unit test representations, resulting in improved generation accuracy and code coverage across all evaluated programming languages. Code and data will be publicly available.

Neural networks excel as function approximators, but their complexity often obscures the types of functions they learn, making it difficult to explain their behavior. To address this, the linearity score lambda(f) is introduced, a simple and interpretable diagnostic that quantifies how well a regression network's output can be mimicked by a linear model. Defined as the R^2 value between the network's predictions and those of a trained linear surrogate, lambda(f) measures linear decodability: the extent to which the network's behavior aligns with a structurally simple model. This framework is evaluated on both synthetic and real-world datasets, using dataset-specific networks and surrogates. High lambda(f) scores reliably indicate alignment with the network's outputs; however, they do not guarantee accuracy with respect to the ground truth. These results highlight the risk of using surrogate fidelity as a proxy for model understanding, especially in high-stakes regression tasks.

We have developed a novel activation function, named the Cauchy Activation Function. This function is derived from the Cauchy Integral Theorem in complex analysis and is specifically tailored for problems requiring high precision. This innovation has led to the creation of a new class of neural networks, which we call (Comple)XNet, or simply XNet. We will demonstrate that XNet is particularly effective for high-dimensional challenges such as image classification and solving Partial Differential Equations (PDEs). Our evaluations show that XNet significantly outperforms established benchmarks like MNIST and CIFAR-10 in computer vision, and offers substantial advantages over Physics-Informed Neural Networks (PINNs) in both low-dimensional and high-dimensional PDE scenarios.

Large Language Models (LLMs) have demonstrated remarkable proficiency in understanding and generating natural language. However, their capabilities wane in highly specialized domains underrepresented in the pretraining corpus, such as physical and biomedical sciences. This work explores how to repurpose general LLMs into effective task solvers for specialized domains. We introduce a novel, model-agnostic framework for learning custom input tags, which are parameterized as continuous vectors appended to the LLM's embedding layer, to condition the LLM. We design two types of input tags: domain tags are used to delimit specialized representations (e.g., chemical formulas) and provide domain-relevant context; function tags are used to represent specific functions (e.g., predicting molecular properties) and compress function-solving instructions. We develop a three-stage protocol to learn these tags using auxiliary data and domain knowledge. By explicitly disentangling task domains from task functions, our method enables zero-shot generalization to unseen problems through diverse combinations of the input tags. It also boosts LLM's performance in various specialized domains, such as predicting protein or chemical properties and modeling drug-target interactions, outperforming expert models tailored to these tasks.

Formulas involving fundamental mathematical constants had a great impact on various fields of science and mathematics, for example aiding in proofs of irrationality of constants. However, the discovery of such formulas has historically remained scarce, often perceived as an act of mathematical genius by great mathematicians such as Ramanujan, Euler, and Gauss. Recent efforts to automate the discovery of formulas for mathematical constants, such as the Ramanujan Machine project, relied on exhaustive search. Despite several successful discoveries, exhaustive search remains limited by the space of options that can be covered and by the need for vast amounts of computational resources. Here we propose a fundamentally different method to search for conjectures on mathematical constants: through analysis of integer sequences. We introduce the Enumerated Signed-continued-fraction Massey Approve (ESMA) algorithm, which builds on the Berlekamp-Massey algorithm to identify patterns in integer sequences that represent mathematical constants. The ESMA algorithm found various known formulas for e, e^2, tan(1), and ratios of values of Bessel functions. The algorithm further discovered a large number of new conjectures for these constants, some providing simpler representations and some providing faster numerical convergence than the corresponding simple continued fractions. Along with the algorithm, we present mathematical tools for manipulating continued fractions. These connections enable us to characterize what space of constants can be found by ESMA and quantify its algorithmic advantage in certain scenarios. Altogether, this work continues in the development of augmenting mathematical intuition by computer algorithms, to help reveal mathematical structures and accelerate mathematical research.

This paper explores the expressive power of deep neural networks through the framework of function compositions. We demonstrate that the repeated compositions of a single fixed-size ReLU network exhibit surprising expressive power, despite the limited expressive capabilities of the individual network itself. Specifically, we prove by construction that L_2circ g^{circ r}circ mathcal{L}_1 can approximate 1-Lipschitz continuous functions on [0,1]^d with an error O(r^{-1/d}), where g is realized by a fixed-size ReLU network, mathcal{L}_1 and L_2 are two affine linear maps matching the dimensions, and g^{circ r} denotes the r-times composition of g. Furthermore, we extend such a result to generic continuous functions on [0,1]^d with the approximation error characterized by the modulus of continuity. Our results reveal that a continuous-depth network generated via a dynamical system has immense approximation power even if its dynamics function is time-independent and realized by a fixed-size ReLU network.

Multitask Gaussian process (MTGP) is powerful for joint learning of multiple tasks with complicated correlation patterns. However, due to the assembling of additive independent latent functions, all current MTGPs including the salient linear model of coregionalization (LMC) and convolution frameworks cannot effectively represent and learn the hierarchical latent interactions between its latent functions. In this paper, we further investigate the interactions in LMC of MTGP and then propose a novel kernel representation of the hierarchical interactions, which ameliorates both the expressiveness and the interpretability of MTGP. Specifically, we express the interaction as a product of function interaction and coefficient interaction. The function interaction is modeled by using cross convolution of latent functions. The coefficient interaction between the LMCs is described as a cross coregionalization term. We validate that considering the interactions can promote knowledge transferring in MTGP and compare our approach with some state-of-the-art MTGPs on both synthetic- and real-world datasets.

This study presents a quantitative evaluation of the code quality and security of five prominent Large Language Models (LLMs): Claude Sonnet 4, Claude 3.7 Sonnet, GPT-4o, Llama 3.2 90B, and OpenCoder 8B. While prior research has assessed the functional performance of LLM-generated code, this research tested LLM output from 4,442 Java coding assignments through comprehensive static analysis using SonarQube. The findings suggest that although LLMs can generate functional code, they also introduce a range of software defects, including bugs, security vulnerabilities, and code smells. These defects do not appear to be isolated; rather, they may represent shared weaknesses stemming from systemic limitations within current LLM code generation methods. In particular, critically severe issues, such as hard-coded passwords and path traversal vulnerabilities, were observed across multiple models. These results indicate that LLM-generated code requires verification in order to be considered production-ready. This study found no direct correlation between a model's functional performance (measured by Pass@1 rate of unit tests) and the overall quality and security of its generated code, measured by the number of SonarQube issues in benchmark solutions that passed the functional tests. This suggests that functional benchmark performance score is not a good indicator of overall code quality and security. The goal of this study is not to rank LLM performance but to highlight that all evaluated models appear to share certain weaknesses. Consequently, these findings support the view that static analysis can be a valuable instrument for detecting latent defects and an important safeguard for organizations that deploy AI in software development.

Unsupervised pretraining, which learns a useful representation using a large amount of unlabeled data to facilitate the learning of downstream tasks, is a critical component of modern large-scale machine learning systems. Despite its tremendous empirical success, the rigorous theoretical understanding of why unsupervised pretraining generally helps remains rather limited -- most existing results are restricted to particular methods or approaches for unsupervised pretraining with specialized structural assumptions. This paper studies a generic framework, where the unsupervised representation learning task is specified by an abstract class of latent variable models Phi and the downstream task is specified by a class of prediction functions Psi. We consider a natural approach of using Maximum Likelihood Estimation (MLE) for unsupervised pretraining and Empirical Risk Minimization (ERM) for learning downstream tasks. We prove that, under a mild ''informative'' condition, our algorithm achieves an excess risk of mathcal{O}(mathcal{C_Phi/m} + mathcal{C_Psi/n}) for downstream tasks, where C_Phi, C_Psi are complexity measures of function classes Phi, Psi, and m, n are the number of unlabeled and labeled data respectively. Comparing to the baseline of mathcal{O}(mathcal{C_{Phi circ Psi}/n}) achieved by performing supervised learning using only the labeled data, our result rigorously shows the benefit of unsupervised pretraining when m gg n and C_{Phicirc Psi} > C_Psi. This paper further shows that our generic framework covers a wide range of approaches for unsupervised pretraining, including factor models, Gaussian mixture models, and contrastive learning.

Neural signed distance functions (SDFs) have been a vital representation to represent 3D shapes or scenes with neural networks. An SDF is an implicit function that can query signed distances at specific coordinates for recovering a 3D surface. Although implicit functions work well on a single shape or scene, they pose obstacles when analyzing multiple SDFs with high-fidelity geometry details, due to the limited information encoded in the latent space for SDFs and the loss of geometry details. To overcome these obstacles, we introduce a method to represent multiple SDFs in a common space, aiming to recover more high-fidelity geometry details with more compact latent representations. Our key idea is to take full advantage of the benefits of generalization-based and overfitting-based learning strategies, which manage to preserve high-fidelity geometry details with compact latent codes. Based on this framework, we also introduce a novel sampling strategy to sample training queries. The sampling can improve the training efficiency and eliminate artifacts caused by the influence of other SDFs. We report numerical and visual evaluations on widely used benchmarks to validate our designs and show advantages over the latest methods in terms of the representative ability and compactness.

We consider the Similarity Sketching problem: Given a universe [u] = {0,ldots, u-1} we want a random function S mapping subsets Asubseteq [u] into vectors S(A) of size t, such that the Jaccard similarity J(A,B) = |Acap B|/|Acup B| between sets A and B is preserved. More precisely, define X_i = [S(A)[i] = S(B)[i]] and X = sum_{iin [t]} X_i. We want E[X_i]=J(A,B), and we want X to be strongly concentrated around E[X] = t cdot J(A,B) (i.e. Chernoff-style bounds). This is a fundamental problem which has found numerous applications in data mining, large-scale classification, computer vision, similarity search, etc. via the classic MinHash algorithm. The vectors S(A) are also called sketches. Strong concentration is critical, for often we want to sketch many sets B_1,ldots,B_n so that we later, for a query set A, can find (one of) the most similar B_i. It is then critical that no B_i looks much more similar to A due to errors in the sketch. The seminal ttimesMinHash algorithm uses t random hash functions h_1,ldots, h_t, and stores left ( min_{ain A} h_1(A),ldots, min_{ain A} h_t(A) right ) as the sketch of A. The main drawback of MinHash is, however, its O(tcdot |A|) running time, and finding a sketch with similar properties and faster running time has been the subject of several papers. (continued...)

The remarkable success of large language models (LLMs) stems from their ability to consolidate vast amounts of knowledge into the memory during pre-training and to retrieve it from the memory during inference, enabling advanced capabilities such as knowledge memorization, instruction-following and reasoning. However, the mechanisms of memory retrieval and consolidation in LLMs remain poorly understood. In this paper, we propose the function token hypothesis to explain the workings of LLMs: During inference, function tokens activate the most predictive features from context and govern next token prediction (memory retrieval). During pre-training, predicting the next tokens (usually content tokens) that follow function tokens increases the number of learned features of LLMs and updates the model parameters (memory consolidation). Function tokens here roughly correspond to function words in linguistics, including punctuation marks, articles, prepositions, and conjunctions, in contrast to content tokens. We provide extensive experimental evidence supporting this hypothesis. Using bipartite graph analysis, we show that a small number of function tokens activate the majority of features. Case studies further reveal how function tokens activate the most predictive features from context to direct next token prediction. We also find that during pre-training, the training loss is dominated by predicting the next content tokens following function tokens, which forces the function tokens to select the most predictive features from context.

When trying to solve a computational problem, we are often faced with a choice between algorithms that are guaranteed to return the right answer but differ in their runtime distributions (e.g., SAT solvers, sorting algorithms). This paper aims to lay theoretical foundations for such choices by formalizing preferences over runtime distributions. It might seem that we should simply prefer the algorithm that minimizes expected runtime. However, such preferences would be driven by exactly how slow our algorithm is on bad inputs, whereas in practice we are typically willing to cut off occasional, sufficiently long runs before they finish. We propose a principled alternative, taking a utility-theoretic approach to characterize the scoring functions that describe preferences over algorithms. These functions depend on the way our value for solving our problem decreases with time and on the distribution from which captimes are drawn. We describe examples of realistic utility functions and show how to leverage a maximum-entropy approach for modeling underspecified captime distributions. Finally, we show how to efficiently estimate an algorithm's expected utility from runtime samples.

The expressivity of Graph Neural Networks (GNNs) is dependent on the aggregation functions they employ. Theoretical works have pointed towards Sum aggregation GNNs subsuming every other GNNs, while certain practical works have observed a clear advantage to using Mean and Max. An examination of the theoretical guarantee identifies two caveats. First, it is size-restricted, that is, the power of every specific GNN is limited to graphs of a specific size. Successfully processing larger graphs may require an other GNN, and so on. Second, it concerns the power to distinguish non-isomorphic graphs, not the power to approximate general functions on graphs, and the former does not necessarily imply the latter. It is desired that a GNN's usability will not be limited to graphs of any specific size. Therefore, we explore the realm of unrestricted-size expressivity. We prove that basic functions, which can be computed exactly by Mean or Max GNNs, are inapproximable by any Sum GNN. We prove that under certain restrictions, every Mean or Max GNN can be approximated by a Sum GNN, but even there, a combination of (Sum, [Mean/Max]) is more expressive than Sum alone. Lastly, we prove further expressivity limitations for GNNs with a broad class of aggregations.

In the artificial neuron, I replace the dot product with the weighted Lehmer mean, which may emulate different cases of a generalized mean. The single neuron instance is replaced by a multiplet of neurons which have the same averaging weights. A group of outputs feed forward, in lieu of the single scalar. The generalization parameter is typically set to a different value for each neuron in the multiplet. I further extend the concept to a multiplet taken from the Gini mean. Derivatives with respect to the weight parameters and with respect to the two generalization parameters are given. Some properties of the network are investigated, showing the capacity to emulate the classical exclusive-or problem organically in two layers and perform some multiplication and division. The network can instantiate truncated power series and variants, which can be used to approximate different functions, provided that parameters are constrained. Moreover, a mean case slope score is derived that can facilitate a learning-rate novelty based on homogeneity of the selected elements. The multiplet neuron equation provides a way to segment regularization timeframes and approaches.

The choice of activation functions in deep networks has a significant effect on the training dynamics and task performance. Currently, the most successful and widely-used activation function is the Rectified Linear Unit (ReLU). Although various hand-designed alternatives to ReLU have been proposed, none have managed to replace it due to inconsistent gains. In this work, we propose to leverage automatic search techniques to discover new activation functions. Using a combination of exhaustive and reinforcement learning-based search, we discover multiple novel activation functions. We verify the effectiveness of the searches by conducting an empirical evaluation with the best discovered activation function. Our experiments show that the best discovered activation function, f(x) = x cdot sigmoid(beta x), which we name Swish, tends to work better than ReLU on deeper models across a number of challenging datasets. For example, simply replacing ReLUs with Swish units improves top-1 classification accuracy on ImageNet by 0.9\% for Mobile NASNet-A and 0.6\% for Inception-ResNet-v2. The simplicity of Swish and its similarity to ReLU make it easy for practitioners to replace ReLUs with Swish units in any neural network.

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular "graph convolutions", a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph---atoms, bonds, distances, etc.---which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

Diffusion models have emerged as a powerful tool rivaling GANs in generating high-quality samples with improved fidelity, flexibility, and robustness. A key component of these models is to learn the score function through score matching. Despite empirical success on various tasks, it remains unclear whether gradient-based algorithms can learn the score function with a provable accuracy. As a first step toward answering this question, this paper establishes a mathematical framework for analyzing score estimation using neural networks trained by gradient descent. Our analysis covers both the optimization and the generalization aspects of the learning procedure. In particular, we propose a parametric form to formulate the denoising score-matching problem as a regression with noisy labels. Compared to the standard supervised learning setup, the score-matching problem introduces distinct challenges, including unbounded input, vector-valued output, and an additional time variable, preventing existing techniques from being applied directly. In this paper, we show that with proper designs, the evolution of neural networks during training can be accurately modeled by a series of kernel regression tasks. Furthermore, by applying an early-stopping rule for gradient descent and leveraging recent developments in neural tangent kernels, we establish the first generalization error (sample complexity) bounds for learning the score function with neural networks, despite the presence of noise in the observations. Our analysis is grounded in a novel parametric form of the neural network and an innovative connection between score matching and regression analysis, facilitating the application of advanced statistical and optimization techniques.

The integration of large language models (LLMs) with function calling has emerged as a crucial capability for enhancing their practical utility in real-world applications. However, effectively combining reasoning processes with accurate function execution remains a significant challenge. Traditional training approaches often struggle to balance the detailed reasoning steps with the precision of function calls, leading to suboptimal performance. To address these limitations, we introduce FunReason, a novel framework that enhances LLMs' function calling capabilities through an automated data refinement strategy and a Self-Refinement Multiscale Loss (SRML) approach. FunReason leverages LLMs' natural reasoning abilities to generate high-quality training examples, focusing on query parseability, reasoning coherence, and function call precision. The SRML approach dynamically balances the contribution of reasoning processes and function call accuracy during training, addressing the inherent trade-off between these two critical aspects. FunReason achieves performance comparable to GPT-4o while effectively mitigating catastrophic forgetting during fine-tuning. FunReason provides a comprehensive solution for enhancing LLMs' function calling capabilities by introducing a balanced training methodology and a data refinement pipeline. For code and dataset, please refer to our repository at GitHub https://github.com/BingguangHao/FunReason