http://jultika.oulu.fi/files/nbnfi-fe2021090645179.pdf

A Review of Uncertainty Quantification in Deep Learning: Techniques, Applications and Challenges

Approximate Methods In Optimization Problems

We present energy-based generative flow networks (EB-GFN), a novel probabilistic modeling algorithm for high-dimensional discrete data. Building upon the theory of generative flow networks (GFlowNets), we model the generation process by a stochastic data construction policy and thus amortize expensive MCMC exploration into a fixed number of actions sampled from a GFlowNet. We show how GFlowNets can approximately perform large-block Gibbs sampling to mix between modes. We propose a framework to jointly train a GFlowNet with an energy function, so that the GFlowNet learns to sample from the energy distribution, while the energy learns with an approximate MLE objective with negative samples from the GFlowNet. We demonstrate EB-GFN's effectiveness on various probabilistic modeling tasks. Code is publicly available at https://github.com/zdhNarsil/EB_GFN.

Generative Flow Networks for Discrete Probabilistic Modeling

Generative flow networks (GFlowNets) are a method for learning a stochastic policy for generating compositional objects, such as graphs or strings, from a given unnormalized density by sequences of actions, where many possible action sequences may lead to the same object. We find previously proposed learning objectives for GFlowNets, flow matching and detailed balance, which are analogous to temporal difference learning, to be prone to inefficient credit propagation across long action sequences. We thus propose a new learning objective for GFlowNets, trajectory balance, as a more efficient alternative to previously used objectives. We prove that any global minimizer of the trajectory balance objective can define a policy that samples exactly from the target distribution. In experiments on four distinct domains, we empirically demonstrate the benefits of the trajectory balance objective for GFlowNet convergence, diversity of generated samples, and robustness to long action sequences and large action spaces.

Trajectory Balance: Improved Credit Assignment in GFlowNets

We develop parallel and distributed Frank-Wolfe algorithms; the former on shared memory machines with mini-batching, and the latter in a delayed update framework. Whenever possible, we perform computations asynchronously, which helps attain speedups on multicore machines as well as in distributed environments. Moreover, instead of worst-case bounded delays, our methods only depend (mildly) on \emph{expected} delays, allowing them to be robust to stragglers and faulty worker threads. Our algorithms assume block-separable constraints, and subsume the recent Block-Coordinate Frank-Wolfe (BCFW) method~\citep{lacoste2013block}. Our analysis reveals problem-dependent quantities that govern the speedups of our methods over BCFW. We present experiments on structural SVM and Group Fused Lasso, obtaining significant speedups over competing state-of-the-art (and synchronous) methods.

Parallel and Distributed Block-Coordinate Frank-Wolfe Algorithms

Design of de novo biological sequences with desired properties, like protein and DNA sequences, often involves an active loop with several rounds of molecule ideation and expensive wet-lab evaluations. These experiments can consist of multiple stages, with increasing levels of precision and cost of evaluation, where candidates are filtered. This makes the diversity of proposed candidates a key consideration in the ideation phase. In this work, we propose an active learning algorithm leveraging epistemic uncertainty estimation and the recently proposed GFlowNets as a generator of diverse candidate solutions, with the objective to obtain a diverse batch of useful (as defined by some utility function, for example, the predicted anti-microbial activity of a peptide) and informative candidates after each round. We also propose a scheme to incorporate existing labeled datasets of candidates, in addition to a reward function, to speed up learning in GFlowNets. We present empirical results on several biological sequence design tasks, and we find that our method generates more diverse and novel batches with high scoring candidates compared to existing approaches.

Biological Sequence Design with GFlowNets

Generative flow networks (GFlowNets) are a family of algorithms for training a sequential sampler of discrete objects under an unnormalized target density and have been successfully used for various probabilistic modeling tasks. Existing training objectives for GFlowNets are either local to states or transitions, or propagate a reward signal over an entire sampling trajectory. We argue that these alternatives represent opposite ends of a gradient bias-variance tradeoff and propose a way to exploit this tradeoff to mitigate its harmful effects. Inspired by the TD($\lambda$) algorithm in reinforcement learning, we introduce subtrajectory balance or SubTB($\lambda$), a GFlowNet training objective that can learn from partial action subsequences of varying lengths. We show that SubTB($\lambda$) accelerates sampler convergence in previously studied and new environments and enables training GFlowNets in environments with longer action sequences and sparser reward landscapes than what was possible before. We also perform a comparative analysis of stochastic gradient dynamics, shedding light on the bias-variance tradeoff in GFlowNet training and the advantages of subtrajectory balance.

Learning GFlowNets from partial episodes for improved convergence and stability

Epistemic uncertainty is the part of out-of-sample prediction error due to the lack of knowledge of the learner. Whereas previous work was focusing on model variance, we propose a principled approach for directly estimating epistemic uncertainty by learning to predict generalization error and subtracting an estimate of aleatoric uncertainty, i.e., intrinsic unpredictability. This estimator of epistemic uncertainty includes the effect of model bias and can be applied in non-stationary learning environments arising in active learning or reinforcement learning. In addition to demonstrating these properties of Direct Epistemic Uncertainty Prediction (DEUP), we illustrate its advantage against existing methods for uncertainty estimation on downstream tasks including sequential model optimization and reinforcement learning. We also evaluate the quality of uncertainty estimates from DEUP for probabilistic classification of images and for estimating uncertainty about synergistic drug combinations.

DEUP: Direct Epistemic Uncertainty Prediction

Continuous normalizing ﬂows (CNFs) are an at-tractive generative modeling technique, but they have thus far been held back by limitations in their simulation-based maximum likelihood training. In this paper, we introduce a new technique called conditional ﬂow matching (CFM), a simulation-free training objective for CNFs. CFM features a stable regression objective like that used to train the stochastic ﬂow in diffusion models but en-joys the efﬁcient inference of deterministic ﬂow models. In contrast to both diffusion models and prior CNF training algorithms, our CFM objective does not require the source distribution to be Gaussian or require evaluation of its density. Based on this new objective, we also introduce optimal transport CFM (OT-CFM), which creates simpler ﬂows that are more stable to train and lead to faster inference, as evaluated in our experiments. Training CNFs with CFM improves results on a variety of conditional and unconditional generation tasks such as inferring single cell dynamics, unsupervised image translation, and Schr ¨ odinger bridge inference. Code is avail-able at https://github.com/atong01/ conditional-flow-matching .

Conditional Flow Matching: Simulation-Free Dynamic Optimal Transport

We revisit the Frank-Wolfe (FW) optimization under strongly convex constraint sets. We provide a faster convergence rate for FW without line search, showing that a previously overlooked variant of FW is indeed faster than the standard variant. With line search, we show that FW can converge to the global optimum, even for smooth functions that are not convex, but are quasi-convex and locally-Lipschitz. We also show that, for the general case of (smooth) non-convex functions, FW with line search converges with high probability to a stationary point at a rate of O(1/t), as long as the constraint set is strongly convex—one of the fastest convergence rates in non-convex optimization.

/pdf/revisiting-projection-free-optimization-for-strongly-convex-2e8lqzhq3j.pdf

Jarrid Rector-Brooks

Papers

Biological Sequence Design with GFlowNets

Learning GFlowNets from partial episodes for improved convergence and stability

DEUP: Direct Epistemic Uncertainty Prediction

Conditional Flow Matching: Simulation-Free Dynamic Optimal Transport

Revisiting Projection-Free Optimization for Strongly Convex Constraint Sets