Publications

Models trained with self-supervised learning objectives have recently matched or surpassed models trained with traditional supervised object recognition in their ability to predict neural responses of object-selective neurons in the primate visual system. A self-supervised learning objective is arguably a more biologically plausible organizing principle, as the optimization does not require a large number of labeled examples. However, typical self-supervised objectives may result in network representations that are overly invariant to changes in the input. Here, we show that a representation with structured variability to input transformations is better aligned with known features of visual perception and neural computation. We introduce a novel framework for converting standard invariant SSL losses into “contrastive-equivariant” versions that encourage preservation of input transformations without supervised access to the transformation parameters. We demonstrate that our proposed method systematically increases the ability of models to predict responses in macaque inferior temporal cortex. Our results demonstrate the promise of incorporating known features of neural computation into task-optimization for building better models of visual cortex.

Quantifying differences across species and individuals is fundamental to many fields of biology. However, it remains challenging to draw detailed functional comparisons between large populations of interacting neurons. Here, we introduce a general framework for comparing neural population activity in terms of shape distances. This approach defines similarity in terms of explicit geometric transformations, which can be flexibly specified to obtain different measures of population-level neural similarity. Moreover, differences between systems are defined by a distance that is symmetric and satisfies the triangle inequality, enabling downstream analyses such as clustering and nearest-neighbor regression. We demonstrate this approach on datasets spanning multiple behavioral tasks (navigation, passive viewing of images, and decision making) and species (mice and non-human primates), highlighting its potential to measure functional variability across subjects and brain regions, as well as its ability to relate neural geometry to animal behavior.

Tensor network quantum states are powerful tools for strongly correlated systems, tailored to capture local correlations such as in ground states with entanglement area laws. When applying tensor network states to interacting fermionic systems, a proper choice of the basis or orbitals can reduce the bond dimension of tensors and provide physically relevant orbitals. We introduce such a change of basis with unitary gates obtained from compressing fermionic Gaussian states into quantum circuits corresponding to various tensor networks. These circuits can reduce the ground-state entanglement entropy and improve the performance of algorithms such as the density matrix renormalization group. We study the Anderson impurity model with one and two impurities to show the potential of the method for improving computational efficiency and interpreting impurity physics. Furthermore, fermionic Gaussian circuits can also suppress entanglement during the time evolution out of low-energy state. Last, we consider Gaussian multiscale entanglement renormalization ansatz (GMERA) circuits which compress fermionic Gaussian states hierarchically. The emergent coarse-grained physical models from these GMERA circuits are studied in terms of their entanglement properties and suitability for performing time evolution.

Neurons in the hippocampus are correlated with different variables, including space, time, sensory cues, rewards and actions, in which the extent of tuning depends on ongoing task demands1,2,3,4,5,6,7,8. However, it remains uncertain whether such diverse tuning corresponds to distinct functions within the hippocampal network or whether a more generic computation can account for these observations9. Here, to disentangle the contribution of externally driven cues versus internal computation, we developed a task in mice in which space, auditory tones, rewards and context were juxtaposed with changing relevance. High-density electrophysiological recordings revealed that neurons were tuned to each of these modalities. By comparing movement paths and action sequences, we observed that external variables had limited direct influence on hippocampal firing. Instead, spiking was influenced by online action plans and modulated by goal uncertainty. Our results suggest that internally generated cell assembly sequences are selected and updated by action plans towards deliberate goals. The apparent tuning of hippocampal neuronal spiking to different sensory modalities might emerge due to alignment to the afforded action progression within a task rather than representation of external cues.

A lack of tools for detecting receptor activity in vivo has limited our ability to fully explore receptor-level control of developmental patterning. Here, we extend a new class of biosensors for receptor tyrosine kinase (RTK) activity, the pYtag system, to visualize endogenous RTK activity in Drosophila. We build biosensors for three Drosophila RTKs that function across developmental stages and tissues. By characterizing Torso::pYtag during terminal patterning in the early embryo, we find that Torso activity differs from downstream ERK activity in two surprising ways: Torso activity is narrowly restricted to the poles but produces a broader gradient of ERK, and Torso activity decreases over developmental time while ERK activity is sustained. This decrease in Torso activity is driven by ERK pathway-dependent negative feedback. Our results suggest an updated model of terminal patterning where a narrow domain of Torso activity, tuned in amplitude by negative feedback, locally activates signaling effectors which diffuse through the syncytial embryo to form the ERK gradient. Altogether, this work highlights the usefulness of pYtags for investigating receptor-level regulation of developmental patterning.

Although optimal control (OC) has been studied in stochastic thermodynamics for systems with continuous state variables, less is known in systems with discrete state variables, such as chemical reaction networks (CRNs). Here, we develop a general theoretical framework to study OC of CRNs for changing the system from an initial distribution of states to a final distribution with minimum dissipation. We derive a “Kirchhoff’s law” for the probability current in the adiabatic limit, from which the optimal kinetic rates are determined analytically for any given probability trajectory allowed by local rate constraints. By using the optimal rates, we show that the total dissipation is determined by a 𝐿2-distance measure in the probability space and derive an analytical expression for the metric tensor that depends on the probability distribution, network topology, and capacity of each link. Minimizing the total dissipation leads to the geodesic trajectory in the probability space and the corresponding OC protocol is determined by the Kirchhoff’s law. To demonstrate our general approach, we use it to find a lower bound for the minimum dissipation that is tighter than existing bounds obtained with only global constraints in the adiabatic limit. We also apply it to simple networks, e.g., fully connected three-state CRNs with different local constraints and show that indirect pathway and nonfunctional transient state can play a crucial role in switching between different probability distributions efficiently. Future directions in studying OC in CRNs by using our general framework are discussed.

The centrosomal aster is a mobile and adaptable cellular organelle that exerts and transmits forces necessary for tasks such as nuclear migration and spindle positioning. Recent experimental and theoretical studies of nematode and human cells demonstrate that pulling forces on asters by cortically anchored force generators are dominant during such processes. Here, we present a comprehensive investigation of the S-model (S for stoichiometry) of aster dynamics based solely on such forces. The model evolves the astral centrosome position, a probability field of cell-surface motor occupancy by centrosomal microtubules (under an assumption of stoichiometric binding), and free boundaries of unattached, growing microtubules. We show how cell shape affects the stability of centering of the aster, and its transition to oscillations with increasing motor number. Seeking to understand observations in single-cell nematode embryos, we use highly accurate simulations to examine the nonlinear structures of the bifurcations, and demonstrate the importance of binding domain overlap to interpreting genetic perturbation experiments. We find a generally rich dynamical landscape, dependent upon cell shape, such as internal constant-velocity equatorial orbits of asters that can be seen as traveling wave solutions. Finally, we study the interactions of multiple asters which we demonstrate an effective mutual repulsion due to their competition for surface force generators. We find, amazingly, that centrosomes can relax onto the vertices of platonic and nonplatonic solids, very closely mirroring the results of the classical Thomson problem for energy-minimizing configurations of electrons constrained to a sphere and interacting via repulsive Coulomb potentials. Our findings both explain experimental observations, providing insights into the mechanisms governing spindle positioning and cell division dynamics, and show the possibility of new nonlinear phenomena in cell biology.

The 2024 New York City Integrative Structural Biology Symposium focused on understanding the challenges and opportunities of applying integrative structural biology techniques to biomedical research. To foster connections across different fields and disciplines, this symposium offered hands-on workshops. These workshops provided attendees an opportunity to use state-of-the-art instrumentation and software programs in the structural biology sciences that they may not have access to in their own laboratories. Moreover, the symposium provided a vibrant environment for scientific discourse where cutting-edge research talks presented the trends in integrative structural biology in the New York City area. In this TrendsTalk, the symposium organizers bring to you the highlights of the workshops and scientific sections from this event.

The discovery of superconductivity in twisted bilayer and twisted trilayer graphene has generated tremendous interest. The key feature of these systems is an interplay between interlayer coupling and a moiré superlattice that gives rise to low-energy flat bands with strong correlations. Flat bands can also be induced by moiré patterns in lattice-mismatched and or twisted heterostructures of other two-dimensional materials such as transition metal dichalcogenides (TMDs). Although a wide range of correlated phenomenon have indeed been observed in the moiré TMDs, robust demonstration of superconductivity has remained absent. Here we report superconductivity in 5 degree twisted bilayer WSe

We solve a model of electrons with Hubbard-U Coulomb repulsion and a random Yukawa coupling to a two-dimensional bosonic bath, using an extended dynamical mean field theory scheme. Our model exhibits a quantum critical point, at which the repulsive component of the electron interactions strongly enhances the effects of the quantum critical bosonic fluctuations on the electrons, leading to a breakdown of Fermi liquid physics and the formation of a strange metal with `Planckian' (O(k