DeepMind, an artificial intelligence (AI) subsidiary of Google parent Alphabet, said it has been successful in predicting the shape of nearly every protein in the human body as well as thousands of other proteins found in 20 additional organisms that scientists rely on for their research, including yeast, fruit flies, and mice. This breakthrough is likely to assist researchers to understand human diseases better and find new drugs to treat or cure them. Some scientists have compared the DeepMind project to the international effort to map every human gene. DeepMind said in a blog post it is releasing the database for free. To set up and run the database, it has partnered with the European Molecular Biology Laboratory.

Back in December 2020, DeepMind took the world of biology by surprise when it solved a 50-year grand challenge with AlphaFold, an AI tool that predicts the structure of proteins. Last week the London-based company published full details of that tool and released its source code. Now the firm has announced that it has used its AI to predict the shapes of nearly every protein in the human body, as well as the shapes of hundreds of thousands of other proteins found in 20 of the most widely studied organisms, including yeast, the fruit fly, and the mouse. The breakthrough could allow biologists from around the world to understand diseases better and develop new drugs. So far the trove consists of 350,000 newly predicted protein structures.

Deng, Geng, Xu, Guangning, Fu, Qiang, Wang, Xindong, Qin, Jing

Recently the shape-restricted inference has gained popularity in statistical and econometric literature in order to relax the linear or quadratic covariate effect in regression analyses. The typical shape-restricted covariate effect includes monotonic increasing, decreasing, convexity or concavity. In this paper, we introduce the shape-restricted inference to the celebrated Cox regression model (SR-Cox), in which the covariate response is modeled as shape-restricted additive functions. The SR-Cox regression approximates the shape-restricted functions using a spline basis expansion with data driven choice of knots. The underlying minimization of negative log-likelihood function is formulated as a convex optimization problem, which is solved with an active-set optimization algorithm. The highlight of this algorithm is that it eliminates the superfluous knots automatically. When covariate effects include combinations of convex or concave terms with unknown forms and linear terms, the most interesting finding is that SR-Cox produces accurate linear covariate effect estimates which are comparable to the maximum partial likelihood estimates if indeed the forms are known. We conclude that concave or convex SR-Cox models could significantly improve nonlinear covariate response recovery and model goodness of fit.

Sundaresan, Priya, Grannen, Jennifer, Thananjeyan, Brijen, Balakrishna, Ashwin, Ichnowski, Jeffrey, Novoseller, Ellen, Hwang, Minho, Laskey, Michael, Gonzalez, Joseph E., Goldberg, Ken

Robot manipulation for untangling 1D deformable structures such as ropes, cables, and wires is challenging due to their infinite dimensional configuration space, complex dynamics, and tendency to self-occlude. Analytical controllers often fail in the presence of dense configurations, due to the difficulty of grasping between adjacent cable segments. We present two algorithms that enhance robust cable untangling, LOKI and SPiDERMan, which operate alongside HULK, a high-level planner from prior work. LOKI uses a learned model of manipulation features to refine a coarse grasp keypoint prediction to a precise, optimized location and orientation, while SPiDERMan uses a learned model to sense task progress and apply recovery actions. We evaluate these algorithms in physical cable untangling experiments with 336 knots and over 1500 actions on real cables using the da Vinci surgical robot. We find that the combination of HULK, LOKI, and SPiDERMan is able to untangle dense overhand, figure-eight, double-overhand, square, bowline, granny, stevedore, and triple-overhand knots. The composition of these methods successfully untangles a cable from a dense initial configuration in 68.3% of 60 physical experiments and achieves 50% higher success rates than baselines from prior work. Supplementary material, code, and videos can be found at https://tinyurl.com/rssuntangling.

Let's make the relevant question more personal: will machines replace me? I'm a mathematician; my profession is often seen from the outside as a very complicated but ultimately purely mechanical game played with fixed rules, like checkers, chess, or Go. These are activities in which machines have already demonstrated superhuman ability. But for me, math is different: it is a creative pursuit that calls on our intuition as much as our ability to compute.

Viswanath, Vainavi, Grannen, Jennifer, Sundaresan, Priya, Thananjeyan, Brijen, Balakrishna, Ashwin, Novoseller, Ellen, Ichnowski, Jeffrey, Laskey, Michael, Gonzalez, Joseph E., Goldberg, Ken

Disentangling two or more cables requires many steps to remove crossings between and within cables. We formalize the problem of disentangling multiple cables and present an algorithm, Iterative Reduction Of Non-planar Multiple cAble kNots (IRON-MAN), that outputs robot actions to remove crossings from multi-cable knotted structures. We instantiate this algorithm with a learned perception system, inspired by prior work in single-cable untying that given an image input, can disentangle two-cable twists, three-cable braids, and knots of two or three cables, such as overhand, square, carrick bend, sheet bend, crown, and fisherman's knots. IRON-MAN keeps track of task-relevant keypoints corresponding to target cable endpoints and crossings and iteratively disentangles the cables by identifying and undoing crossings that are critical to knot structure. Using a da Vinci surgical robot, we experimentally evaluate the effectiveness of IRON-MAN on untangling multi-cable knots of types that appear in the training data, as well as generalizing to novel classes of multi-cable knots. Results suggest that IRON-MAN is effective in disentangling knots involving up to three cables with 80.5% success and generalizing to knot types that are not present during training, with cables of both distinct or identical colors.

We introduce a density-based clustering method called skeleton clustering that can detect clusters in multivariate and even high-dimensional data with irregular shapes. To bypass the curse of dimensionality, we propose surrogate density measures that are less dependent on the dimension but have intuitive geometric interpretations. The clustering framework constructs a concise representation of the given data as an intermediate step and can be thought of as a combination of prototype methods, density-based clustering, and hierarchical clustering. We show by theoretical analysis and empirical studies that the skeleton clustering leads to reliable clusters in multivariate and high-dimensional scenarios.

Basna, Rani, Nassar, Hiba, Podgórski, Krzysztof

In implementations of the functional data methods, the effect of the initial choice of an orthonormal basis has not gained much attention in the past. Typically, several standard bases such as Fourier, wavelets, splines, etc. are considered to transform observed functional data and a choice is made without any formal criteria indicating which of the bases is preferable for the initial transformation of the data into functions. In an attempt to address this issue, we propose a strictly data-driven method of orthogonal basis selection. The method uses recently introduced orthogonal spline bases called the splinets obtained by efficient orthogonalization of the B-splines. The algorithm learns from the data in the machine learning style to efficiently place knots. The optimality criterion is based on the average (per functional data point) mean square error and is utilized both in the learning algorithms and in comparison studies. The latter indicates efficiency that is particularly evident for the sparse functional data and to a lesser degree in analyses of responses to complex physical systems.

Moscato, Pablo, Haque, Mohammad Nazmul, Huang, Kevin, Sloan, Julia, de Oliveira, Jon C.

In Artificial Intelligence we often seek to identify an unknown target function of many variables $y=f(\mathbf{x})$ giving a limited set of instances $S=\{(\mathbf{x^{(i)}},y^{(i)})\}$ with $\mathbf{x^{(i)}} \in D$ where $D$ is a domain of interest. We refer to $S$ as the training set and the final quest is to identify the mathematical model that approximates this target function for new $\mathbf{x}$; with the set $T=\{ \mathbf{x^{(j)}} \} \subset D$ with $T \neq S$ (i.e. thus testing the model generalisation). However, for some applications, the main interest is approximating well the unknown function on a larger domain $D'$ that contains $D$. In cases involving the design of new structures, for instance, we may be interested in maximizing $f$; thus, the model derived from $S$ alone should also generalize well in $D'$ for samples with values of $y$ larger than the largest observed in $S$. In that sense, the AI system would provide important information that could guide the design process, e.g., using the learned model as a surrogate function to design new lab experiments. We introduce a method for multivariate regression based on iterative fitting of a continued fraction by incorporating additive spline models. We compared it with established methods such as AdaBoost, Kernel Ridge, Linear Regression, Lasso Lars, Linear Support Vector Regression, Multi-Layer Perceptrons, Random Forests, Stochastic Gradient Descent and XGBoost. We tested the performance on the important problem of predicting the critical temperature of superconductors based on physical-chemical characteristics.

Training-serving skew: The offline numbers may look great, but what if your model will be evaluated on a different or broader set of examples than those found in the training set? This phenomenon, more generally referred to as "dataset shift" or "distribution shift", happens all the time in real-world situations. Models are trained on a curated set of examples, or clicks on top-ranked recommendations, or a specific geographical region, and then applied to every user or use case. Curiosities and anomalies in your training and testing data become genuine and sustained loss patterns. Bad individual errors: Models are often judged by their worst behavior --- a single egregious outcome can damage the faith that important stakeholders have in the model and even cause serious reputational harm to your business or institution.