Topic models infer latent topic distributions based on observed word co-occurrences in a text corpus. While typically a corpus contains documents of variable lengths, most previous topic models treat documents of different lengths uniformly, assuming that each document is sufficiently informative. However, shorter documents may have only a few word co-occurrences, resulting in inferior topic quality. Some other previous works assume that all documents are short, and leverage external auxiliary data, e.g., pretrained word embeddings and document connectivity. Orthogonal to existing works, we remedy this problem within the corpus itself by proposing a Meta-Complement Topic Model, which improves topic quality of short texts by transferring the semantic knowledge learned on long documents to complement semantically limited short texts. As a self-contained module, our framework is agnostic to auxiliary data and can be further improved by flexibly integrating them into our framework. Specifically, when incorporating document connectivity, we further extend our framework to complement documents with limited edges. Experiments demonstrate the advantage of our framework.

Mechanistic interpretability aims to understand neural networks by identifying which learned features mediate specific behaviors. Attribution graphs reveal these feature pathways, but interpreting them requires extensive manual analysis -- a single prompt can take approximately 2 hours for an experienced circuit tracer. We present probe prompting, an automated pipeline that transforms attribution graphs into compact, interpretable subgraphs built from concept-aligned supernodes. Starting from a seed prompt and target logit, we select high-influence features, generate concept-targeted yet context-varying probes, and group features by cross-prompt activation signatures into Semantic, Relationship, and Say-X categories using transparent decision rules. Across five prompts including classic "capitals" circuits, probe-prompted subgraphs preserve high explanatory coverage while compressing complexity (Completeness 0.83, mean across circuits; Replacement 0.54). Compared to geometric clustering baselines, concept-aligned groups exhibit higher behavioral coherence: 2.3x higher peak-token consistency (0.425 vs 0.183) and 5.8x higher activation-pattern similarity (0.762 vs 0.130), despite lower geometric compactness. Entity-swap tests reveal a layerwise hierarchy: early-layer features transfer robustly (64% transfer rate, mean layer 6.3), while late-layer Say-X features specialize for output promotion (mean layer 16.4), supporting a backbone-and-specialization view of transformer computation. We release code (https://github.com/peppinob-ol/attribution-graph-probing), an interactive demo (https://huggingface.co/spaces/Peppinob/attribution-graph-probing), and minimal artifacts enabling immediate reproduction and community adoption.

Modern answer set programming solvers such as CLINGO support advanced language constructs that improve the expressivity and conciseness of logic programs. Conditional literals are one such construct. They form "subformulas" that behave as nested implications within the bodies of logic rules. Their inclusion brings the form of rules closer to the less restrictive syntax of first-order logic. These qualities make conditional literals useful tools for knowledge representation. In this paper, we propose a semantics for logic programs with conditional literals and arithmetic based on the SM operator. These semantics do not require grounding, unlike the established semantics for such programs that relies on a translation to infinitary propositional logic. The main result of this paper establishes the precise correspondence between the proposed and existing semantics.

A formalization of a subject-event ontology is proposed for modeling complex dynamic systems without reliance on global time. Key principles: (1) event as an act of fixation - a subject discerns and fixes changes according to models (conceptual templates) available to them; (2) causal order via happens-before - the order of events is defined by explicit dependencies, not timestamps; (3) making the ontology executable via a declarative dataflow mechanism, ensuring determinism; (4) models as epistemic filters - a subject can only fix what falls under its known concepts and properties; (5) presumption of truth - the declarative content of an event is available for computation from the moment of fixation, without external verification. The formalization includes nine axioms (A1-A9), ensuring the correctness of executable ontologies: monotonicity of history (I1), acyclicity of causality (I2), traceability (I3). Special attention is given to the model-based approach (A9): event validation via schemas, actor authorization, automatic construction of causal chains (W3) without global time. Practical applicability is demonstrated on the boldsea system - a workflow engine for executable ontologies, where the theoretical constructs are implemented in BSL (Boldsea Semantic Language). The formalization is applicable to distributed systems, microservice architectures, DLT platforms, and multiperspectivity scenarios (conflicting facts from different subjects).

Out-of-distribution (OOD) detection remains challenging in text-rich networks, where textual features intertwine with topological structures. Existing methods primarily address label shifts or rudimentary domain-based splits, overlooking the intricate textual-structural diversity. For example, in social networks, where users represent nodes with textual features (name, bio) while edges indicate friendship status, OOD may stem from the distinct language patterns between bot and normal users. To address this gap, we introduce the TextTopoOOD framework for evaluating detection across diverse OOD scenarios: (1) attribute-level shifts via text augmentations and embedding perturbations; (2) structural shifts through edge rewiring and semantic connections; (3) thematically-guided label shifts; and (4) domain-based divisions. Furthermore, we propose TNT-OOD to model the complex interplay between Text aNd Topology using: 1) a novel cross-attention module to fuse local structure into node-level text representations, and 2) a HyperNetwork to generate node-specific transformation parameters. This aligns topological and semantic features of ID nodes, enhancing ID/OOD distinction across structural and textual shifts. Experiments on 11 datasets across four OOD scenarios demonstrate the nuanced challenge of TextTopoOOD for evaluating OOD detection in text-rich networks.

In this paper, we study a functional programming approach to natural language semantics, allowing us to increase the expressiveness of a more traditional denotation style. We will formalize a category based type and effect system to represent the semantic difference between syntactically equivalent expressions. We then construct a diagrammatic calculus to model parsing and handling of effects, providing a method to efficiently compute the denotations for sentences.

Scientific applications of machine learning often rely on small, specialized models tuned to particular domains. Such models often achieve excellent performance, but lack flexibility. Foundation models offer versatility, but typically underperform specialized approaches, especially on non-traditional modalities and long-tail domains. We propose MARVIS (Modality Adaptive Reasoning over VISualizations), a training-free method that enables even small vision-language models to predict any data modality with high accuracy. MARVIS transforms latent embedding spaces into visual representations and then leverages the spatial and fine-grained reasoning skills of VLMs to successfully interpret and utilize them. MARVIS achieves competitive performance on vision, audio, biological, and tabular domains using a single 3B parameter model, achieving results that beat Gemini by 16\% on average and approach specialized methods, without exposing personally identifiable information (P.I.I.) or requiring any domain-specific training. We open source our code and datasets at https://github.com/penfever/marvis

Large Language Models (LLMs) have shown impressive capabilities in downstream software engineering tasks such as Automated Program Repair (APR). In particular, there has been a lot of research on repository-level issue-resolution benchmarks such as SWE-Bench. Although there has been significant progress on this topic, we notice that in the process of solving such issues, existing agentic systems tend to hyper-localize on immediately suspicious lines of code and fix them in isolation, without a deeper understanding of the issue semantics, code semantics, or execution semantics. Consequently, many existing systems generate patches that overfit to the user issue, even when a more general fix is preferable. To address this limitation, we introduce SemAgent, a novel workflow-based procedure that leverages issue, code, and execution semantics to generate patches that are complete - identifying and fixing all lines relevant to the issue. We achieve this through a novel pipeline that (a) leverages execution semantics to retrieve relevant context, (b) comprehends issue-semantics via generalized abstraction, (c) isolates code-semantics within the context of this abstraction, and (d) leverages this understanding in a two-stage architecture: a repair stage that proposes fine-grained fixes, followed by a reviewer stage that filters relevant fixes based on the inferred issue-semantics. Our evaluations show that our methodology achieves a solve rate of 44.66% on the SWEBench-Lite benchmark beating all other workflow-based approaches, and an absolute improvement of 7.66% compared to our baseline, which lacks such deep semantic understanding. We note that our approach performs particularly well on issues requiring multi-line reasoning (and editing) and edge-case handling, suggesting that incorporating issue and code semantics into APR pipelines can lead to robust and semantically consistent repairs.

Activity cliff prediction is a critical task in drug discovery and material design. Existing computational methods are limited to handling single binding targets, which restricts the applicability of these prediction models. In this paper, we present the Multi-Grained Target Perception network (MTPNet) to incorporate the prior knowledge of interactions between the molecules and their target proteins. Specifically, MTPNet is a unified framework for activity cliff prediction, which consists of two components: Macro-level Target Semantic (MTS) guidance and Micro-level Pocket Semantic (MPS) guidance. By this way, MTPNet dynamically optimizes molecular representations through multi-grained protein semantic conditions. To our knowledge, it is the first time to employ the receptor proteins as guiding information to effectively capture critical interaction details. Extensive experiments on 30 representative activity cliff datasets demonstrate that MTPNet significantly outperforms previous approaches, achieving an average RMSE improvement of 18.95% on top of several mainstream GNN architectures. Overall, MTPNet internalizes interaction patterns through conditional deep learning to achieve unified predictions of activity cliffs, helping to accelerate compound optimization and design. Codes are available at: https://github.com/ZishanShu/MTPNet.

We present the Semantics-aware Dataset and Benchmark Generation Pipeline for Open-vocabulary Object Navigation in Dynamic Scenes (SD-OVON). It utilizes pretraining multimodal foundation models to generate infinite unique photo-realistic scene variants that adhere to real-world semantics and daily commonsense for the training and the evaluation of navigation agents, accompanied with a plugin for generating object navigation task episodes compatible to the Habitat simulator. In addition, we offer two pre-generated object navigation task datasets, SD-OVON-3k and SD-OVON-10k, comprising respectively about 3k and 10k episodes of the open-vocabulary object navigation task, derived from the SD-OVON-Scenes dataset with 2.5k photo-realistic scans of real-world environments and the SD-OVON-Objects dataset with 0.9k manually inspected scanned and artist-created manipulatable object models. Unlike prior datasets limited to static environments, SD-OVON covers dynamic scenes and manipulatable objects, facilitating both real-to-sim and sim-to-real robotic applications. This approach enhances the realism of navigation tasks, the training and the evaluation of open-vocabulary object navigation agents in complex settings. To demonstrate the effectiveness of our pipeline and datasets, we propose two baselines and evaluate them along with state-of-the-art baselines on SD-OVON-3k. The datasets, benchmark and source code are publicly available.