Wang-Zhou Dai

Lun Ai, Shi-Shun Liang, Wang-Zhou Dai et al.

An important application of Synthetic Biology is the engineering of the host cell system to yield useful products. However, an increase in the scale of the host system leads to huge design space and requires a large number of validation trials with high experimental costs. A comprehensible machine learning approach that efficiently explores the hypothesis space and guides experimental design is urgently needed for the Design-Build-Test-Learn (DBTL) cycle of the host cell system. We introduce a novel machine learning framework ILP-iML1515 based on Inductive Logic Programming (ILP) that performs abductive logical reasoning and actively learns from training examples. In contrast to numerical models, ILP-iML1515 is built on comprehensible logical representations of a genome-scale metabolic model and can update the model by learning new logical structures from auxotrophic mutant trials. The ILP-iML1515 framework 1) allows high-throughput simulations and 2) actively selects experiments that reduce the experimental cost of learning gene functions in comparison to randomly selected experiments.

Yifei Peng, Zijie Zha, Yu Jin et al.

Making neural visual generative models controllable by logical reasoning systems is promising for improving faithfulness, transparency, and generalizability. We propose the Abductive visual Generation (AbdGen) approach to build such logic-integrated models. A vector-quantized symbol grounding mechanism and the corresponding disentanglement training method are introduced to enhance the controllability of logical symbols over generation. Furthermore, we propose two logical abduction methods to make our approach require few labeled training data and support the induction of latent logical generative rules from data. We experimentally show that our approach can be utilized to integrate various neural generative models with logical reasoning systems, by both learning from scratch or utilizing pre-trained models directly. The code is released at https://github.com/future-item/AbdGen.

Lue Tao, Yu-Xuan Huang, Wang-Zhou Dai et al.

Neuro-symbolic hybrid systems are promising for integrating machine learning and symbolic reasoning, where perception models are facilitated with information inferred from a symbolic knowledge base through logical reasoning. Despite empirical evidence showing the ability of hybrid systems to learn accurate perception models, the theoretical understanding of learnability is still lacking. Hence, it remains unclear why a hybrid system succeeds for a specific task and when it may fail given a different knowledge base. In this paper, we introduce a novel way of characterising supervision signals from a knowledge base, and establish a criterion for determining the knowledge's efficacy in facilitating successful learning. This, for the first time, allows us to address the two questions above by inspecting the knowledge base under investigation. Our analysis suggests that many knowledge bases satisfy the criterion, thus enabling effective learning, while some fail to satisfy it, indicating potential failures. Comprehensive experiments confirm the utility of our criterion on benchmark tasks.

Yu-Ning Qiu, Lin-Feng Zou, Jiong-Da Wang et al.

In complex code-generation tasks, conversation-based LLM code repair exhibits limited ability to recover from first-pass programming errors, as such code revisions are usually driven by LLMs' "plausible reasoning" rather than a formal, algorithmic debugging procedure. However, a formal foundation for such debugging exists in Udi Shapiro's theory of algorithmic program debugging (APD), which frames program repair as an explicit, stepwise procedural refinement process. In this paper, we propose a neuro-symbolic procedural refinement approach, Abduction-Based Procedural Refinement (ABPR), which couples an LLM with a meta-interpreter that materialises program execution into compact, declarative tree-structured traces, following the principles of APD. We evaluate ABPR on ARC-AGI-2, a benchmark requiring strong abstraction and debugging capabilities, and adopt Prolog as the target language due to its declarative semantics, which are well-suited to algorithmic program debugging. Our experiments show that ABPR paired with Gemini-3-Flash achieves a Pass@2 score of 56.67\% even in a language in which contemporary LLMs typically underperform. These results point towards a more auditable paradigm for program repair by integrating LLMs with classical formal methods.

Xiao-Wen Yang, Jie-Jing Shao, Lan-Zhe Guo et al.

Large Language Models (LLMs) have shown promising results across various tasks, yet their reasoning capabilities remain a fundamental challenge. Developing AI systems with strong reasoning capabilities is regarded as a crucial milestone in the pursuit of Artificial General Intelligence (AGI) and has garnered considerable attention from both academia and industry. Various techniques have been explored to enhance the reasoning capabilities of LLMs, with neuro-symbolic approaches being a particularly promising way. This paper comprehensively reviews recent developments in neuro-symbolic approaches for enhancing LLM reasoning. We first present a formalization of reasoning tasks and give a brief introduction to the neurosymbolic learning paradigm. Then, we discuss neuro-symbolic methods for improving the reasoning capabilities of LLMs from three perspectives: Symbolic->LLM, LLM->Symbolic, and LLM+Symbolic. Finally, we discuss several key challenges and promising future directions. We have also released a GitHub repository including papers and resources related to this survey: https://github.com/LAMDASZ-ML/Awesome-LLM-Reasoning-with-NeSy.

Yifei Peng, Yaoli Liu, Enbo Xia et al.

We propose ILP-CoT, a method that bridges Inductive Logic Programming (ILP) and Multimodal Large Language Models (MLLMs) for abductive logical rule induction. The task involves both discovering logical facts and inducing logical rules from a small number of unstructured textual or visual inputs, which still remain challenging when solely relying on ILP, due to the requirement of specified background knowledge and high computational cost, or MLLMs, due to the appearance of perceptual hallucinations. Based on the key observation that MLLMs could propose structure-correct rules even under hallucinations, our approach automatically builds ILP tasks with pruned search spaces based on the rule structure proposals from MLLMs, and utilizes ILP system to output rules built upon rectified logical facts and formal inductive reasoning. Its effectiveness is verified through challenging logical induction benchmarks, as well as a potential application of our approach, namely text-to-image customized generation with rule induction. Our code and data are released at https://github.com/future-item/ILP-CoT.

Yu Jin, Jingming Liu, Zhexu Luo et al.

Visual generative abductive learning studies jointly training symbol-grounded neural visual generator and inducing logic rules from data, such that after learning, the visual generation process is guided by the induced logic rules. A major challenge for this task is to reduce the time cost of logic abduction during learning, an essential step when the logic symbol set is large and the logic rule to induce is complicated. To address this challenge, we propose a pre-training method for obtaining meta-rule selection policy for the recently proposed visual generative learning approach AbdGen [Peng et al., 2023], aiming at significantly reducing the candidate meta-rule set and pruning the search space. The selection model is built based on the embedding representation of both symbol grounding of cases and meta-rules, which can be effectively integrated with both neural model and logic reasoning system. The pre-training process is done on pure symbol data, not involving symbol grounding learning of raw visual inputs, making the entire learning process low-cost. An additional interesting observation is that the selection policy can rectify symbol grounding errors unseen during pre-training, which is resulted from the memorization ability of attention mechanism and the relative stability of symbolic patterns. Experimental results show that our method is able to effectively address the meta-rule selection problem for visual abduction, boosting the efficiency of visual generative abductive learning. Code is available at https://github.com/future-item/metarule-select.

Naaisha Agarwal, Yihan Wu, Yichang Jian et al.

Building AI systems that can plan, act, and create in the physical world requires more than pattern recognition. Such systems must understand the causal mechanisms and constraints governing physical processes in order to guide sequential decisions. This capability relies on internal representations, analogous to an internal language model, that relate observations, actions, and resulting environmental changes. However, many existing benchmarks treat visual perception and programmatic reasoning as separate problems, focusing either on visual recognition or on symbolic tasks. The domain of origami provides a natural testbed that integrates these modalities. Constructing shapes through folding operations requires visual perception, reasoning about geometric and physical constraints, and sequential planning, while remaining sufficiently structured for systematic evaluation. We introduce OrigamiBench, an interactive benchmark in which models iteratively propose folds and receive feedback on physical validity and similarity to a target configuration. Experiments with modern vision-language models show that scaling model size alone does not reliably produce causal reasoning about physical transformations. Models fail to generate coherent multi-step folding strategies, suggesting that visual and language representations remain weakly integrated.

Wen-Chao Hu, Wang-Zhou Dai, Yuan Jiang et al.

Neuro-Symbolic (NeSy) AI could be regarded as an analogy to human dual-process cognition, modeling the intuitive System 1 with neural networks and the algorithmic System 2 with symbolic reasoning. However, for complex learning targets, NeSy systems often generate outputs inconsistent with domain knowledge and it is challenging to rectify them. Inspired by the human Cognitive Reflection, which promptly detects errors in our intuitive response and revises them by invoking the System 2 reasoning, we propose to improve NeSy systems by introducing Abductive Reflection (ABL-Refl) based on the Abductive Learning (ABL) framework. ABL-Refl leverages domain knowledge to abduce a reflection vector during training, which can then flag potential errors in the neural network outputs and invoke abduction to rectify them and generate consistent outputs during inference. ABL-Refl is highly efficient in contrast to previous ABL implementations. Experiments show that ABL-Refl outperforms state-of-the-art NeSy methods, achieving excellent accuracy with fewer training resources and enhanced efficiency.

Runzhi Deng, Yundi Hu, Xinshuang Zhang et al.

Few-shot multi-class industrial anomaly detection remains a challenging task. Vision-language models need to be both category-adaptive and sharply discriminative, yet data scarcity often blurs the boundary between normal and abnormal states. This ambiguity leads to missed subtle defects and the rejection of atypical normal samples. We propose ABounD, an Adversarial Boundary-Driven few-shot learning for multi-class anomaly detection, which is a unified learning framework that integrates semantic concept learning with decision boundary shaping. The Dynamic Concept Fusion (DCF) module produces class-adaptive prompts by fusing generalizable priors with class-specific cues, conditioned on image features. Meanwhile, Adversarial Boundary Forging (ABF) sculpts a more precise decision margin by generating boundary-level fence features via PGD-style perturbations. Training is conducted in a single stage under a Concept-Boundary Loss, where ABF provides the main supervisory signal and semantic-spatial regularizers stabilize the optimization. This synergy yields a decision boundary that closely follows normal data while preserving flexibility and robust semantic alignment. Experiments on MVTec-AD and VisA datasets demonstrate state-of-the-art performance in the task of few-shot multi-class anomaly detection.

Wang-Zhou Dai, Liam Hallett, Stephen H. Muggleton et al.

The application of Artificial Intelligence (AI) to synthetic biology will provide the foundation for the creation of a high throughput automated platform for genetic design, in which a learning machine is used to iteratively optimise the system through a design-build-test-learn (DBTL) cycle. However, mainstream machine learning techniques represented by deep learning lacks the capability to represent relational knowledge and requires prodigious amounts of annotated training data. These drawbacks strongly restrict AI's role in synthetic biology in which experimentation is inherently resource and time intensive. In this work, we propose an automated biodesign engineering framework empowered by Abductive Meta-Interpretive Learning ($Meta_{Abd}$), a novel machine learning approach that combines symbolic and sub-symbolic machine learning, to further enhance the DBTL cycle by enabling the learning machine to 1) exploit domain knowledge and learn human-interpretable models that are expressed by formal languages such as first-order logic; 2) simultaneously optimise the structure and parameters of the models to make accurate numerical predictions; 3) reduce the cost of experiments and effort on data annotation by actively generating hypotheses and examples. To verify the effectiveness of $Meta_{Abd}$, we have modelled a synthetic dataset for the production of proteins from a three gene operon in a microbial host, which represents a common synthetic biology problem.

Wang-Zhou Dai, Stephen H. Muggleton

For many reasoning-heavy tasks involving raw inputs, it is challenging to design an appropriate end-to-end learning pipeline. Neuro-Symbolic Learning, divide the process into sub-symbolic perception and symbolic reasoning, trying to utilise data-driven machine learning and knowledge-driven reasoning simultaneously. However, they suffer from the exponential computational complexity within the interface between these two components, where the sub-symbolic learning model lacks direct supervision, and the symbolic model lacks accurate input facts. Hence, most of them assume the existence of a strong symbolic knowledge base and only learn the perception model while avoiding a crucial problem: where does the knowledge come from? In this paper, we present Abductive Meta-Interpretive Learning ($Meta_{Abd}$) that unites abduction and induction to learn neural networks and induce logic theories jointly from raw data. Experimental results demonstrate that $Meta_{Abd}$ not only outperforms the compared systems in predictive accuracy and data efficiency but also induces logic programs that can be re-used as background knowledge in subsequent learning tasks. To the best of our knowledge, $Meta_{Abd}$ is the first system that can jointly learn neural networks from scratch and induce recursive first-order logic theories with predicate invention.

Wang-Zhou Dai, Qiu-Ling Xu, Yang Yu et al.

Perception and reasoning are basic human abilities that are seamlessly connected as part of human intelligence. However, in current machine learning systems, the perception and reasoning modules are incompatible. Tasks requiring joint perception and reasoning ability are difficult to accomplish autonomously and still demand human intervention. Inspired by the way language experts decoded Mayan scripts by joining two abilities in an abductive manner, this paper proposes the abductive learning framework. The framework learns perception and reasoning simultaneously with the help of a trial-and-error abductive process. We present the Neural-Logical Machine as an implementation of this novel learning framework. We demonstrate that--using human-like abductive learning--the machine learns from a small set of simple hand-written equations and then generalizes well to complex equations, a feat that is beyond the capability of state-of-the-art neural network models. The abductive learning framework explores a new direction for approaching human-level learning ability.

Wang-Zhou Dai, Zhi-Hua Zhou

Recent years have seen a surge of interest in Probabilistic Logic Programming (PLP) and Statistical Relational Learning (SRL) models that combine logic with probabilities. Structure learning of these systems is an intersection area of Inductive Logic Programming (ILP) and statistical learning (SL). However, ILP cannot deal with probabilities, SL cannot model relational hypothesis. The biggest challenge of integrating these two machine learning frameworks is how to estimate the probability of a logic clause only from the observation of grounded logic atoms. Many current methods models a joint probability by representing clause as graphical model and literals as vertices in it. This model is still too complicate and only can be approximate by pseudo-likelihood. We propose Inductive Logic Boosting framework to transform the relational dataset into a feature-based dataset, induces logic rules by boosting Problog Rule Trees and relaxes the independence constraint of pseudo-likelihood. Experimental evaluation on benchmark datasets demonstrates that the AUC-PR and AUC-ROC value of ILP learned rules are higher than current state-of-the-art SRL methods.