Author name cluster

David van Dijk

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8 papers

2 author rows

ICLR Conference 2025 Conference Paper

Intelligence at the Edge of Chaos

Shiyang Zhang
Aakash Patel
Syed Asad Rizvi
Nianchen Liu
Sizhuang He
Amin Karbasi
Emanuele Zappala
David van Dijk

We explore the emergence of intelligent behavior in artificial systems by investigating how the complexity of rule-based systems influences the capabilities of models trained to predict these rules. Our study focuses on elementary cellular automata (ECA), simple yet powerful one-dimensional systems that generate behaviors ranging from trivial to highly complex. By training distinct Large Language Models (LLMs) on different ECAs, we evaluated the relationship between the complexity of the rules' behavior and the intelligence exhibited by the LLMs, as reflected in their performance on downstream tasks. Our findings reveal that rules with higher complexity lead to models exhibiting greater intelligence, as demonstrated by their performance on reasoning and chess move prediction tasks. Both uniform and periodic systems, and often also highly chaotic systems, resulted in poorer downstream performance, highlighting a sweet spot of complexity conducive to intelligence. We conjecture that intelligence arises from the ability to predict complexity and that creating intelligence may require only exposure to complexity.

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NeurIPS Conference 2025 Conference Paper

Non-Markovian Discrete Diffusion with Causal Language Models

Yangtian Zhang
Sizhuang He
Daniel Levine
Lawrence Zhao
David Zhang
Syed Rizvi
Shiyang Zhang
Emanuele Zappala

Discrete diffusion models offer a flexible, controllable approach to structured sequence generation, yet they still lag behind causal language models in expressive power. A key limitation lies in their reliance on the Markovian assumption, which restricts each step to condition only on the current state, leading to potential uncorrectable error accumulation. In this paper, We introduce CaDDi, a discrete diffusion model that conditions on the entire generative trajectory, thereby lifting the Markov constraint and allowing the model to revisit and improve past states. By unifying sequential (causal) and temporal (diffusion) reasoning in a single non‑Markovian transformer, CaDDi also treats standard causal language models as a special case and permits the direct reuse of pretrained LLM weights with no architectural changes. Empirically, CaDDi outperforms state‑of‑the‑art discrete diffusion baselines on natural‑language benchmarks, substantially narrowing the remaining gap to large autoregressive transformers.

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ICLR Conference 2024 Conference Paper

BrainLM: A foundation model for brain activity recordings

Josue Ortega Caro
Antonio Henrique de Oliveira Fonseca
Syed Asad Rizvi
Matteo Rosati
Christopher L. Averill
James L. Cross
Prateek Mittal
Emanuele Zappala

We introduce the Brain Language Model (BrainLM), a foundation model for brain activity dynamics trained on 6,700 hours of fMRI recordings. Utilizing self-supervised masked-prediction training, BrainLM demonstrates proficiency in both fine-tuning and zero-shot inference tasks. Fine-tuning allows for the accurate prediction of clinical variables like age, anxiety, and PTSD as well as forecasting of future brain states. Critically, the model generalizes well to entirely new external cohorts not seen during training. In zero-shot inference mode, BrainLM can identify intrinsic functional networks directly from raw fMRI data without any network-based supervision during training. The model also generates interpretable latent representations that reveal relationships between brain activity patterns and cognitive states. Overall, BrainLM offers a versatile and interpretable framework for elucidating the complex spatiotemporal dynamics of human brain activity. It serves as a powerful "lens" through which massive repositories of fMRI data can be analyzed in new ways, enabling more effective interpretation and utilization at scale. The work demonstrates the potential of foundation models to advance computational neuroscience research.

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ICML Conference 2024 Conference Paper

Cell2Sentence: Teaching Large Language Models the Language of Biology

Daniel LeVine
Syed Asad Rizvi
Sacha Lévy
Nazreen Pallikkavaliyaveetil
David Zhang
Xingyu Chen
Sina Ghadermarzi
Ruiming Wu

We introduce Cell2Sentence (C2S), a novel method to directly adapt large language models to a biological context, specifically single-cell transcriptomics. By transforming gene expression data into "cell sentences, " C2S bridges the gap between natural language processing and biology. We demonstrate cell sentences enable the fine-tuning of language models for diverse tasks in biology, including cell generation, complex cell-type annotation, and direct data-driven text generation. Our experiments reveal that GPT-2, when fine-tuned with C2S, can generate biologically valid cells based on cell type inputs, and accurately predict cell types from cell sentences. This illustrates that language models, through C2S fine-tuning, can acquire a significant understanding of single-cell biology while maintaining robust text generation capabilities. C2S offers a flexible, accessible framework to integrate natural language processing with transcriptomics, utilizing existing models and libraries for a wide range of biological applications.

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ICML Conference 2023 Conference Paper

Continuous Spatiotemporal Transformer

Antonio Henrique de Oliveira Fonseca
Emanuele Zappala
Josue Ortega Caro
David van Dijk

Modeling spatiotemporal dynamical systems is a fundamental challenge in machine learning. Transformer models have been very successful in NLP and computer vision where they provide interpretable representations of data. However, a limitation of transformers in modeling continuous dynamical systems is that they are fundamentally discrete time and space models and thus have no guarantees regarding continuous sampling. To address this challenge, we present the Continuous Spatiotemporal Transformer (CST), a new transformer architecture that is designed for modeling of continuous systems. This new framework guarantees a continuous and smooth output via optimization in Sobolev space. We benchmark CST against traditional transformers as well as other spatiotemporal dynamics modeling methods and achieve superior performance in a number of tasks on synthetic and real systems, including learning brain dynamics from calcium imaging data.

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AAAI Conference 2023 Conference Paper

Neural Integro-Differential Equations

Emanuele Zappala
Antonio H. de O. Fonseca
Andrew H. Moberly
Michael J. Higley
Chadi Abdallah
Jessica A. Cardin
David van Dijk

Modeling continuous dynamical systems from discretely sampled observations is a fundamental problem in data science. Often, such dynamics are the result of non-local processes that present an integral over time. As such, these systems are modeled with Integro-Differential Equations (IDEs); generalizations of differential equations that comprise both an integral and a differential component. For example, brain dynamics are not accurately modeled by differential equations since their behavior is non-Markovian, i.e. dynamics are in part dictated by history. Here, we introduce the Neural IDE (NIDE), a novel deep learning framework based on the theory of IDEs where integral operators are learned using neural networks. We test NIDE on several toy and brain activity datasets and demonstrate that NIDE outperforms other models. These tasks include time extrapolation as well as predicting dynamics from unseen initial conditions, which we test on whole-cortex activity recordings in freely behaving mice. Further, we show that NIDE can decompose dynamics into their Markovian and non-Markovian constituents, via the learned integral operator, which we test on fMRI brain activity recordings of people on ketamine. Finally, the integrand of the integral operator provides a latent space that gives insight into the underlying dynamics, which we demonstrate on wide-field brain imaging recordings. Altogether, NIDE is a novel approach that enables modeling of complex non-local dynamics with neural networks.

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AAAI Conference 2021 Conference Paper

Gaining Insight into SARS-CoV-2 Infection and COVID-19 Severity Using Self-supervised Edge Features and Graph Neural Networks

Arijit Sehanobish
Neal Ravindra
David van Dijk

A molecular and cellular understanding of how SARS-CoV- 2 variably infects and causes severe COVID-19 remains a bottleneck in developing interventions to end the pandemic. We sought to use deep learning (DL) to study the biology of SARS-CoV-2 infection and COVID-19 severity by identifying transcriptomic patterns and cell types associated with SARS-CoV-2 infection and COVID-19 severity. To do this, we developed a new approach to generating self-supervised edge features. We propose a model that builds on Graph Attention Networks (GAT), creates edge features using selfsupervised learning, and ingests these edge features via a Set Transformer. This model achieves significant improvements in predicting the disease state of individual cells, given their transcriptome. We apply our model to single-cell RNA sequencing datasets of SARS-CoV-2 infected lung organoids and bronchoalveolar lavage fluid samples of patients with COVID-19, achieving state-of-the-art performance on both datasets with our model. We then borrow from the field of explainable AI (XAI) to identify the features (genes) and cell types that discriminate bystander vs. infected cells across time and moderate vs. severe COVID-19 disease. To the best of our knowledge, this represents the first application of DL to identifying the molecular and cellular determinants of SARS- CoV-2 infection and COVID-19 severity using single-cell omics data.

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ICML Conference 2020 Conference Paper

TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics

Alexander Tong 0001
Jessie Huang
Guy Wolf
David van Dijk
Smita Krishnaswamy

It is increasingly common to encounter data in the form of cross-sectional population measurements over time, particularly in biomedical settings. Recent attempts to model individual trajectories from this data use optimal transport to create pairwise matchings between time points. However, these methods cannot model non-linear paths common in many underlying dynamic systems. We establish a link between continuous normalizing flows and dynamic optimal transport to model the expected paths of points over time. Continuous normalizing flows are generally under constrained, as they are allowed to take an arbitrary path from the source to the target distribution. We present \emph{TrajectoryNet}, which controls the continuous paths taken between distributions. We show how this is particularly applicable for studying cellular dynamics in data from single-cell RNA sequencing (scRNA-seq) technologies, and that TrajectoryNet improves upon recently proposed static optimal transport-based models that can be used for interpolating cellular distributions.

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