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- ShortScience.org is a platform for post-publication discussion aiming to improve accessibility and reproducibility of research ideas.
- The website has 1584 public summaries, mostly in machine learning, written by the community and organized by paper, conference, and year.
- Reading summaries of papers is useful to obtain the perspective and insight of another reader, why they liked or disliked it, and their attempt to demystify complicated sections.
- Also, writing summaries is a good exercise to understand the content of a paper because you are forced to challenge your assumptions when explaining it.
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Automatic chemical design using a data-driven continuous representation of molecules

Gómez-Bombarelli, Rafael and Duvenaud, David and Hernández-Lobato, José Miguel and Aguilera-Iparraguirre, Jorge and Hirzel, Timothy D. and Adams, Ryan P. and Aspuru-Guzik, Alán

arXiv e-Print archive - 2016 via Local Bibsonomy

Keywords: dblp

Gómez-Bombarelli, Rafael and Duvenaud, David and Hernández-Lobato, José Miguel and Aguilera-Iparraguirre, Jorge and Hirzel, Timothy D. and Adams, Ryan P. and Aspuru-Guzik, Alán

arXiv e-Print archive - 2016 via Local Bibsonomy

Keywords: dblp

[link]
I'll admit that I found this paper a bit of a letdown to read, relative to expectations rooted in its high citation count, and my general excitement and interest to see how deep learning could be brought to bear on molecular design. But before a critique, let's first walk through the mechanics of how the authors' approach works. The method proposed is basically a very straightforward Variational Auto Encoder, or VAE. It takes in a textual SMILES string representation of a molecular structure, uses an encoder to map that into a continuous vector representation, a decoder to map the vector representation back into a a SMILES string, and an auxiliary predictor to predict properties of a molecule given the continuous representation. So, the training loss is a combination of the reconstruction loss (log probability of the true molecule under the distribution produced by the decoder) and the semi-supervised predictive loss. The hope with this model is that it would allow you to sample from a space of potential molecules by starting from an existing molecule, and then optimizing the the vector representation of that molecule to make it score higher on whatever property you want to optimize for. https://i.imgur.com/WzZsCOB.png The authors acknowledge that, in this setup, you're just producing a probability distribution over characters, and that the continuous vectors sampled from the latent space might not actually map to valid SMILES strings, and beyond that may well not correspond to chemically valid molecules. Empirically, they said that the proportion of valid generated molecules ranged between 1 and 70%. But they argue that it'd be too difficult to enforce those constraints, and instead just sample from the model and run the results through a hand-designed filter for molecular validity. In my view, this is the central weakness of the method proposed in this paper: that they seem to have not tackled the question of either chemical viability or even syntactic correctness of the produced molecules. I found it difficult to nail down from the paper what the ultimate percentage of valid molecules was from points in latent space that were off of the training . A table reports "percentage of 5000 randomly-selected latent points that decode to valid molecules after 1000 attempts," but I'm confused by what the 1000 attempts means here - does that mean we draw 1000 samples from the distribution given by the decoder, and see if *any* of those samples are valid? That would be a strange metric, if so, and perhaps it means something different, but it's hard to tell. https://i.imgur.com/9sy0MXB.png This paper made me really curious to see whether a GAN could do better in this space, since it would presumably be better at the task of incentivizing syntactic correctness of produced strings (given that any deviation from correctness could be signal for the discriminator), but it might also lead to issues around mode collapse, and when I last checked the literature, GANs on text data in particular were still not great. |

Deep Residual Learning for Image Recognition

He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian

arXiv e-Print archive - 2015 via Local Bibsonomy

Keywords: dblp

He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian

arXiv e-Print archive - 2015 via Local Bibsonomy

Keywords: dblp

[link]
Deeper networks should never have a higher **training** error than smaller ones. In the worst case, the layers should "simply" learn identities. It seems as this is not so easy with conventional networks, as they get much worse with more layers. So the idea is to add identity functions which skip some layers. The network only has to learn the **residuals**. Advantages: * Learning the identity becomes learning 0 which is simpler * Loss in information flow in the forward pass is not a problem anymore * No vanishing / exploding gradient * Identities don't have parameters to be learned ## Evaluation The learning rate starts at 0.1 and is divided by 10 when the error plateaus. Weight decay of 0.0001 ($10^{-4}$), momentum of 0.9. They use mini-batches of size 128. * ImageNet ILSVRC 2015: 3.57% (ensemble) * CIFAR-10: 6.43% * MS COCO: 59.0% mAp@0.5 (ensemble) * PASCAL VOC 2007: 85.6% mAp@0.5 * PASCAL VOC 2012: 83.8% mAp@0.5 ## See also * [DenseNets](http://www.shortscience.org/paper?bibtexKey=journals/corr/1608.06993) |

Cutting out the Middle-Man: Training and Evaluating Energy-Based Models without Sampling

Grathwohl, Will and Wang, Kuan-Chieh and Jacobsen, Jorn-Henrik and Duvenaud, David and Zemel, Richard

- 2020 via Local Bibsonomy

Keywords: bayesian, generative-models, energy-models, uncertainty

Grathwohl, Will and Wang, Kuan-Chieh and Jacobsen, Jorn-Henrik and Duvenaud, David and Zemel, Richard

- 2020 via Local Bibsonomy

Keywords: bayesian, generative-models, energy-models, uncertainty

[link]
The authors introduce a new, sampling-free method for training and evaluating energy-based models (aka EBMs, aka unnormalized density models). There are two broad approches for training EBMs. Sampling-based approaches like contrastive divergence try to estimate the likelihood with MCMC, but can be biased if the chain is not sufficiently long. The speed of training also greatly depends on the sampling parameters. Other approches, like score matching, avoid sampling by solving a surrogate objective that approximates the likelihood. However, using a surrogate objective also introduces bias in the solution. In any case, comparing goodness of fit of different models is challenging, regardless of how the models were trained. The authors introduce a measure of probability distance between distributions $p$ and $q$ called the Learned Stein Discrepancy ($LSD$): $$ LSD(f_{\phi}, p, q) = \mathbb{E}_{p(x)} [\nabla_x \log q(x)^T f_{\phi}(x) + Tr(\nabla_x f_{\phi} (x)) $$ This measure is derived from the Stein Discrepancy $SD(p,q)$. Note that like the $SD$, the $LSD$ is 0 iff $p = q$. Typically, $p$ is the data distribution and $q$ is the learned approximate distribution (an EBM), although this doesn't have to be the case. Note also that this objective only requires a differentiable unnormalized distribution $\tilde{q}$, and does not require MCMC sampling or computation of the normalizing constant $Z$, since $\nabla_x \log q(x) = \nabla_x \log \tilde{q}(x) - \nabla_x \log Z = \nabla_x \log \tilde{q}(x)$. $f_\phi$ is known as the critic function, and minimizing the $LSD$ with respect to $\phi$ (i.e. with gradient descent) over a bounded space of functions $\mathcal{F}$ can approximate the $SD$ over that space. The authors choose to define the function space $\mathcal{F} = \{ f: \mathbb{E}_{p(x)} [f(x)^Tf(x)] < \infty \}$, which is convenient because it can be optimized by introducing a simple L2 regularizer on the critic's output: $\mathcal{R}_\lambda (f_\phi) = \lambda \mathbb{E}_{p(x)} [f_\phi(x)^T f_\phi(x)]$. Since the trace of a matrix is expensive to backpropagate through, the authors use a single-sample Monte Carlo estimate $Tr(\nabla_x f_\phi(x)) \approx \mathbb{E}_{\mathbb{N}(\epsilon|0,1)} [\epsilon^T \nabla_x f_\phi(x) \epsilon] $, which is more efficient since $\epsilon^T \nabla_x f_\phi(x)$ is a vector-Jacobian product. The overall objective is thus the following: $$ \text{arg} \max_\phi \mathbb{E}_{p(x)} [\nabla_x \log q(x)^T f_{\phi}(x) + \mathbb{E}_{\epsilon} [\epsilon^T \nabla_x f_{\phi} (x) \epsilon)] - \lambda f_\phi(x)^T f_\phi(x)] $$ It is possible to compare two different EBMs $q_1$ and $q_2$ by optimizing the above objective for two different critic parameters $\phi_1$ and $\phi_2$, using the training and validation data for critic optimization (then evaluating on the held-out test set). Note that when computing the $LSD$ on the test set, the exact trace can be computed instead of the Monte Carlo approximation to reduce variance, since gradients are no longer required. The model that is closer to 0 has achieved a better fit. Similarly, a hypothesis test using the $LSD$ can be used to test if $p = q$ for the data distribution $p$ and model distribution $q$. The authors then show how EBM parameters $\theta$ can actually be optimized by gradient descent on the $LSD$ objective, in a minimax problem that is similar to the problem of optimizing a generative adversarial network (GAN). For given $\theta$, you first optimize the critic $f_\phi$ w.r.t. $\phi$ to try to get the $LSD(f_\phi, p, q_\theta)$ close to its theoretical optimum with the current $q_\theta$, then you take a single gradient step $\nabla_\theta LSD$ to minimize the $LSD$. They show some experiments that indicates that this works pretty well. One thing that was not clear to me when reading this paper is whether the $LSD(f_\phi,p,q)$ should be minimized or maximized with respect to $\phi$ to get it close to the true $SD(p,q)$. Although it it possible for $LSD$ to be above or below 0 for a given choice of $q$ and $f_\phi$, the problem can always be formulated as minimization by simply changing the sign of $f_\phi$ at the beginning such that the $LSD$ is positive (or as maximization by making it negative). |

Critic Regularized Regression

Ziyu Wang and Alexander Novikov and Konrad Zolna and Jost Tobias Springenberg and Scott Reed and Bobak Shahriari and Noah Siegel and Josh Merel and Caglar Gulcehre and Nicolas Heess and Nando de Freitas

arXiv e-Print archive - 2020 via Local arXiv

Keywords: cs.LG, cs.AI, stat.ML

**First published:** 2024/05/22 (just now)

**Abstract:** Offline reinforcement learning (RL), also known as batch RL, offers the
prospect of policy optimization from large pre-recorded datasets without online
environment interaction. It addresses challenges with regard to the cost of
data collection and safety, both of which are particularly pertinent to
real-world applications of RL. Unfortunately, most off-policy algorithms
perform poorly when learning from a fixed dataset. In this paper, we propose a
novel offline RL algorithm to learn policies from data using a form of
critic-regularized regression (CRR). We find that CRR performs surprisingly
well and scales to tasks with high-dimensional state and action spaces --
outperforming several state-of-the-art offline RL algorithms by a significant
margin on a wide range of benchmark tasks.
more
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Ziyu Wang and Alexander Novikov and Konrad Zolna and Jost Tobias Springenberg and Scott Reed and Bobak Shahriari and Noah Siegel and Josh Merel and Caglar Gulcehre and Nicolas Heess and Nando de Freitas

arXiv e-Print archive - 2020 via Local arXiv

Keywords: cs.LG, cs.AI, stat.ML

[link]
Offline reinforcement learning is potentially high-value thing for the machine learning community learn to do well, because there are many applications where it'd be useful to generate a learnt policy for responding to a dynamic environment, but where it'd be too unsafe or expensive to learn in an on-policy or online way, where we continually evaluate our actions in the environment to test their value. In such settings, we'd like to be able to take a batch of existing data - collected from a human demonstrator, or from some other algorithm - and be able to learn a policy from those pre-collected transitions, without being able to query the environment further by taking arbitrary actions. There are two broad strategies for learning a policy from precollected transitions. One is to simply learn to mimic the action policy used by the demonstrator, predicting the action the demonstrator would take in a given state, without making use of reward data at all. This is Behavioral Cloning, and has the advantage of being somewhat more conservative (in terms of not experimenting with possibly-unsafe-or-low-reward actions the demonstrator never took), but this is also a disadvantage, because it's not possible to get higher reward than the demonstrator themselves got if you're simply copying their behavior. Another approach is to learn a Q function - estimating the value of a given action in a given state - using the reward data from the precollected transitions. This can also have some downsides, mostly in the direction of overconfidence. Q value Temporal Difference learning works by using the current reward added to the max Q value over possible next actions as the target for the current-state Q estimate. This tends to lead to overestimates, because regression to the mean effects mean that the highest value Q estimates are disproportionately likely to be noisy (possibly because they correspond to an action with little data in the demonstrator dataset). In on-policy Q learning, this is less problematic, because the agent can take the action associated with their noisily inaccurate estimate, and as a result get more data for that action, and get an estimate that is less noisy in future. But when we're in a fully offline setting, all our learning is completed before we actually start taking actions with our policy, so taking high-uncertainty actions isn't a valuable source of new information, but just risky. The approach suggested by this DeepMind paper - Critic Regularized Regression, or CRR - is essentially a synthesis of these two possible approaches. The method learns a Q function as normal, using temporal difference methods. The distinction in this method comes from how to get a policy, given a learned Q function. Rather than simply taking the action your Q estimate says is highest-value at a particular point, CRR optimizes a policy according to the formula shown below. The f() function is a stand-in for various potential functions, all of which are monotonic with respect to the Q function, meaning they increase when the Q function does. https://i.imgur.com/jGmhYdd.png This basically amounts to a form of a behavioral cloning loss (with the part that maximizes the probability under your policy of the actions sampled from the demonstrator dataset), but weighted or, as the paper terms it, filtered, by the learned Q function. The higher the estimated q value for a transition, the more weight is placed on that transition from the demo dataset having high probability under your policy. Rather than trying to mimic all of the actions of the demonstrator, the policy preferentially tries to mimic the demonstrator actions that it estimates were particularly high-quality. Different f() functions lead to different kinds of filtration. The `binary`version is an indicator function for the Advantage of an action (the Q value for that action at that state minus some reference value for the state, describing how much better the action is than other alternatives at that state) being greater than zero. Another, `exp`, uses exponential weightings which do a more "soft" upweighting or downweighting of transitions based on advantage, rather than the sharp binary of whether an actions advantage is above 1. The authors demonstrate that, on multiple environments from three different environment suites, CRR outperforms other off-policy baselines - either more pure behavioral cloning, or more pure RL - and in many cases does so quite dramatically. They find that the sharper binary weighting scheme does better on simpler tasks, since the trade-off of fewer but higher-quality samples to learn from works there. However, on more complex tasks, the policy benefits from the exp weighting, which still uses and learns from more samples (albeit at lower weights), which introduces some potential mimicking of lower-quality transitions, but at the trade of a larger effective dataset size to learn from. |

Imagenet classification with deep convolutional neural networks

Krizhevsky, Alex and Sutskever, Ilya and Hinton, Geoffrey E

Neural Information Processing Systems Conference - 2012 via Local Bibsonomy

Keywords: image, imagenet, thema:deepwalk, classification

Krizhevsky, Alex and Sutskever, Ilya and Hinton, Geoffrey E

Neural Information Processing Systems Conference - 2012 via Local Bibsonomy

Keywords: image, imagenet, thema:deepwalk, classification

[link]
This paper is about Convolutional Neural Networks for Computer Vision. It was the first break-through in the ImageNet classification challenge (LSVRC-2010, 1000 classes). ReLU was a key aspect which was not so often used before. The paper also used Dropout in the last two layers. ## Training details * Momentum of 0.9 * Learning rate of $\varepsilon$ (initialized at 0.01) * Weight decay of $0.0005 \cdot \varepsilon$. * Batch size of 128 * The training took 5 to 6 days on two NVIDIA GTX 580 3GB GPUs. ## See also * [Stanford presentation](http://vision.stanford.edu/teaching/cs231b_spring1415/slides/alexnet_tugce_kyunghee.pdf) |

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