Section: New Results

Learning in Graphs

Correlation Clustering with Adaptive Similarity Queries In correlation clustering, we are given $n$ objects together with a binary similarity score between each pair of them. The goal is to partition the objects into clusters so to minimise the disagreements with the scores. In [6], we investigate correlation clustering as an active learning problem: each similarity score can be learned by making a query, and the goal is to minimise both the disagreements and the total number of queries. On the one hand, we describe simple active learning algorithms, which provably achieve an almost optimal trade-off while giving cluster recovery guarantees, and we test them on different datasets. On the other hand, we prove information-theoretical bounds on the number of queries necessary to guarantee a prescribed disagreement bound. These results give a rich characterization of the trade-off between queries and clustering error.

Flattening a Hierarchical Clustering through Active Learning In [12], we investigate active learning by pairwise similarity over the leaves of trees originating from hierarchical clustering procedures. In the realizable setting, we provide a full characterization of the number of queries needed to achieve perfect reconstruction of the tree cut. In the non-realizable setting, we rely on known important-sampling procedures to obtain regret and query complexity bounds. Our algorithms come with theoretical guarantees on the statistical error and, more importantly, lend themselves to linear-time implementations in the relevant parameters of the problem. We discuss such implementations, prove running time guarantees for them, and present preliminary experiments on real-world datasets showing the compelling practical performance of our algorithms as compared to both passive learning and simple active learning baselines.

MaxHedge: Maximising a Maximum Online In [10], we introduce a new online learning framework where, at each trial, the learner is required to select a subset of actions from a given known action set. Each action is associated with an energy value, a reward and a cost. The sum of the energies of the actions selected cannot exceed a given energy budget. The goal is to maximise the cumulative profit, where the profit obtained on a single trial is defined as the difference between the maximum reward among the selected actions and the sum of their costs. Action energy values and the budget are known and fixed. All rewards and costs associated with each action change over time and are revealed at each trial only after the learner's selection of actions. Our framework encompasses several online learning problems where the environment changes over time; and the solution trades-off between minimising the costs and maximising the maximum reward of the selected subset of actions, while being constrained to an action energy budget. The algorithm that we propose is efficient, general and may be specialised to multiple natural online combinatorial problems.

Closed-loop cycles of experiment design, execution, and learning accelerate systems biology model development in yeast One of the most challenging tasks in modern science is the development of systems biology models: Existing models are often very complex but generally have low predictive performance. The construction of high-fidelity models will require hundreds/thousands of cycles of model improvement, yet few current systems biology research studies complete even a single cycle. In [2], we combined multiple software tools with integrated laboratory robotics to execute three cycles of model improvement of the prototypical eukaryotic cellular transformation, the yeast (Saccharomyces cerevisiae) diauxic shift. In the first cycle, a model outperforming the best previous diauxic shift model was developed using bioinformatic and systems biology tools. In the second cycle, the model was further improved using automatically planned experiments. In the third cycle, hypothesis-led experiments improved the model to a greater extent than achieved using high-throughput experiments. All of the experiments were formalized and communicated to a cloud laboratory automation system (Eve) for automatic execution, and the results stored on the semantic web for reuse. The final model adds a substantial amount of knowledge about the yeast diauxic shift: 92 genes (+45%), and 1 048 interactions (+147%). This knowledge is also relevant to understanding cancer, the immune system, and aging. We conclude that systems biology software tools can be combined and integrated with laboratory robots in closed-loop cycles.