arXiv subjects

Michael Bain

Publications and source records attributed to Michael Bain.

13 recordsLinked to original sources

arXiv2026

Identifying Latent Declarative Representations of Code for Assisting Repository Migration

Legacy software repositories embed decades of domain knowledge in undocumented code, making understanding and modernization difficult. We treat a program as the implementation of an unobserved, declarative description of its computation and investigate whether making this latent declarative representation explicit improves repository-scale porting. ADFD-Migrate approximates the latent representation with an annotated data-flow diagram (ADFD) of processes, data stores, external entities, flows, and behavioral contracts. An LLM infers the source ADFD from bounded repository context, guided by static-analysis coverage checks. Dependency-aware chunking orders bounded process groups for target-language generation. Differences between the source ADFD and a statically recovered target ADFD then guide regeneration. We evaluate ADFD-Migrate on f2x50, a new benchmark of 50~Fortran repositories spanning 1.5k--1.6M lines of code and three complexity tiers, and assess the resulting ports along two dimensions: porting soundness, measured by source-oracle behavioral agreement, and porting completeness, measured by a composite migration outcome index. Against 382 curated Fortran-oracle probes, the generated Python passes 327 (85.6\%), with 40 repositories passing every attempted probe. ADFD-Migrate exposes all 382 planned behaviors as runnable targets, compared with 99 and 98 for direct and repository-context translation and 69 and 30 for the static-profile and dependency-chunking ablations. It also achieves a 93.1\% mean migration outcome index and a 17--59 percentage-point outcome-index advantage over direct translation on 47 repositories. These results suggest that an inspectable semantic bottleneck can improve the coverage and integration of repository-scale migration while enabling lower-cost generation for many repositories.

cs.SE↗

arXiv2026

Interpretable Column Annotation with LLM-Symbolized Decision Process Materialization

Column annotation (CA), including column type annotation (CTA) and column property annotation (CPA), aims to identify the meanings of table columns and the semantic relationships among them. Recent CA methods usually use various neural models to learn column representations and directly map them to label categories, thereby (1) sacrificing model interpretability and adaptivity, and (2) overlooking rich label semantics and ultimately limiting accuracy. To address these limitations, we propose SymCA, an LLM-empowered interpretable CA framework that materializes column annotation as a global-to-local symbolic decision process. SymCA consists of two components: (1) global skeleton induction, which constructs a semantic skeleton over the label space, and (2) local substrate evolution, which evolves predictive substrates within the skeleton. Specifically, to exploit label semantics while preserving an interpretable decision process, the global skeleton induction module leverages LLMs to generate candidate hypernym-inspired tree-structured semantic skeletons and employs a Minimum Bayes Risk (MBR)-based consensus strategy to select a robust skeleton against generation variance. Since different internal nodes require different evidence to distinguish among their child nodes, the local substrate evolution module materializes each internal node as an executable and evolvable predictive substrate. Over multiple evolution rounds, each substrate trains an interpretable random forest classifier with the current operator set, leverages the LLM to propose node-specific operator modifications, and uses an exploration-exploitation strategy to prioritize promising substrates. Extensive experiments demonstrate that SymCA is accurate, robust, and interpretable, outperforming the strongest baselines by an average of 6.42% in Micro-F1 and 11.03% in Macro-F1.

cs.CL↗

arXiv2025

Ensembling LLM-Induced Decision Trees for Explainable and Robust Error Detection

Error detection (ED), which aims to identify incorrect or inconsistent cell values in tabular data, is important for ensuring data quality. Recent state-of-the-art ED methods leverage the pre-trained knowledge and semantic capability of large language models (LLMs) to directly label whether a cell is erroneous. However, this LLM-as-a-labeler pipeline produces predictions through an implicit black-box process with limited traceability and explicit justification, and relies on stochastic single-pass inference, resulting in inconsistent and insufficiently robust detections across contexts. To address these limitations, we propose an LLM-as-an-inducer framework that uses an LLM to induce a decision tree for ED, termed TreeED, and ensembles multiple such trees for consensus detection, termed ForestED. Based on prompts derived from data context, decision tree specifications, and output requirements, TreeED queries the LLM to induce a decision tree skeleton whose root-to-leaf paths specify the stepwise procedure for evaluating a sample. Each tree contains three types of nodes: (1) rule nodes that perform simple validation checks, such as format or range constraints; (2) Graph Neural Network (GNN) nodes that capture complex patterns, such as functional dependencies; and (3) leaf nodes that output the final decision as error or clean. ForestED employs uncertainty sampling to obtain multiple informative row subsets and constructs a decision tree for each subset using TreeED. It then applies an Expectation-Maximization-based algorithm to jointly estimate tree reliability and optimize the consensus ED prediction. Experiments demonstrate that our methods are accurate, explainable, and robust, achieving an average F1-score improvement of 16.1% over the best baseline.

cs.CL↗

arXiv2025

Symbolic Neural Generation with Applications to Lead Discovery in Drug Design

We investigate a relatively under-explored class of hybrid neurosymbolic models that integrate symbolic learning with neural reasoning to construct data generators meeting formal correctness criteria. In Symbolic Neural Generators (SNGs), symbolic learners examine logical specifications of feasible data from a small set of instances -- sometimes just one. Each specification in turn constrains the conditional information supplied to a neural-based generator, which rejects any instance violating the symbolic specification. Like other neurosymbolic approaches, SNG exploits the complementary strengths of symbolic and neural methods. The outcome of an SNG is a pair $(H, X)$, where $H$ is a symbolic description of feasible instances constructed from data, and $X$ a set of generated new instances that satisfy the description. We introduce a semantics for such systems, based on the construction of appropriate base and fibre partially-ordered sets combined into an overall partial order. We implement an SNG combining a restricted form of Inductive Logic Programming (ILP) with a large language model (LLM) and evaluate it on early-stage drug design. Our main interest is the description and the set of potential inhibitor molecules generated by the SNG. On benchmark problems -- where drug targets are well understood -- SNG performance is statistically comparable to state-of-the-art methods. On exploratory problems with poorly understood targets, generated molecules exhibit binding affinities on par with leading clinical candidates. Experts further find the symbolic specifications useful as preliminary filters, with several generated molecules identified as viable for synthesis and wet-lab testing.

cs.LG↗

arXiv2025

Structured Program Synthesis using LLMs: Results and Insights from the IPARC Challenge

The IPARC Challenge, inspired by ARC, provides controlled program synthesis tasks over synthetic images to evaluate automatic program construction, focusing on sequence, selection, and iteration. This set of 600 tasks has resisted automated solutions. This paper presents a structured inductive programming approach with LLMs that successfully solves tasks across all IPARC categories. The controlled nature of IPARC reveals insights into LLM-based code generation, including the importance of prior structuring, LLMs' ability to aid structuring (requiring human refinement), the need to freeze correct code, the efficiency of code reuse, and how LLM-generated code can spark human creativity. These findings suggest valuable mechanisms for human-LLM collaboration in tackling complex program synthesis.

cs.SE↗

arXiv2025

Engineering Systems for Data Analysis Using Interactive Structured Inductive Programming

Engineering information systems for scientific data analysis presents significant challenges: complex workflows requiring exploration of large solution spaces, close collaboration with domain specialists, and the need for maintainable, interpretable implementations. Traditional manual development is time-consuming, while "No Code" approaches using large language models (LLMs) often produce unreliable systems. We present iProg, a tool implementing Interactive Structured Inductive Programming. iProg employs a variant of a '2-way Intelligibility' communication protocol to constrain collaborative system construction by a human and an LLM. Specifically, given a natural-language description of the overall data analysis task, iProg uses an LLM to first identify an appropriate decomposition of the problem into a declarative representation, expressed as a Data Flow Diagram (DFD). In a second phase, iProg then uses an LLM to generate code for each DFD process. In both stages, human feedback, mediated through the constructs provided by the communication protocol, is used to verify LLMs' outputs. We evaluate iProg extensively on two published scientific collaborations (astrophysics and biochemistry), demonstrating that it is possible to identify appropriate system decompositions and construct end-to-end information systems with better performance, higher code quality, and order-of-magnitude faster development compared to Low Code/No Code alternatives. The tool is available at: https://shraddhasurana.github.io/dhaani/

cs.AI↗

arXiv2025

A Comprehensive Survey on Integrating Large Language Models with Knowledge-Based Methods

The rapid development of artificial intelligence has led to marked progress in the field. One interesting direction for research is whether Large Language Models (LLMs) can be integrated with structured knowledge-based systems. This approach aims to combine the generative language understanding of LLMs and the precise knowledge representation systems by which they are integrated. This article surveys the relationship between LLMs and knowledge bases, looks at how they can be applied in practice, and discusses related technical, operational, and ethical challenges. Utilizing a comprehensive examination of the literature, the study both identifies important issues and assesses existing solutions. It demonstrates the merits of incorporating generative AI into structured knowledge-base systems concerning data contextualization, model accuracy, and utilization of knowledge resources. The findings give a full list of the current situation of research, point out the main gaps, and propose helpful paths to take. These insights contribute to advancing AI technologies and support their practical deployment across various sectors.

cs.CL↗

arXiv2023

Defining Reference Sequences for Nocardia Species by Similarity and Clustering Analyses of 16S rRNA Gene Sequence Data

The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia. A total of 364 16S rRNA gene sequences of Nocardia species were studied. In addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level at the time of submission to GenBank were used for machine learning classification experiments. Different clustering algorithms were compared with a novel algorithm or the linear mapping (LM) of the distance matrix. Principal Components Analysis was used for the dimensionality reduction and visualization. Results: The LM algorithm achieved the highest performance and classified the set of 364 16S rRNA sequences into 80 clusters, the majority of which (83.52%) corresponded with the original species. The most representative 16S rRNA sequences for individual Nocardia species have been identified as 'centroids' in respective clusters from which the distances to all other sequences were minimized; 110 16S rRNA gene sequences with identifications recorded only at the genus level were classified using machine learning methods. Simple kNN machine learning demonstrated the highest performance and classified Nocardia species sequences with an accuracy of 92.7% and a mean frequency of 0.578.

q-bio.GN↗

arXiv2023

A Model for Intelligible Interaction Between Agents That Predict and Explain

Machine Learning (ML) has emerged as a powerful form of data modelling with widespread applicability beyond its roots in the design of autonomous agents. However, relatively little attention has been paid to the interaction between people and ML systems. In this paper we view interaction between humans and ML systems within the broader context of communication between agents capable of prediction and explanation. We formalise the interaction model by taking agents to be automata with some special characteristics and define a protocol for communication between such agents. We define One- and Two-Way Intelligibility as properties that emerge at run-time by execution of the protocol. The formalisation allows us to identify conditions under which run-time sequences are bounded, and identify conditions under which the protocol can correctly implement an axiomatic specification of intelligible interaction between a human and an ML system. We also demonstrate using the formal model to: (a) identify instances of One- and Two-Way Intelligibility in literature reports on humans interacting with ML systems providing logic-based explanations, as is done in Inductive Logic Programming (ILP); and (b) map interactions between humans and machines in an elaborate natural-language based dialogue-model to One- or Two-Way Intelligible interactions in the formal model.

cs.AI↗

arXiv2022

One-way Explainability Isn't The Message

Recent engineering developments in specialised computational hardware, data-acquisition and storage technology have seen the emergence of Machine Learning (ML) as a powerful form of data analysis with widespread applicability beyond its historical roots in the design of autonomous agents. However -- possibly because of its origins in the development of agents capable of self-discovery -- relatively little attention has been paid to the interaction between people and ML. In this paper we are concerned with the use of ML in automated or semi-automated tools that assist one or more human decision makers. We argue that requirements on both human and machine in this context are significantly different to the use of ML either as part of autonomous agents for self-discovery or as part statistical data analysis. Our principal position is that the design of such human-machine systems should be driven by repeated, two-way intelligibility of information rather than one-way explainability of the ML-system's recommendations. Iterated rounds of intelligible information exchange, we think, will characterise the kinds of collaboration that will be needed to understand complex phenomena for which neither man or machine have complete answers. We propose operational principles -- we call them Intelligibility Axioms -- to guide the design of a collaborative decision-support system. The principles are concerned with: (a) what it means for information provided by the human to be intelligible to the ML system; and (b) what it means for an explanation provided by an ML system to be intelligible to a human. Using examples from the literature on the use of ML for drug-design and in medicine, we demonstrate cases where the conditions of the axioms are met. We describe some additional requirements needed for the design of a truly collaborative decision-support system.

cs.LG↗

arXiv2018

Logical Explanations for Deep Relational Machines Using Relevance Information

Our interest in this paper is in the construction of symbolic explanations for predictions made by a deep neural network. We will focus attention on deep relational machines (DRMs, first proposed by H. Lodhi). A DRM is a deep network in which the input layer consists of Boolean-valued functions (features) that are defined in terms of relations provided as domain, or background, knowledge. Our DRMs differ from those proposed by Lodhi, which use an Inductive Logic Programming (ILP) engine to first select features (we use random selections from a space of features that satisfies some approximate constraints on logical relevance and non-redundancy). But why do the DRMs predict what they do? One way of answering this is the LIME setting, in which readable proxies for a black-box predictor. The proxies are intended only to model the predictions of the black-box in local regions of the instance-space. But readability alone may not enough: to be understandable, the local models must use relevant concepts in an meaningful manner. We investigate the use of a Bayes-like approach to identify logical proxies for local predictions of a DRM. We show: (a) DRM's with our randomised propositionalization method achieve state-of-the-art predictive performance; (b) Models in first-order logic can approximate the DRM's prediction closely in a small local region; and (c) Expert-provided relevance information can play the role of a prior to distinguish between logical explanations that perform equivalently on prediction alone.

cs.LG↗

arXiv2017

B-CNN: Branch Convolutional Neural Network for Hierarchical Classification

Convolutional Neural Network (CNN) image classifiers are traditionally designed to have sequential convolutional layers with a single output layer. This is based on the assumption that all target classes should be treated equally and exclusively. However, some classes can be more difficult to distinguish than others, and classes may be organized in a hierarchy of categories. At the same time, a CNN is designed to learn internal representations that abstract from the input data based on its hierarchical layered structure. So it is natural to ask if an inverse of this idea can be applied to learn a model that can predict over a classification hierarchy using multiple output layers in decreasing order of class abstraction. In this paper, we introduce a variant of the traditional CNN model named the Branch Convolutional Neural Network (B-CNN). A B-CNN model outputs multiple predictions ordered from coarse to fine along the concatenated convolutional layers corresponding to the hierarchical structure of the target classes, which can be regarded as a form of prior knowledge on the output. To learn with B-CNNs a novel training strategy, named the Branch Training strategy (BT-strategy), is introduced which balances the strictness of the prior with the freedom to adjust parameters on the output layers to minimize the loss. In this way we show that CNN based models can be forced to learn successively coarse to fine concepts in the internal layers at the output stage, and that hierarchical prior knowledge can be adopted to boost CNN models' classification performance. Our models are evaluated to show that the B-CNN extensions improve over the corresponding baseline CNN on the benchmark datasets MNIST, CIFAR-10 and CIFAR-100.

cs.CV↗

arXiv2017

Word Vector Enrichment of Low Frequency Words in the Bag-of-Words Model for Short Text Multi-class Classification Problems

The bag-of-words model is a standard representation of text for many linear classifier learners. In many problem domains, linear classifiers are preferred over more complex models due to their efficiency, robustness and interpretability, and the bag-of-words text representation can capture sufficient information for linear classifiers to make highly accurate predictions. However in settings where there is a large vocabulary, large variance in the frequency of terms in the training corpus, many classes and very short text (e.g., single sentences or document titles) the bag-of-words representation becomes extremely sparse, and this can reduce the accuracy of classifiers. A particular issue in such settings is that short texts tend to contain infrequently occurring or rare terms which lack class-conditional evidence. In this work we introduce a method for enriching the bag-of-words model by complementing such rare term information with related terms from both general and domain-specific Word Vector models. By reducing sparseness in the bag-of-words models, our enrichment approach achieves improved classification over several baseline classifiers in a variety of text classification problems. Our approach is also efficient because it requires no change to the linear classifier before or during training, since bag-of-words enrichment applies only to text being classified.

cs.CL↗