Singapore

Single-cell foundation models (scFMs) have demonstrated state-of-the-art performance on various tasks, such as cell-type annotation and perturbation response prediction, by learning gene regulatory networks from large-scale transcriptome data. However, a significant challenge remains: the decision-making processes of these models are less interpretable compared to traditional methods like differential gene expression analysis. Recently, transcoders have emerged as a promising approach for extracting interpretable decision circuits from large language models (LLMs). In this work, we train transcoders on all 24 layers of the cell2sentence (C2S) model, a state-of-the-art scFM, and develop systematic pipelines for biological interpretation. Our analysis reveals that over 80\% of transcoder features across most layers are biologically interpretable through Gene Set Enrichment Analysis (GSEA). Through a case study on endothelial cell classification, we demonstrate that extracted circuits correctly identify cell-type-specific genes and significantly enrich for relevant pathways (FDR = 0.0013), confirming that transcoders can uncover biologically plausible decision-making mechanisms within complex single-cell models.

AAAI 2026

Transcoder-based Circuit Analysis for Interpretable single-Cell Foundation Models

transcoder

circuit analysis

mechanistic interpretability

single-cell analysis

### Welcome to The 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025)

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*It is my great pleasure and honor to welcome you to the 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025), held in beautiful Vienna, Austria, from July 27 to August 1, 2025. ACL2025continues our field’s tradition of excellence in scholarship, innovation, and inclusivity, and I am deeply grateful to the many volunteers who have worked tirelessly to bring this event to life.* 
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ACL 2025

Welcome to The 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025)

workshop paper

We are pleased to announce the Fortieth AAAI Conference on Artificial Intelligence (AAAI-26), which will be held in Singapore EXPO from January 20 to January 27, 2026.

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We are pleased to announce the Fortieth AAAI Conference on Artificial Intelligence (AAAI-26), which will be held in Singapore EXPO from January 20 to January 27, 2026.

We introduce PerturbAgent, a large language model (LLM)-based multi-agent system for single-cell genetic perturbation studies. In biomedical research, understanding cellular responses to perturbations is essential for interpreting gene function and regulatory pathways in single-cell data. Existing methods focus only on either single-cell analysis pipelines or perturbation prediction models, and often lack this necessary biological interpretation. PerturbAgent addresses these limitations, targeting both analysis and prediction tasks while also generating comprehensive biological interpretations with results grounded in mechanisms, pathways, and existing knowledge. We further propose MAST++, a general framework that evaluates agentic performance across profile, reasoning, perception, interaction, and memory, and complement it with biological validity assessments. On public single-cell Perturb-seq and RNA-seq datasets, PerturbAgent reliably achieves high task completion and delivers citation-backed biological summaries, representing progress toward practical and interpretable agent workflows for scientific discovery.

PerturbAgent: An Agentic AI system for Analysis and Prediction of Genetic Perturbations

Transformer-based language models excel at both recall (retrieving memorized facts) and reasoning (performing multistep inference), yet it remains unclear whether these functions rely on overlapping or separable internal circuits. Understanding these mechanisms is critical for building trustworthy and scientifically interpretable AI systems.We address this question through mechanistic interpretability, using controlled linguistic puzzles to probe transformer models at the layer, head, and neuron levels. By combining layer-wise activation tracing, attention-head specialization metrics, and causal activation patching, we identify subnetworks whose perturbation selectively disrupts either factual retrieval or reasoning. Across the Qwen, LLaMA-3 and Mistral families, we find a consistent pattern: the early and middle layers primarily support recall, while the deeper layers and specific MLP pathways enable reasoning. Interventions in distinct components lead to selective impairments: Disabling identified recall circuits reduces the factual precision by up to 15 % while leaving the reasoning intact, while disabling reasoning circuits yields a comparable drop in multistep inference. These findings offer causal, interpretable evidence that recall and reasoning arise from partially distinct but complementary computational processes, advancing the mechanistic foundations of explainable AI.

Disentangling Recall and Reasoning in Transformer Models through Layer-wise Attention and Activation Analysis

There is a substantial body of literature examining the mathematical reasoning capabilities of large language models (LLMs), particularly their performance on precise arithmetic operations in autoregressive architectures. However, their ability to perform approximate reasoning in informal, fast-paced mathematical operations has received far less attention, especially among non-autoregressive decoder models. Our work addresses this gap by introducing StreetMath, a benchmark designed to evaluate models’ approximation abilities under real-world approximation scenarios. We conduct extensive evaluations across different LLM architectures: Qwen3-4B-Instruct-2507, Qwen3-4B-Thinking-2507, Dream-v0-Instruct-7B, Falcon-Mamba-7B-Instruct, and Mamba-GPT-3B. Furthermore, we apply mechanistic interpretability techniques to probe their internal computational states. Our analysis reveals that LLMs generally attempt to compute exact values or invoke external tools even in tasks that call for approximation. Moreover, while models sometimes reach the correct answer in early layers or steps, they still consume more tokens when solving approximation tasks. Additional experiments indicate that exact and approximate arithmetic operations rely on largely separate neural components. Drawing upon research on cognitive psychology, we argue that LLMs do not exhibit cognitive miserliness in the same way humans do in street math settings. We open source our work https://anonymous.4open.science/r/StreetMath-1/

StreetMath: Understanding How LLMs Approximate Mathematical Reasoning

Retrieval-Augmented Generation (RAG) systems enhance large language models (LLMs) by grounding responses in external evidence, mitigating hallucinations, and enabling access to up-to-date, domain-specific knowledge. However, existing RAG frameworks often suffer from unstable self-supervised optimization signals and inconsistent factual grounding. We introduce CREAM-RAG (Consistency-Regularized Enhanced Augmented Model for RAG), a unified framework that integrates retrieval, Direct Preference Optimization (DPO)-based self-reward reinforcement learning, and a consistency regularization objective to stabilize reward dynamics during fine-tuning. By enforcing alignment between multiple retrieved contexts and generated responses, CREAM-RAG improves factual faithfulness and semantic coherence without external supervision. Empirical evaluations on the LLaMA-2-7B model demonstrate that CREAM-RAG achieves a 35.04% average improvement over the base model across reasoning and factuality benchmarks, highlighting its effectiveness in reducing hallucinations and enhancing retrieval-grounded reasoning.

CREAM-RAG: Enhanced Retrieval Augmented Generation to Limit Hallucination through Consistency-based Self-RAG

Large language models (LLMs) often generate fluent but factually incorrect statements despite having access to relevant evidence, a failure mode rooted in how they allocate attention between contextual and parametric knowledge. Understanding and steering this internal behavior is key both for trustworthy deployment and for scientific interpretability of model mechanisms. We introduce COMPASS (Context-Modulated PID Attention Steering System), a lightweight, interpretable control framework that embeds a model-based feedback loop directly within decoding. COMPASS quantifies context reliance via a transparent metric, the Context Reliance Score (CRS), which serves as an online probe of how attention heads ground generation in evidence. Using this interpretable signal, a PID controller dynamically modulates attention heads to maintain factual consistency without retraining or multi-pass decoding. Across benchmarks (HotpotQA, XSum, HaluEval, RAGTruth), COMPASS consistently reduces contextual hallucination rates (2.8–5.8\% absolute) while revealing how distinct attention heads contribute to evidence alignment. These results highlight feedback-driven interpretability as a pathway toward scientific understanding of LLM behavior.

COMPASS: Context-Modulated PID Attention Steering System for Hallucination Mitigation

Large reasoning models trained via reinforcement learning (RL) substantially outperform their supervised counterparts on tasks requiring logic and mathematical reasoning, yet the mechanistic basis for these improvements remains unclear. We investigate this phenomenon through an integrated behavioral-mechanistic analysis of mathematical reasoning, asking: what internal differences enable RL models' superior performance? We present three converging lines of evidence that RL models develop higher-quality reasoning representations earlier in their networks. First, linear probes trained on layer-wise hidden states reveal that RL models achieve 11% higher accuracy in predicting answer correctness, with this capability emerging earlier than in base models—suggesting RL training produces more structured, reasoning-relevant representations throughout the network. Second, soft-mean ablation studies show RL models exhibit greater performance degradation when early-layer representations are perturbed, confirming that critical reasoning computations occur earlier and that these representations are functionally important for downstream generation. These representational differences manifest behaviorally in how models allocate computational resources during generation. Analyzing within-problem token generation variability across 50 responses per problem, we find that Qwen3-Thinking maintains remarkably consistent token usage (CV = 0.25-0.33) across all difficulty levels while achieving 97.7% accuracy, suggesting its superior representations enable efficient, reliable solution paths. In contrast, DeepSeek-Math models exhibit elevated variability specifically at capability boundaries (CV >0.8 at 20-60% accuracy), indicating adaptive computational effort where problems strain model capacity—yet DeepSeek's RL and supervised variants show nearly identical variability profiles, suggesting current reward structures may not fully exploit the potential for adaptive token allocation. Together, these findings suggest that RL training fundamentally restructures how models represent and process reasoning problems, building more robust and accessible reasoning representations. This mechanistic understanding provides actionable insights for designing more reliable reasoning systems and highlights the value of probing internal representations to understand capability improvements.

Probing the Origins of Reasoning Performance: Representational Quality for Mathematical Problem-Solving in RL vs SFT Finetuned Models

Recent studies have revealed that LLMs can exhibit behavioral self-awareness — the ability to accurately describe or predict their own learned behaviors without explicit supervision. This capability raises safety concerns, as it may allow models to intentionally conceal their true abilities during evaluation. We attempt to better understand this phenomenon by investigating how and when self-awareness emerges during fine-tuning, and whether it can be mechanistically localized. Through controlled fine-tuning experiments on instruction-tuned LLMs with low-rank adapters (LoRA), we find: (1) that across domains and layers, fine-tuning consistently elicits self-aware behavior early on in the training process; (2) that self-awareness can be reliably induced using a single rank-1 LoRA adapter; and (3) that the learned self-aware behavior is largely captured by a single steering vector in activation space, recovering nearly all of the fine-tune’s behavioral effect. Together, these findings suggest that self-awareness exhibits a rapid transition and is captured by a linear direction rather than a distributed introspective mechanism.

Emergent Mechanisms of Self-Awareness in LLMs

We introduce a diagnostic for symmetry learning in PDE surrogates: the influence function computed across symmetry- related states. On compressible Euler flows, our diagnostic reveals that a UNet exhibits partial but unstable influence across square group actions and translations, whereas a ViT reaches lower prediction error yet shows largely orthogonal updates across orbits. This exposes an optimization-symmetry tradeoff: stronger inductive biases promote data efficiency but can couple updates rigidly; flexible architectures optimize easily but ignore physical structure. Our diagnostic offers a reproducible test for whether training dynamics propagate information across symmetry orbits, a necessary ingredient for robust generalization in scientific machine learning.

Loss Landscape Geometry and the Learning of Symmetries: Or, What Influence Functions Reveal About Memorization and Generalization

Additive manufacturing enables the layer-by-layer fabrication of complex and customizable structures but remains prone to internal defects that are difficult to detect during fabrication. This work presents an anomaly detection framework for real-time defect monitoring using a custom-designed wireless antenna sensor. The sensor consists of an aluminum split-ring resonator patterned with gold conductive ink and mounted on a ceramic substrate. It passively responds to structural and thermal changes during the manufacturing process by producing frequency-domain scattering parameter signals. To process these high-dimensional signals without requiring defect-labeled data, we develop a zero-bias deep neural network trained exclusively on normal-class samples. The model constructs a class-structured latent space using cosine similarity to learned templates and applies Mahalanobis distance to define statistical decision boundaries. Anomalies are identified when inputs deviate significantly from the expected distribution of normal data. The framework is designed around two deployment-oriented principles. Explainability enables users and domain experts to understand detection decisions through latent space visualization, feature attribution, and statistical reasoning that connects model outputs to interpretable signal characteristics. Instructibility allows users to tune detection sensitivity through threshold control without retraining, adapting the system to different quality requirements and process tolerances. The system is evaluated using experimental data collected from the antenna sensor under controlled thermal variation. Results demonstrate that the proposed method accurately detects anomalous signal patterns without using defect supervision, while maintaining interpretability and user control. This approach offers a transparent, adaptive, and data-efficient solution for in situ defect monitoring in additive manufacturing environments.

Anomaly Detection for Antenna-Based Defect Detection in Additive Manufacturing: An Explainable, Instructive Learning Framework

Reports of “emergent” capabilities in transformer-based LLMs (abrupt, non-linear improvements in task performance) remain controversial due to post-hoc measurement and ambiguous definitions. We investigate whether such transitions can be predicted pre-hoc from internal representations. For each training checkpoint, we train sparse autoencoders (SAEs) on model activations, construct a co-activation graph over SAE features, and track graph statistics (e.g. density, clustering, etc.). We analyze a 2-layer grokking-style transformer with aggregate graph metrics over eight SAE initializations, and test lead-lag relationships between changes in graph metrics and subsequent changes in accuracy under a formalized emergence criterion. Across both settings, we find no statistically significant evidence that global co-activation topology forecasts emergent jumps in performance. If pre-hoc indicators exist, they may lie outside the global graph measures analyzed here (e.g., in task-specific circuits or localized subgraphs).

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PerturbAgent: An Agentic AI system for Analysis and Prediction of Genetic Perturbations

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Next from AAAI 2026

PerturbAgent: An Agentic AI system for Analysis and Prediction of Genetic Perturbations

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A Survey on Foundation Language Models for Single-cell Biology

Stay up to date with the latest Underline news!

PRESENTATIONS

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RESOURCES

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