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Efficiently exploring complex loss landscapes is key to the performance of deep neural networks. While momentum-based optimizers are widely … (voir plus)used in state-of-the-art setups, classical momentum can still struggle with large, misaligned gradients, leading to oscillations. To address this, we propose Torque-Aware Momentum (TAM), which introduces a damping factor based on the angle between the new gradients and previous momentum, stabilizing the update direction during training. Empirical results show that TAM, which can be combined with both SGD and Adam, enhances exploration, handles distribution shifts more effectively, and improves generalization performance across various tasks, including image classification and large language model fine-tuning, when compared to classical momentum-based optimizers.
Creativity is a cornerstone of human evolution and is typically defined as the multifaceted ability to produce novel and useful artifacts. A… (voir plus)lthough much research has focused on divergent thinking, growing evidence underscores the importance of perceptual processing in fostering creativity, particularly through perceptual flexibility. The present work aims to offer a framework that relates creativity to perception, showing how sensory affordances, especially in ambiguous stimuli, can contribute to the generation of novel ideas. In doing so, we contextualize the phenomenon of pareidolia, which involves seeing familiar patterns in noisy or ambiguous stimuli, as a key perceptual mechanism of idea generation—one of the central stages of the creative process. We introduce “divergent perception” to describe the process by which individuals actively engage with the perceptual affordances provided by ambiguous sensory information, and illustrate how this concept could account for the heightened creativity observed in psychedelic and psychotic states. Moreover, we explore how divergent perception relates to cognitive mechanisms crucial in creative thinking, particularly focusing on the role of attention. Finally, we discuss future paths for the exploration of divergent perception, including targeted manipulation of stimulus characteristics and the investigation of the intricate interplay between bottom‐up and top‐down cognitive processes.
Annotating chromatin loops is essential for understanding the 3D genome’s role in gene regulation, but current methods struggle with low c… (voir plus)overage, particularly in single-cell datasets. Chromatin loops are kilo-to mega-range structures that exhibit broader features, such as co-occurring loops, stripes, and domain boundaries along axial directions of Hi-C contact maps. However, existing tools primarily focus on detecting localized, highly-concentrated, interactions. Furthermore, the wide variety of available chromatin conformation datasets is rarely utilized in developing effective loop callers. Here, we present Polaris, a universal tool that integrates axial attention with a U-shaped backbone to accurately detect loops across different 3D genome assays. By leveraging extensive Hi-C contact maps in a pretrain-finetune paradigm, Polaris achieves consistent performance across various datasets. We compare Polaris against existing tools in loop annotation from both bulk and single-cell data and find that Polaris outperforms other programs across different cell types, species, sequencing depths, and assays.
Large language models (LLMs) possess vast semantic knowledge but often struggle with complex reasoning tasks, particularly in relational rea… (voir plus)soning problems such as kinship or spatial reasoning. In this paper, we present Path-of-Thoughts (PoT), a novel framework designed to tackle relation reasoning by decomposing the task into three key stages: graph extraction, path identification, and reasoning. Unlike previous approaches, PoT efficiently extracts a task-agnostic graph that identifies crucial entities, relations, and attributes within the problem context. Subsequently, PoT identifies relevant reasoning chains within the graph corresponding to the posed question, facilitating inference of potential answers. Experimental evaluations on four benchmark datasets, demanding long reasoning chains, demonstrate that PoT surpasses state-of-the-art baselines by a significant margin (maximum 21.3%) without necessitating fine-tuning or extensive LLM calls. Furthermore, as opposed to prior neuro-symbolic methods, PoT exhibits improved resilience against LLM errors by leveraging the compositional nature of graphs.
Large language models (LLMs) possess vast semantic knowledge but often struggle with complex reasoning tasks, particularly in relational rea… (voir plus)soning problems such as kinship or spatial reasoning. In this paper, we present Path-of-Thoughts (PoT), a novel framework designed to tackle relation reasoning by decomposing the task into three key stages: graph extraction, path identification, and reasoning. Unlike previous approaches, PoT efficiently extracts a task-agnostic graph that identifies crucial entities, relations, and attributes within the problem context. Subsequently, PoT identifies relevant reasoning chains within the graph corresponding to the posed question, facilitating inference of potential answers. Experimental evaluations on four benchmark datasets, demanding long reasoning chains, demonstrate that PoT surpasses state-of-the-art baselines by a significant margin (maximum 21.3%) without necessitating fine-tuning or extensive LLM calls. Furthermore, as opposed to prior neuro-symbolic methods, PoT exhibits improved resilience against LLM errors by leveraging the compositional nature of graphs.
Ensuring long-term fairness is crucial when developing automated decision making systems, specifically in dynamic and sequential environment… (voir plus)s. By maximizing their reward without consideration of fairness, AI agents can introduce disparities in their treatment of groups or individuals. In this paper, we establish the connection between bisimulation metrics and group fairness in reinforcement learning. We propose a novel approach that leverages bisimulation metrics to learn reward functions and observation dynamics, ensuring that learners treat groups fairly while reflecting the original problem. We demonstrate the effectiveness of our method in addressing disparities in sequential decision making problems through empirical evaluation on a standard fairness benchmark consisting of lending and college admission scenarios.
Ensuring long-term fairness is crucial when developing automated decision making systems, specifically in dynamic and sequential environment… (voir plus)s. By maximizing their reward without consideration of fairness, AI agents can introduce disparities in their treatment of groups or individuals. In this paper, we establish the connection between bisimulation metrics and group fairness in reinforcement learning. We propose a novel approach that leverages bisimulation metrics to learn reward functions and observation dynamics, ensuring that learners treat groups fairly while reflecting the original problem. We demonstrate the effectiveness of our method in addressing disparities in sequential decision making problems through empirical evaluation on a standard fairness benchmark consisting of lending and college admission scenarios.
Time-series studies are critical for uncovering dynamic biological processes, but achieving comprehensive profiling and resolution across mu… (voir plus)ltiple time points and modalities (multi-omics) remains challenging due to cost and scalability constraints. Current methods for studying temporal dynamics, whether at the bulk or single-cell level, often require extensive sampling, making it impractical to deeply profile all time points and modalities. To overcome these limitations, we present DTPSP, a deep learning framework designed to identify the most informative time points in any time-series study, enabling resource-efficient and targeted analyses. DTPSP models temporal gene expression patterns using readily obtainable data, such as bulk RNA-seq, to select time points that capture key system dynamics. It also integrates a deep generative module to infer data for non-sampled time points based on the selected time points, reconstructing the full temporal trajectory. This dual capability enables DTPSP to prioritize key time points for in-depth profiling, such as single-cell sequencing or multi-omics analyses, while filling gaps in the temporal landscape with high fidelity. We apply DTPSP to developmental and disease-associated time courses, demonstrating its ability to optimize experimental designs across bulk and single-cell studies. By reducing costs, enabling strategic multi-omics profiling, and enhancing biological insights, DTPSP provides a scalable and generalized solution for investigating dynamic systems.
In single-cell sequencing analysis, several computational methods have been developed to map the cellular state space, but little has been d… (voir plus)one to map or create embeddings of the gene space. Here, we formulate the gene embedding problem, design tasks with simulated single-cell data to evaluate representations, and establish ten relevant baselines. We then present a graph signal processing approach we call gene signal pattern analysis (GSPA) that learns rich gene representations from single-cell data using a dictionary of diffusion wavelets on the cell-cell graph. GSPA enables characterization of genes based on their patterning on the cellular manifold. It also captures how localized or diffuse the expression of a gene is, for which we present a score called the gene localization score. We motivate and demonstrate the efficacy of GSPA as a framework for a range of biological tasks, such as capturing gene coexpression modules, condition-specific enrichment, and perturbation-specific gene-gene interactions. Then, we showcase the broad utility of gene rep-resentations derived from GSPA, including for cell-cell communication (GSPA-LR), spatial transcriptomics (GSPA-multimodal), and patient response (GSPA-Pt) analysis.
One of the most fundamental laws of physics is the principle of least action. Motivated by its predictive power, we introduce a neuronal lea… (voir plus)st-action principle for cortical processing of sensory streams to produce appropriate behavioural outputs in real time. The principle postulates that the voltage dynamics of cortical pyramidal neurons prospectively minimize the local somato-dendritic mismatch error within individual neurons. For motor output neurons, it implies minimizing an instantaneous behavioural error. For deep network neurons, it implies a prospective firing to overcome integration delays and correct for possible output errors right in time. The neuron-specific errors are extracted in the apical dendrites of pyramidal neurons through a cortical microcircuit that tries to explain away the feedback from the periphery, and correct the trajectory on the fly. Any motor output is in a moving equilibrium with the sensory inputs and the motor feedback during the whole sensory-motor trajectory. Ongoing synaptic plasticity reduces the somato-dendritic mismatch error within each cortical neuron and performs gradient descent on the output cost at any moment in time. The neuronal least-action principle offers an axiomatic framework to derive local neuronal and synaptic dynamics for global real-time computation and learning in the brain and in physical substrates in general.
