Cyclic peptides, characterized by geometric constraints absent in linear peptides, offer enhanced biochemical properties, presenting new opportunities to address unmet medical needs. However, designing target-specific cyclic peptides remains underexplored due to limited training data. To bridge the gap, we propose CP-Composer, a novel generative framework that enables zero-shot cyclic peptide generation via composable geometric constraints. Our approach decomposes complex cyclization patterns into unit constraints, which are incorporated into a diffusion model through geometric conditioning on nodes and edges. During training, the model learns from unit constraints and their random combinations in linear peptides, while at inference, novel constraint combinations required for cyclization are imposed as input. Experiments show that our model, despite trained with linear peptides, is capable of generating diverse target-binding cyclic peptides, reaching success rates from 38% to 84% on different cyclization strategies.

This paper proposes a formal framework based on symbolic compression, integrating combinatory logic, information-theoretic optimal encoding, and context-aware inference techniques to achieve a step-change improvement in token efficiency while preserving semantic integrity. We establish a mathematical framework within a functional programming paradigm, derive the quantitative relationship between symbolic density and model interpretability, and propose a differentiable compression factor metric to evaluate encoding efficiency. Furthermore, we leverage parameter-efficient fine-tuning (PEFT) techniques to achieve a low-cost application of the GAEL language. Experimental results show that this method achieves a 78.3% token compression rate in code generation tasks while improving logical traceability by 62% through structural explicitness. This research provides new theoretical tools for efficient inference in LLMs and opens a symbolic path for model interpretability research.

Increase in data, size, or compute can lead to sudden learning of specific capabilities by a neural network -- a phenomenon often called "emergence''. Beyond scientific understanding, establishing the causal factors underlying such emergent capabilities is crucial to enable risk regulation frameworks for AI. In this work, we seek inspiration from study of emergent properties in other fields and propose a phenomenological definition for the concept in the context of neural networks. Our definition implicates the acquisition of general structures underlying the data-generating process as a cause of sudden performance growth for specific, narrower tasks. We empirically investigate this definition by proposing an experimental system grounded in a context-sensitive formal language and find that Transformers trained to perform tasks on top of strings from this language indeed exhibit emergent capabilities. Specifically, we show that once the language's underlying grammar and context-sensitivity inducing structures are learned by the model, performance on narrower tasks suddenly begins to improve. We then analogize our network's learning dynamics with the process of percolation on a bipartite graph, establishing a formal phase transition model that predicts the shift in the point of emergence observed in our experiments when changing the data structure. Overall, our experimental and theoretical frameworks yield a step towards better defining, characterizing, and predicting emergence in neural networks.

We present Score, a rule engine designed and implemented for the Scone knowledge base system. Scone is a knowledge base system designed for storing and manipulating rich representations of general knowledge in symbolic form. It represents knowledge in the form of nodes and links in a network structure, and it can perform basic inference about the relationships between different elements efficiently. On its own, Scone acts as a sort of "smart memory" that can interface with other software systems. One area of improvement for Scone is how useful it can be in supplying knowledge to an intelligent agent that can use the knowledge to perform actions and update the knowledge base with its observations. We augment the Scone system with a production rule engine that automatically performs simple inference based on existing and newly-added structures in Scone's knowledge base, potentially improving the capabilities of any planning systems built on top of Scone. Production rule systems consist of "if-then" production rules that try to match their predicates to existing knowledge and fire their actions when their predicates are satisfied. We propose two kinds of production rules, if-added and if-needed rules, that differ in how they are checked and fired to cover multiple use cases. We then implement methods to efficiently check and fire these rules in a large knowledge base. The new rule engine is not meant to be a complex stand-alone planner, so we discuss how it fits into the context of Scone and future work on planning systems.

Wikidata has been increasingly adopted by many communities for a wide variety of applications, which demand high-quality knowledge to deliver successful results. In this paper, we develop a framework to detect and analyze low-quality statements in Wikidata by shedding light on the current practices exercised by the community. We explore three indicators of data quality in Wikidata, based on: 1) community consensus on the currently recorded knowledge, assuming that statements that have been removed and not added back are implicitly agreed to be of low quality; 2) statements that have been deprecated; and 3) constraint violations in the data. We combine these indicators to detect low-quality statements, revealing challenges with duplicate entities, missing triples, violated type rules, and taxonomic distinctions. Our findings complement ongoing efforts by the Wikidata community to improve data quality, aiming to make it easier for users and editors to find and correct mistakes.

With the overwhelming popularity of Knowledge Graphs (KGs), researchers have poured attention to link prediction to fill in missing facts for a long time. However, they mainly focus on link prediction on binary relational data, where facts are usually represented as triples in the form of (head entity, relation, tail entity). In practice, n-ary relational facts are also ubiquitous. When encountering such facts, existing studies usually decompose them into triples by introducing a multitude of auxiliary virtual entities and additional triples. These conversions result in the complexity of carrying out link prediction on n-ary relational data. It has even proven that they may cause loss of structure information. To overcome these problems, in this paper, we represent each n-ary relational fact as a set of its role and role-value pairs. We then propose a method called NaLP to conduct link prediction on n-ary relational data, which explicitly models the relatedness of all the role and role-value pairs in an n-ary relational fact. We further extend NaLP by introducing type constraints of roles and role-values without any external type-specific supervision, and proposing a more reasonable negative sampling mechanism. Experimental results validate the effectiveness and merits of the proposed methods.

Wikidata constraints, albeit useful, are represented and processed in an incomplete, ad hoc fashion. Constraint declarations do not fully express their meaning, and thus do not provide a precise, unambiguous basis for constraint specification, or a logical foundation for constraint-checking implementations. In prior work we have proposed a logical framework for Wikidata as a whole, based on multi-attributed relational structures (MARS) and related logical languages. In this paper we explain how constraints are handled in the proposed framework, and show that nearly all of Wikidata's existing property constraints can be completely characterized in it, in a natural and economical fashion. We also give characterizations for several proposed property constraints, and show that a variety of non-property constraints can be handled in the same framework.

Statistical models with constrained probability distributions are abundant in machine learning. Some examples include regression models with norm constraints (e.g., Lasso), probit, many copula models, and latent Dirichlet allocation (LDA). Bayesian inference involving probability distributions confined to constrained domains could be quite challenging for commonly used sampling algorithms. In this paper, we propose a novel augmentation technique that handles a wide range of constraints by mapping the constrained domain to a sphere in the augmented space. By moving freely on the surface of this sphere, sampling algorithms handle constraints implicitly and generate proposals that remain within boundaries when mapped back to the original space. Our proposed method, called {Spherical Augmentation}, provides a mathematically natural and computationally efficient framework for sampling from constrained probability distributions. We show the advantages of our method over state-of-the-art sampling algorithms, such as exact Hamiltonian Monte Carlo, using several examples including truncated Gaussian distributions, Bayesian Lasso, Bayesian bridge regression, reconstruction of quantized stationary Gaussian process, and LDA for topic modeling.