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Shi Gu

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Published work

18 published item(s)

preprint2026arXiv

Knowledge Transfer Scaling Laws for 3D Medical Imaging

Vision foundation models are increasingly moving beyond 2D to volumetric domains such as 3D medical imaging, where unified pretraining across different imaging modalities (i.e. CT, MRI, and PET) could provide foundational models for diverse clinical tasks. However, training such models requires mixing heterogeneous imaging domains, and current mixture strategies remain largely heuristic. In this work, we observe that different medical imaging domains scale at variable rates during pretraining, and knowledge transfer between domains is strongly asymmetric: training on one domain can substantially improve another, but the reverse may be much weaker. Interestingly, both MAE reconstruction loss and cross-domain transfer follow predictable power-law trends with domain-specific behaviors. Motivated by these findings, we formulate data allocation as a scaling-law optimization problem. The derived allocations reveal an interpretable hub-and-island structure: highly transferable domains emerge as hubs that benefit many others and deserve strategic allocation, while isolated domains act as islands requiring direct investment. Empirically, transfer-aware allocation outperforms data-proportional sampling by up to 58% and generalizes well to unseen budgets with r=0.989. Downstream validation on disease classification and organ/lesion segmentation further confirms that the derived transfer-aware mixtures provide stronger pretrained representations for clinical 3D medical imaging tasks.

preprint2022arXiv

Control Theory Illustrates the Energy Efficiency in the Dynamic Reconfiguration of Functional Connectivity

The brain's functional connectivity fluctuates over time instead of remaining steady in a stationary mode even during the resting state. This fluctuation establishes the dynamical functional connectivity that transitions in a non-random order between multiple modes. Yet it remains unexplored how the transition facilitates the entire brain network as a dynamical system and what utility this mechanism for dynamic reconfiguration can bring over the widely used graph theoretical measurements. To address these questions, we propose to conduct an energetic analysis of functional brain networks using resting-state fMRI and behavioral measurements from the Human Connectome Project. Through comparing the state transition energy under distinct adjacent matrices, we justify that dynamic functional connectivity leads to 60% less energy cost to support the resting state dynamics than static connectivity when driving the transition through default mode network. Moreover, we demonstrate that combining graph theoretical measurements and our energy-based control measurements as the feature vector can provide complementary prediction power for the behavioral scores. Our approach integrates statistical inference and dynamical system inspection towards understanding brain networks.

preprint2022arXiv

Converting Artificial Neural Networks to Spiking Neural Networks via Parameter Calibration

Spiking Neural Network (SNN), originating from the neural behavior in biology, has been recognized as one of the next-generation neural networks. Conventionally, SNNs can be obtained by converting from pre-trained Artificial Neural Networks (ANNs) by replacing the non-linear activation with spiking neurons without changing the parameters. In this work, we argue that simply copying and pasting the weights of ANN to SNN inevitably results in activation mismatch, especially for ANNs that are trained with batch normalization (BN) layers. To tackle the activation mismatch issue, we first provide a theoretical analysis by decomposing local conversion error to clipping error and flooring error, and then quantitatively measure how this error propagates throughout the layers using the second-order analysis. Motivated by the theoretical results, we propose a set of layer-wise parameter calibration algorithms, which adjusts the parameters to minimize the activation mismatch. Extensive experiments for the proposed algorithms are performed on modern architectures and large-scale tasks including ImageNet classification and MS COCO detection. We demonstrate that our method can handle the SNN conversion with batch normalization layers and effectively preserve the high accuracy even in 32 time steps. For example, our calibration algorithms can increase up to 65% accuracy when converting VGG-16 with BN layers.

preprint2022arXiv

MixMix: All You Need for Data-Free Compression Are Feature and Data Mixing

User data confidentiality protection is becoming a rising challenge in the present deep learning research. Without access to data, conventional data-driven model compression faces a higher risk of performance degradation. Recently, some works propose to generate images from a specific pretrained model to serve as training data. However, the inversion process only utilizes biased feature statistics stored in one model and is from low-dimension to high-dimension. As a consequence, it inevitably encounters the difficulties of generalizability and inexact inversion, which leads to unsatisfactory performance. To address these problems, we propose MixMix based on two simple yet effective techniques: (1) Feature Mixing: utilizes various models to construct a universal feature space for generalized inversion; (2) Data Mixing: mixes the synthesized images and labels to generate exact label information. We prove the effectiveness of MixMix from both theoretical and empirical perspectives. Extensive experiments show that MixMix outperforms existing methods on the mainstream compression tasks, including quantization, knowledge distillation, and pruning. Specifically, MixMix achieves up to 4% and 20% accuracy uplift on quantization and pruning, respectively, compared to existing data-free compression work.

preprint2022arXiv

Temporal Efficient Training of Spiking Neural Network via Gradient Re-weighting

Recently, brain-inspired spiking neuron networks (SNNs) have attracted widespread research interest because of their event-driven and energy-efficient characteristics. Still, it is difficult to efficiently train deep SNNs due to the non-differentiability of its activation function, which disables the typically used gradient descent approaches for traditional artificial neural networks (ANNs). Although the adoption of surrogate gradient (SG) formally allows for the back-propagation of losses, the discrete spiking mechanism actually differentiates the loss landscape of SNNs from that of ANNs, failing the surrogate gradient methods to achieve comparable accuracy as for ANNs. In this paper, we first analyze why the current direct training approach with surrogate gradient results in SNNs with poor generalizability. Then we introduce the temporal efficient training (TET) approach to compensate for the loss of momentum in the gradient descent with SG so that the training process can converge into flatter minima with better generalizability. Meanwhile, we demonstrate that TET improves the temporal scalability of SNN and induces a temporal inheritable training for acceleration. Our method consistently outperforms the SOTA on all reported mainstream datasets, including CIFAR-10/100 and ImageNet. Remarkably on DVS-CIFAR10, we obtained 83$\%$ top-1 accuracy, over 10$\%$ improvement compared to existing state of the art. Codes are available at \url{https://github.com/Gus-Lab/temporal_efficient_training}.

preprint2021arXiv

Optimal Conversion of Conventional Artificial Neural Networks to Spiking Neural Networks

Spiking neural networks (SNNs) are biology-inspired artificial neural networks (ANNs) that comprise of spiking neurons to process asynchronous discrete signals. While more efficient in power consumption and inference speed on the neuromorphic hardware, SNNs are usually difficult to train directly from scratch with spikes due to the discreteness. As an alternative, many efforts have been devoted to converting conventional ANNs into SNNs by copying the weights from ANNs and adjusting the spiking threshold potential of neurons in SNNs. Researchers have designed new SNN architectures and conversion algorithms to diminish the conversion error. However, an effective conversion should address the difference between the SNN and ANN architectures with an efficient approximation \DSK{of} the loss function, which is missing in the field. In this work, we analyze the conversion error by recursive reduction to layer-wise summation and propose a novel strategic pipeline that transfers the weights to the target SNN by combining threshold balance and soft-reset mechanisms. This pipeline enables almost no accuracy loss between the converted SNNs and conventional ANNs with only $\sim1/10$ of the typical SNN simulation time. Our method is promising to get implanted onto embedded platforms with better support of SNNs with limited energy and memory.

preprint2020arXiv

Controllability Analysis of Functional Brain Networks

Network control theory has recently emerged as a promising approach for understanding brain function and dynamics. By operationalizing notions of control theory for brain networks, it offers a fundamental explanation for how brain dynamics may be regulated by structural connectivity. While powerful, the approach does not currently consider other non-structural explanations of brain dynamics. Here we extend the analysis of network controllability by formalizing the evolution of neural signals as a function of effective inter-regional coupling and pairwise signal covariance. We find that functional controllability characterizes a region's impact on the capacity for the whole system to shift between states, and significantly predicts individual difference in performance on cognitively demanding tasks including those task working memory, language, and emotional intelligence. When comparing measurements from functional and structural controllability, we observed consistent relations between average and modal controllability, supporting prior work. In the same comparison, we also observed distinct relations between controllability and synchronizability, reflecting the additional information obtained from functional signals. Our work suggests that network control theory can serve as a systematic analysis tool to understand the energetics of brain state transitions, associated cognitive processes, and subsequent behaviors.

preprint2018arXiv

On Structural Controllability of Symmetric (Brain) Networks

The question of controllability of natural and man-made network systems has recently received considerable attention. In the context of the human brain, the study of controllability may not only shed light into the organization and function of different neural circuits, but also inform the design and implementation of minimally invasive yet effective intervention protocols to treat neurological disorders. While the characterization of brain controllability is still in its infancy, some results have recently appeared and given rise to scientific debate. Among these, [1] has numerically shown that a class of brain networks constructed from DSI/DTI imaging data are controllable from one brain region. That is, a single brain region is theoretically capable of moving the whole brain network towards any desired target state. In this note we provide evidence supporting controllability of brain networks from a single region as discussed in [1], thus contradicting the main conclusion and methods developed in [2].

preprint2016arXiv

Autaptic Connections Shift Network Excitability and Bursting

Network architecture forms a critical constraint on neuronal function. Here we examine the role of structural autapses, when a neuron synapses onto itself, in driving network-wide bursting behavior. Using a simple spiking model of neuronal activity, we study how autaptic connections affect activity patterns, and evaluate if neuronal degree or controllability are significant factors that affect changes in bursting from these autaptic connections. We observed that adding increasing numbers of autaptic connections to excitatory neurons increased the number of spiking events in the network and the number of network-wide bursts, particularly in the portion of the phase space in which excitatory synapses were stronger contributors to bursting behavior than inhibitory synapses. In comparison, autaptic connections to excitatory neurons with high average controllability led to higher burst frequencies than adding the same number of self-looping connections to neurons with high modal controllability. The number of autaptic connections required to induce bursting behavior could be lowered by selectively adding autapses to high degree excitatory neurons. These results suggest a role of autaptic connections in controlling network-wide bursts in diverse cortical and subcortical regions of mammalian brain. Moreover, they open up new avenues for the study of dynamic neurophysiological correlates of structural controllability.

preprint2016arXiv

Cognitive Control in the Controllable Connectome

Cognition is supported by neurophysiological processes that occur both in local anatomical neighborhoods and in distributed large-scale circuits. Recent evidence from network control theory suggests that white matter pathways linking large-scale brain regions provide a critical substrate constraining the ability of single areas to affect control on those processes. Yet, no direct evidence exists for a relationship between brain network controllability and cognitive control performance. Here, we address this gap by constructing structural brain networks from diffusion tensor imaging data acquired in 125 healthy adult individuals. We define a simplified model of brain dynamics and simulate network control to quantify modal and boundary controllability, which together describe complementary features of a region's theoretically predicted preference to drive the brain into different cognitive states. We observe that individual differences in these control features derived from structural connectivity are significantly correlated with individual differences in cognitive control performance, as measured by a continuous performance attention test, a color/shape switching task, the Stroop inhibition task, and a spatial n-back working memory task. Indeed, control hubs like anterior cingulate are distinguished from default mode and frontal association areas in terms of the relationship between their control properties and individual differences in cognitive function. These results provide the first empirical evidence that network control forms a fundamental mechanism of cognitive control.

preprint2016arXiv

Explicitly Linking Regional Activation and Function Connectivity: Community Structure of Weighted Networks with Continuous Annotation

A major challenge in neuroimaging is understanding the mapping of neurophysiological dynamics onto cognitive functions. Traditionally, these maps have been constructed by examining changes in the activity magnitude of regions related to task performance. Recently, network neuroscience has produced methods to map connectivity patterns among many regions to certain cognitive functions by drawing on tools from network science and graph theory. However, these two different views are rarely addressed simultaneously, largely because few tools exist that account for patterns between nodes while simultaneously considering activation of nodes. We address this gap by solving the problem of community detection on weighted networks with continuous (non-integer) annotations by deriving a generative probabilistic model. This model generates communities whose members connect densely to nodes within their own community, and whose members share similar annotation values. We demonstrate the utility of the model in the context of neuroimaging data gathered during a motor learning paradigm, where edges are task-based functional connectivity and annotations to each node are beta weights from a general linear model that encoded a linear decrease in blood-oxygen-level-dependent signal with practice. Interestingly, we observe that individuals who learn at a faster rate exhibit the greatest dissimilarity between functional connectivity and activation magnitudes, suggesting that activation and functional connectivity are distinct dimensions of neurophysiology that track behavioral change. More generally, the tool that we develop offers an explicit, mathematically principled link between functional activation and functional connectivity, and can readily be applied to a other similar problems in which one set of imaging data offers network data, and a second offers a regional attribute.

preprint2016arXiv

Functional Hypergraph Uncovers Novel Covariant Structures over Neurodevelopment

Brain development during adolescence is marked by substantial changes in brain structure and function, leading to a stable network topology in adulthood. However, most prior work has examined the data through the lens of brain areas connected to one another in large-scale functional networks. Here, we apply a recently-developed hypergraph approach that treats network connections (edges) rather than brain regions as the unit of interest, allowing us to describe functional network topology from a fundamentally different perspective. Capitalizing on a sample of 780 youth imaged as part of the Philadelphia Neurodevelopmental Cohort, this hypergraph representation of resting-state functional MRI data reveals three distinct classes of sub-networks (hyperedges): clusters, bridges, and stars, which represent spatially distributed, bipartite, and focal architectures, respectively. Cluster hyperedges show a strong resemblance to the functional modules of the brain including somatomotor, visual, default mode, and salience systems. In contrast, star hyperedges represent highly localized subnetworks centered on a small set of regions, and are distributed across the entire cortex. Finally, bridge hyperedges link clusters and stars in a core-periphery organization. Notably, developmental changes within hyperedges are ordered in a similar core-periphery fashion, with the greatest developmental effects occurring in networked hyperedges within the functional core. Taken together, these results emphasize that the network organization of human brain emerges across multiple scales and evolves substantially through the adolescent period.

preprint2016arXiv

Optimally controlling the human connectome: the role of network topology

To meet ongoing cognitive demands, the human brain must seamlessly transition from one brain state to another, in the process drawing on different cognitive systems. How does the brain's network of anatomical connections help facilitate such transitions? Which features of this network contribute to making one transition easy and another transition difficult? Here, we address these questions using network control theory. We calculate the optimal input signals to drive the brain to and from states dominated by different cognitive systems. The input signals allow us to assess the contributions made by different brain regions. We show that such contributions, which we measure as energy, are correlated with regions' weighted degrees. We also show that the network communicability, a measure of direct and indirect connectedness between brain regions, predicts the extent to which brain regions compensate when input to another region is suppressed. Finally, we identify optimal states in which the brain should start (and finish) in order to minimize transition energy. We show that the optimal target states display high activity in hub regions, implicating the brain's rich club. Furthermore, when rich club organization is destroyed, the energy cost associated with state transitions increases significantly, demonstrating that it is the richness of brain regions that makes them ideal targets.

preprint2016arXiv

Stimulation-based control of dynamic brain networks

The ability to modulate brain states using targeted stimulation is increasingly being employed to treat neurological disorders and to enhance human performance. Despite the growing interest in brain stimulation as a form of neuromodulation, much remains unknown about the network-level impact of these focal perturbations. To study the system wide impact of regional stimulation, we employ a data-driven computational model of nonlinear brain dynamics to systematically explore the effects of targeted stimulation. Validating predictions from network control theory, we uncover the relationship between regional controllability and the focal versus global impact of stimulation, and we relate these findings to differences in the underlying network architecture. Finally, by mapping brain regions to cognitive systems, we observe that the default mode system imparts large global change despite being highly constrained by structural connectivity. This work forms an important step towards the development of personalized stimulation protocols for medical treatment or performance enhancement.

preprint2016arXiv

The Energy Landscape of Neurophysiological Activity Implicit in Brain Network Structure

A critical mystery in neuroscience lies in determining how anatomical structure impacts the complex functional dynamics of human thought. How does large-scale brain circuitry constrain states of neuronal activity and transitions between those states? We address these questions using a maximum entropy model of brain dynamics informed by white matter tractography. We demonstrate that the most probable brain states -- characterized by minimal energy -- display common activation profiles across brain areas: local spatially-contiguous sets of brain regions reminiscent of cognitive systems are co-activated frequently. The predicted activation rate of these systems is highly correlated with the observed activation rate measured in a separate resting state fMRI data set, validating the utility of the maximum entropy model in describing neurophysiologial dynamics. This approach also offers a formal notion of the energy of activity within a system, and the energy of activity shared between systems. We observe that within- and between-system energies cleanly separate cognitive systems into distinct categories, optimized for differential contributions to integrated v.s. segregated function. These results support the notion that energetic and structural constraints circumscribe brain dynamics, offering novel insights into the roles that cognitive systems play in driving whole-brain activation patterns.

preprint2016arXiv

The Energy Landscape Underpinning Module Dynamics in the Human Brain Connectome

Human brain dynamics can be profitably viewed through the lens of statistical mechanics, where neurophysiological activity evolves around and between local attractors representing preferred mental states. Many physically-inspired models of these dynamics define the state of the brain based on instantaneous measurements of regional activity. Yet, recent work in network neuroscience has provided initial evidence that the brain might also be well-characterized by time-varying states composed of locally coherent activity or functional modules. Here we study this network-based notion of brain state to understand how functional modules dynamically interact with one another to perform cognitive functions. We estimate the functional relationships between regions of interest (ROIs) by fitting a pair-wise maximum entropy model to each ROI's pattern of allegiance to functional modules. Local minima in this model represent attractor states characterized by specific patterns of modular structure. The clustering of local minima highlights three classes of ROIs with similar patterns of allegiance to community states. Visual, attention, sensorimotor, and subcortical ROIs tend to form a single functional community. The remaining ROIs tend to form a putative executive control community or a putative default mode and salience community. We simulate the brain's dynamic transitions between these community states using a Markov Chain Monte Carlo random walk. We observe that simulated transition probabilities between basins resemble empirically observed transitions between community allegiance states in resting state fMRI data. These results collectively offer a view of the brain as a dynamical system that transitions between basins of attraction characterized by coherent activity in small groups of brain regions, and that the strength of these attractors depends on the cognitive computations being performed.

preprint2014arXiv

Controllability of Brain Networks

Cognitive function is driven by dynamic interactions between large-scale neural circuits or networks, enabling behavior. Fundamental principles constraining these dynamic network processes have remained elusive. Here we use network control theory to offer a mechanistic explanation for how the brain moves between cognitive states drawn from the network organization of white matter microstructure. Our results suggest that densely connected areas, particularly in the default mode system, facilitate the movement of the brain to many easily-reachable states. Weakly connected areas, particularly in cognitive control systems, facilitate the movement of the brain to difficult-to-reach states. Areas located on the boundary between network communities, particularly in attentional control systems, facilitate the integration or segregation of diverse cognitive systems. Our results suggest that structural network differences between the cognitive circuits dictate their distinct roles in controlling dynamic trajectories of brain network function.

preprint2010arXiv

Phase Conjugation and Negative Refraction Using Nonlinear Active Metamaterials

We present experimental demonstration of phase conjugation using nonlinear metamaterial elements. Active split-ring resonators loaded with varactor diodes are demonstrated theoretically to act as phase-conjugating or time-reversing discrete elements when parametrically pumped and illuminated with appropriate frequencies. The metamaterial elements were fabricated and shown experimentally to produce a time reversed signal. Measurements confirm that a discrete array of phase-conjugating elements act as a negatively-refracting time reversal RF lens only 0.12$λ$ thick.