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Timewarp: Transferable Acceleration of Molecular Dynamics by Learning Time-Coarsened Dynamics

Neural Information Processing Systems

MD is often used to compute equilibrium properties, which requires sampling from an equilibrium distribution such as the Boltzmann distribution. However, many important processes, such as binding and folding, occur over timescales of milliseconds or beyond, and cannot be efficiently sampled with conventional MD.Furthermore, new MD simulations need to be performed for each molecular system studied.We present *Timewarp*, an enhanced sampling method which uses a normalising flow as a proposal distribution in a Markov chain Monte Carlo method targeting the Boltzmann distribution. The flow is trained offline on MD trajectories and learns to make large steps in time, simulating the molecular dynamics of $10^{5} - 10^{6} \textrm{fs}$.Crucially, Timewarp is *transferable* between molecular systems: once trained, we show that it generalises to unseen small peptides (2-4 amino acids) at all-atom resolution, exploring their metastable states and providing wall-clock acceleration of sampling compared to standard MD.Our method constitutes an important step towards general, transferable algorithms for accelerating MD.


Towards a Zero-One Law for Column Subset Selection

Neural Information Processing Systems

There are a number of approximation algorithms for NP-hard versions of low rank approximation, such as finding a rank-$k$ matrix $B$ minimizing the sum of absolute values of differences to a given $n$-by-$n$ matrix $A$, $\min_{\textrm{rank-}k~B}\|A-B\|_1$, or more generally finding a rank-$k$ matrix $B$ which minimizes the sum of $p$-th powers of absolute values of differences, $\min_{\textrm{rank-}k~B}\|A-B\|_p^p$. Many of these algorithms are linear time columns subset selection algorithms, returning a subset of $\poly(k \log n)$ columns whose cost is no more than a $\poly(k)$ factor larger than the cost of the best rank-$k$ matrix.



Learning (Very) Simple Generative Models Is Hard

Neural Information Processing Systems

Motivated by the recent empirical successes of deep generative models, we study the computational complexity of the following unsupervised learning problem.


(\textrm{Implicit}) 2 : Implicit Layers for Implicit Representations

Neural Information Processing Systems

Recent research in deep learning has investigated two very different forms of ''implicitness'': implicit representations model high-frequency data such as images or 3D shapes directly via a low-dimensional neural network (often using e.g., sinusoidal bases or nonlinearities); implicit layers, in contrast, refer to techniques where the forward pass of a network is computed via non-linear dynamical systems, such as fixed-point or differential equation solutions, with the backward pass computed via the implicit function theorem. In this work, we demonstrate that these two seemingly orthogonal concepts are remarkably well-suited for each other. In particular, we show that by exploiting fixed-point implicit layer to model implicit representations, we can substantially improve upon the performance of the conventional explicit-layer-based approach. Additionally, as implicit representation networks are typically trained in large-batch settings, we propose to leverage the property of implicit layers to amortize the cost of fixed-point forward/backward passes over training steps -- thereby addressing one of the primary challenges with implicit layers (that many iterations are required for the black-box fixed-point solvers). We empirically evaluated our method on learning multiple implicit representations for images, videos and audios, showing that our $(\textrm{Implicit})^2$ approach substantially improve upon existing models while being both faster to train and much more memory efficient.


Reviews: Causal Confusion in Imitation Learning

Neural Information Processing Systems

Summary: This paper has a very interesting claim: distributional shift in imitation learning settings is primarily caused by causal misidentification of the features by the learning algorithm. An interesting example is that of a self-driving car policy trained on a dataset of paired image-control datapoints collected by an expert human driving the car. If the images contain the turn signal on the dashboard then the supervised learner learns to have very good predictive power by indexing on that feature in the image. Clearly that does not generalize during test time. While this is a pathological example, such behavior is present in most settings where usually the state is blown-up by appending past states and actions.


Timewarp: Transferable Acceleration of Molecular Dynamics by Learning Time-Coarsened Dynamics

Neural Information Processing Systems

MD is often used to compute equilibrium properties, which requires sampling from an equilibrium distribution such as the Boltzmann distribution. However, many important processes, such as binding and folding, occur over timescales of milliseconds or beyond, and cannot be efficiently sampled with conventional MD.Furthermore, new MD simulations need to be performed for each molecular system studied.We present *Timewarp*, an enhanced sampling method which uses a normalising flow as a proposal distribution in a Markov chain Monte Carlo method targeting the Boltzmann distribution. The flow is trained offline on MD trajectories and learns to make large steps in time, simulating the molecular dynamics of 10 {5} - 10 {6} \textrm{fs} .Crucially, Timewarp is *transferable* between molecular systems: once trained, we show that it generalises to unseen small peptides (2-4 amino acids) at all-atom resolution, exploring their metastable states and providing wall-clock acceleration of sampling compared to standard MD.Our method constitutes an important step towards general, transferable algorithms for accelerating MD.


Learning (Very) Simple Generative Models Is Hard

Neural Information Processing Systems

Motivated by the recent empirical successes of deep generative models, we study the computational complexity of the following unsupervised learning problem. We show under the statistical query (SQ) model that no polynomial-time algorithm can solve this problem even when the output coordinates of F are one-hidden-layer ReLU networks with \log(d) neurons. Previously, the best lower bounds for this problem simply followed from lower bounds for *supervised learning* and required at least two hidden layers and \textrm{poly}(d) neurons [Daniely-Vardi '21, Chen-Gollakota-Klivans-Meka '22]. The key ingredient in our proof is an ODE-based construction of a compactly supported, piecewise-linear function f with polynomially-bounded slopes such that the pushforward of \mathcal{N}(0,1) under f matches all low-degree moments of \mathcal{N}(0,1) .


Towards a Zero-One Law for Column Subset Selection

Neural Information Processing Systems

There are a number of approximation algorithms for NP-hard versions of low rank approximation, such as finding a rank- k matrix B minimizing the sum of absolute values of differences to a given n -by- n matrix A, \min_{\textrm{rank-}k B}\ A-B\ _1, or more generally finding a rank- k matrix B which minimizes the sum of p -th powers of absolute values of differences, \min_{\textrm{rank-}k B}\ A-B\ _p p . Many of these algorithms are linear time columns subset selection algorithms, returning a subset of \poly(k \log n) columns whose cost is no more than a \poly(k) factor larger than the cost of the best rank- k matrix. The above error measures are special cases of the following general entrywise low rank approximation problem: given an arbitrary function g:\mathbb{R} \rightarrow \mathbb{R}_{\geq 0}, find a rank- k matrix B which minimizes \ A-B\ _g \sum_{i,j}g(A_{i,j}-B_{i,j}) . A natural question is which functions g admit efficient approximation algorithms? Indeed, this is a central question of recent work studying generalized low rank models.


Tight Dimensionality Reduction for Sketching Low Degree Polynomial Kernels

Neural Information Processing Systems

We revisit the classic randomized sketch of a tensor product of q vectors x_i\in\mathbb{R} n . However, in their analysis C_{\Omega} 2 can be as large as \Theta(n {2q}), even for a set \Omega of O(1) vectors x . We give a new analysis of this sketch, providing nearly optimal bounds. For the important case of q 2 and \delta 1/\poly(n), this shows that m \Theta(\epsilon {-2} \log(n) \epsilon {-1} \log 2(n)), demonstrating that the \epsilon {-2} and \log 2(n) terms do not multiply each other. In a number of applications, one has \Omega \poly(n) and in this case our bounds are optimal up to a constant factor.