AutoSAM: an Agentic Framework for Automating Input File Generation for the SAM Code with Multi-Modal Retrieval-Augmented Generation

In the design and safety analysis of advanced reactor systems, constructing input files for system-level thermal-hydraulics codes such as the System Analysis Module (SAM) remains a labor-intensive task. Analysts must extract and reconcile design data from heterogeneous engineering documents and manually translate it into solver-specific syntax. In this paper, we present AutoSAM, an agentic framework that automates SAM input file generation. The framework combines a large language model agent with retrieval-augmented generation over the solver's user guide and theory manual, together with specialized tools for analyzing PDFs, images, spreadsheets, and text files. AutoSAM ingests unstructured engineering documents, including system diagrams, design reports, and data tables, extracts simulation-relevant parameters into a human-auditable intermediate representation, and synthesizes validated, solver-compatible input decks. Its multimodal retrieval pipeline integrates scientific text extraction, vision-based figure interpretation, semantic embedding, and query answering. We evaluate AutoSAM on four case studies of increasing complexity: a single-pipe steady-state model, a solid-fuel channel with temperature reactivity feedback, the Advanced Burner Test Reactor core, and the Molten Salt Reactor Experiment primary loop. Across all cases, the agent produces runnable SAM models consistent with expected thermal-hydraulic behavior while explicitly identifying missing data and labeling assumed values. The framework achieves 100% utilization of structured inputs, about 88% extraction from PDF text, and 100% completeness in vision-based geometric extraction. These results demonstrate a practical path toward prompt-driven reactor modeling, in which analysts provide system descriptions and supporting documentation while the agent translates them into transparent, and executable, SAM simulations.

When Language Models Lose Their Mind: The Consequences of Brain Misalignment

While brain-aligned large language models (LLMs) have garnered attention for their potential as cognitive models and for potential for enhanced safety and trustworthiness in AI, the role of this brain alignment for linguistic competence remains uncertain. In this work, we investigate the functional implications of brain alignment by introducing brain-misaligned models--LLMs intentionally trained to predict brain activity poorly while maintaining high language modeling performance. We evaluate these models on over 200 downstream tasks encompassing diverse linguistic domains, including semantics, syntax, discourse, reasoning, and morphology. By comparing brain-misaligned models with well-matched brain-aligned counterparts, we isolate the specific impact of brain alignment on language understanding. Our experiments reveal that brain misalignment substantially impairs downstream performance, highlighting the critical role of brain alignment in achieving robust linguistic competence. These findings underscore the importance of brain alignment in LLMs and offer novel insights into the relationship between neural representations and linguistic processing.

Beyond Local Code Optimization: Multi-Agent Reasoning for Software System Optimization

Large language models and AI agents have recently shown promise in automating software performance optimization, but existing approaches predominantly rely on local, syntax-driven code transformations. This limits their ability to reason about program behavior and capture whole system performance interactions. As modern software increasingly comprises interacting components - such as microservices, databases, and shared infrastructure - effective code optimization requires reasoning about program structure and system architecture beyond individual functions or files. This paper explores the feasibility of whole system optimization for microservices. We introduce a multi-agent framework that integrates control-flow and data-flow representations with architectural and cross-component dependency signals to support system-level performance reasoning. The proposed system is decomposed into coordinated agent roles - summarization, analysis, optimization, and verification - that collaboratively identify cross-cutting bottlenecks and construct multi-step optimization strategies spanning the software stack. We present a proof-of-concept on a microservice-based system that illustrates the effectiveness of our proposed framework, achieving a 36.58% improvement in throughput and a 27.81% reduction in average response time.

LingoMotion: An Interpretable and Unambiguous Symbolic Representation for Human Motion

Existing representations for human motion, such as MotionGPT, often operate as black-box latent vectors with limited interpretability and build on joint positions which can cause ambiguity. Inspired by the hierarchical structure of natural languages - from letters to words, phrases, and sentences - we propose LingoMotion, a motion language that facilitates interpretable and unambiguous symbolic representation for both simple and complex human motion. In this paper, we introduce the concept design of LingoMotion, including the definitions of motion alphabet based on joint angles, the morphology for forming words and phrases to describe simple actions like walking and their attributes like speed and scale, as well as the syntax for describing more complex human activities with sequences of words and phrases. The preliminary results, including the implementation and evaluation of motion alphabet using a large-scale motion dataset Motion-X, demonstrate the high fidelity of motion representation.

Distilling Formal Logic into Neural Spaces: A Kernel Alignment Approach for Signal Temporal Logic

We introduce a framework for learning continuous neural representations of formal specifications by distilling the geometry of their semantics into a latent space. Existing approaches rely either on symbolic kernels -- which preserve behavioural semantics but are computationally prohibitive, anchor-dependent, and non-invertible -- or on syntax-based neural embeddings that fail to capture underlying structures. Our method bridges this gap: using a teacher-student setup, we distill a symbolic robustness kernel into a Transformer encoder. Unlike standard contrastive methods, we supervise the model with a continuous, kernel-weighted geometric alignment objective that penalizes errors in proportion to their semantic discrepancies. Once trained, the encoder produces embeddings in a single forward pass, effectively mimicking the kernel's logic at a fraction of its computational cost. We apply our framework to Signal Temporal Logic (STL), demonstrating that the resulting neural representations faithfully preserve the semantic similarity of STL formulae, accurately predict robustness and constraint satisfaction, and remain intrinsically invertible. Our proposed approach enables highly efficient, scalable neuro-symbolic reasoning and formula reconstruction without repeated kernel computation at runtime.

MetaOthello: A Controlled Study of Multiple World Models in Transformers

Foundation models must handle multiple generative processes, yet mechanistic interpretability largely studies capabilities in isolation; it remains unclear how a single transformer organizes multiple, potentially conflicting "world models". Previous experiments on Othello playing neural-networks test world-model learning but focus on a single game with a single set of rules. We introduce MetaOthello, a controlled suite of Othello variants with shared syntax but different rules or tokenizations, and train small GPTs on mixed-variant data to study how multiple world models are organized in a shared representation space. We find that transformers trained on mixed-game data do not partition their capacity into isolated sub-models; instead, they converge on a mostly shared board-state representation that transfers causally across variants. Linear probes trained on one variant can intervene on another's internal state with effectiveness approaching that of matched probes. For isomorphic games with token remapping, representations are equivalent up to a single orthogonal rotation that generalizes across layers. When rules partially overlap, early layers maintain game-agnostic representations while a middle layer identifies game identity, and later layers specialize. MetaOthello offers a path toward understanding not just whether transformers learn world models, but how they organize many at once.

Explicit Grammar Semantic Feature Fusion for Robust Text Classification

Natural Language Processing enables computers to understand human language by analysing and classifying text efficiently with deep-level grammatical and semantic features. Existing models capture features by learning from large corpora with transformer models, which are computationally intensive and unsuitable for resource-constrained environments. Therefore, our proposed study incorporates comprehensive grammatical rules alongside semantic information to build a robust, lightweight classification model without resorting to full parameterised transformer models or heavy deep learning architectures. The novelty of our approach lies in its explicit encoding of sentence-level grammatical structure, including syntactic composition, phrase patterns, and complexity indicators, into a compact grammar vector, which is then fused with frozen contextual embeddings. These heterogeneous elements unified a single representation that captures both the structural and semantic characteristics of the text. Deep learning models such as Deep Belief Networks (DBNs), Long Short-Term Memory (LSTMs), BiLSTMs, and transformer-based BERT and XLNET were used to train and evaluate the model, with the number of epochs varied. Based on experimental results, the unified feature representation model captures both the semantic and structural properties of text, outperforming baseline models by 2%-15%, enabling more effective learning across heterogeneous domains. Unlike prior syntax-aware transformer models that inject grammatical structure through additional attention layers, tree encoders, or full fine-tuning, the proposed framework treats grammar as an explicit inductive bias rather than a learnable module, resulting in a very lightweight model that delivers better performance on edge devices

From Logs to Language: Learning Optimal Verbalization for LLM-Based Recommendation in Production

Large language models (LLMs) are promising backbones for generative recommender systems, yet a key challenge remains underexplored: verbalization, i.e., converting structured user interaction logs into effective natural language inputs. Existing methods rely on rigid templates that simply concatenate fields, yielding suboptimal representations for recommendation. We propose a data-centric framework that learns verbalization for LLM-based recommendation. Using reinforcement learning, a verbalization agent transforms raw interaction histories into optimized textual contexts, with recommendation accuracy as the training signal. This agent learns to filter noise, incorporate relevant metadata, and reorganize information to improve downstream predictions. Experiments on a large-scale industrial streaming dataset show that learned verbalization delivers up to 93% relative improvement in discovery item recommendation accuracy over template-based baselines. Further analysis reveals emergent strategies such as user interest summarization, noise removal, and syntax normalization, offering insights into effective context construction for LLM-based recommender systems.

JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures

Genomic Foundation Models (GFMs) have largely relied on Masked Language Modeling (MLM) or Next Token Prediction (NTP) to learn the language of life. While these paradigms excel at capturing local genomic syntax and fine-grained motif patterns, they often fail to capture the broader functional context, resulting in representations that lack a global biological perspective. We introduce JEPA-DNA, a novel pre-training framework that integrates the Joint-Embedding Predictive Architecture (JEPA) with traditional generative objectives. JEPA-DNA introduces latent grounding by coupling token-level recovery with a predictive objective in the latent space by supervising a CLS token. This forces the model to predict the high-level functional embeddings of masked genomic segments rather than focusing solely on individual nucleotides. JEPA-DNA extends both NTP and MLM paradigms and can be deployed either as a standalone from-scratch objective or as a continual pre-training enhancement for existing GFMs. Our evaluations across a diverse suite of genomic benchmarks demonstrate that JEPA-DNA consistently yields superior performance in supervised and zero-shot tasks compared to generative-only baselines. By providing a more robust and biologically grounded representation, JEPA-DNA offers a scalable path toward foundation models that understand not only the genomic alphabet, but also the underlying functional logic of the sequence.

dnaHNet: A Scalable and Hierarchical Foundation Model for Genomic Sequence Learning

Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff in their input representation. Standard fixed-vocabulary tokenizers fragment biologically meaningful motifs such as codons and regulatory elements, while nucleotide-level models preserve biological coherence but incur prohibitive computational costs for long contexts. We introduce dnaHNet, a state-of-the-art tokenizer-free autoregressive model that segments and models genomic sequences end-to-end. Using a differentiable dynamic chunking mechanism, dnaHNet compresses raw nucleotides into latent tokens adaptively, balancing compression with predictive accuracy. Pretrained on prokaryotic genomes, dnaHNet outperforms leading architectures including StripedHyena2 in scaling and efficiency. This recursive chunking yields quadratic FLOP reductions, enabling $>3 \times$ inference speedup over Transformers. On zero-shot tasks, dnaHNet achieves superior performance in predicting protein variant fitness and gene essentiality, while automatically discovering hierarchical biological structures without supervision. These results establish dnaHNet as a scalable, interpretable framework for next-generation genomic modeling.