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Thomas McGee

Publications and source records attributed to Thomas McGee.

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AlgoTrace: Algorithmic Primitives and Compositional Geometry of Reasoning in Language Models

How do inference time and latent computations enable large language models (LLMs) to solve multi-step reasoning problems? We introduce AlgoTrace, a framework for tracing and steering algorithmic operations in the model latent space for multi-step reasoning. We operationalize primitives by clustering latent activations of the model when solving four benchmarks: Traveling Salesperson Problem (TSP), 3SAT, AIME, and Graph Navigation. We annotate the clusters using their corresponding tokens in the reasoning trace. We then apply function vector methods to extract primitive vectors as reusable compositional building blocks of reasoning. We find that a) injecting a primitive vector into models (Phi, Qwen, Llama) elicits the associated algorithmic operation in the reasoning trace, b) injecting primitives can steer behavior across tasks, c) primitive vectors can be composed through algebraic operations, revealing a geometric logic in activation space, and d) a fine-tuned model exhibits improved composition of primitives (Phi-4-Reasoning vs. Phi-4). These findings demonstrate that LLM reasoning can be understood as a walk through algorithmic primitives in the latent space governed by compositional geometry. These primitives transfer across tasks, and reasoning finetuning strengthens algorithmic generalization and composition across domains.

cs.LG

Time-Resolved EEG Decoding of Semantic Processing Reveals Altered Neural Dynamics in Depression and Suicidality

Depression and suicidality affect cognitive and emotional processes, yet objective, task-evoked neural readouts of mental health remain limited. We investigated the spatiotemporal dynamics of affective semantic processing using multivariate decoding of time-resolved, 64-channel electroencephalography (EEG). Participants (N=137) performed a sentence-evaluation task with emotionally salient, self-referential statements. We identified robust neural signatures of semantic processing, with peak decoding accuracy between 300-600 ms -- a window associated with rapid, stimulus-driven semantic evaluation and conflict monitoring. Relative to healthy controls, individuals with depression and suicidal ideation showed earlier onset, longer duration, and greater amplitude decoding responses, along with broader cross-temporal generalization and enhanced contributions from frontocentral and parietotemporal components. These findings suggest altered sensitivity and impaired disengagement from emotionally salient content in the clinical groups, advancing our understanding of the neurocognitive basis of mental health and establishing a compact and interpretable EEG-based index of semantic-evaluation dynamics with potential diagnostic relevance.

q-bio.NC

Position: We Need An Algorithmic Understanding of Generative AI

What algorithms do LLMs actually learn and use to solve problems? Studies addressing this question are sparse, as research priorities are focused on improving performance through scale, leaving a theoretical and empirical gap in understanding emergent algorithms. This position paper proposes AlgEval: a framework for systematic research into the algorithms that LLMs learn and use. AlgEval aims to uncover algorithmic primitives, reflected in latent representations, attention, and inference-time compute, and their algorithmic composition to solve task-specific problems. We highlight potential methodological paths and a case study toward this goal, focusing on emergent search algorithms. Our case study illustrates both the formation of top-down hypotheses about candidate algorithms, and bottom-up tests of these hypotheses via circuit-level analysis of attention patterns and hidden states. The rigorous, systematic evaluation of how LLMs actually solve tasks provides an alternative to resource-intensive scaling, reorienting the field toward a principled understanding of underlying computations. Such algorithmic explanations offer a pathway to human-understandable interpretability, enabling comprehension of the model's internal reasoning performance measures. This can in turn lead to more sample-efficient methods for training and improving performance, as well as novel architectures for end-to-end and multi-agent systems.

cs.AI

Neural Responses to Affective Sentences Reveal Signatures of Depression

Major Depressive Disorder (MDD) is a highly prevalent mental health condition, and a deeper understanding of its neurocognitive foundations is essential for identifying how core functions such as emotional and self-referential processing are affected. We investigate how depression alters the temporal dynamics of emotional processing by measuring neural responses to self-referential affective sentences using surface electroencephalography (EEG) in healthy and depressed individuals. Our results reveal significant group-level differences in neural activity during sentence viewing, suggesting disrupted integration of emotional and self-referential information in depression. Deep learning model trained on these responses achieves an area under the receiver operating curve (AUC) of 0.707 in distinguishing healthy from depressed participants, and 0.624 in differentiating depressed subgroups with and without suicidal ideation. Spatial ablations highlight anterior electrodes associated with semantic and affective processing as key contributors. These findings suggest stable, stimulus-driven neural signatures of depression that may inform future diagnostic tools.

cs.LG

Deep Learning Characterizes Depression and Suicidal Ideation from Eye Movements

Identifying physiological and behavioral markers for mental health conditions is a longstanding challenge in psychiatry. Depression and suicidal ideation, in particular, lack objective biomarkers, with screening and diagnosis primarily relying on self-reports and clinical interviews. Here, we investigate eye tracking as a potential marker modality for screening purposes. Eye movements are directly modulated by neuronal networks and have been associated with attentional and mood-related patterns; however, their predictive value for depression and suicidality remains unclear. We recorded eye-tracking sequences from 126 young adults as they read and responded to affective sentences, and subsequently developed a deep learning framework to predict their clinical status. The proposed model included separate branches for trials of positive and negative sentiment, and used 2D time-series representations to account for both intra-trial and inter-trial variations. We were able to identify depression and suicidal ideation with an area under the receiver operating curve (AUC) of 0.793 (95% CI: 0.765-0.819) against healthy controls, and suicidality specifically with 0.826 AUC (95% CI: 0.797-0.852). The model also exhibited moderate, yet significant, accuracy in differentiating depressed from suicidal participants, with 0.609 AUC (95% CI 0.571-0.646). Discriminative patterns emerge more strongly when assessing the data relative to response generation than relative to the onset time of the final word of the sentences. The most pronounced effects were observed for negative-sentiment sentences, that are congruent to depressed and suicidal participants. Our findings highlight eye tracking as an objective tool for mental health assessment and underscore the modulatory impact of emotional stimuli on cognitive processes affecting oculomotor control.

cs.LG