A Comparative Study of Modern Inference Techniques for Structured Discrete Energy Minimization Problems

International audienceSzeliski et al. published an influential study in 2006 on energy minimization methods for Markov Random Fields (MRF). This study provided valuable insights in choosing the best optimization technique for certain classes of problems. While these insights remain generally useful today, the phenomenal success of random field models means that the kinds of inference problems that have to be solved changed significantly. Specifically , the models today often include higher order interactions, flexible connectivity structures, large label-spaces of different car-dinalities, or learned energy tables. To reflect these changes, we provide a modernized and enlarged study. We present an empirical comparison of more than 27 state-of-the-art optimization techniques on a corpus of 2,453 energy minimization instances from diverse applications in computer vision. To ensure reproducibility, we evaluate all methods in the OpenGM 2 framework and report extensive results regarding runtime and solution quality. Key insights from our study agree with the results of Szeliski et al. for the types of models they studied. However, on new and challenging types of models our findings disagree and suggest that polyhedral methods and integer programming solvers are competitive in terms of runtime and solution quality over a large range of model types

Lifted graphical models: a survey

Lifted graphical models provide a language for expressing dependencies between different types of entities, their attributes, and their diverse relations, as well as techniques for probabilistic reasoning in such multi-relational domains. In this survey, we review a general form for a lifted graphical model, a par-factor graph, and show how a number of existing statistical relational representations map to this formalism. We discuss inference algorithms, including lifted inference algorithms, that efficiently compute the answers to probabilistic queries over such models. We also review work in learning lifted graphical models from data. There is a growing need for statistical relational models (whether they go by that name or another), as we are inundated with data which is a mix of structured and unstructured, with entities and relations extracted in a noisy manner from text, and with the need to reason effectively with this data. We hope that this synthesis of ideas from many different research groups will provide an accessible starting point for new researchers in this expanding field

Automatically Selecting Inference Algorithms for Discrete Energy Minimisation

Minimisation of discrete energies defined over factors is an important problem in computer vision, and a vast number of MAP inference algorithms have been proposed. Different inference algorithms perform better on factor graph models (GMs) from different underlying problem classes, and in general it is difficult to know which algorithm will yield the lowest energy for a given GM. To mitigate this difficulty, survey papers advise the practitioner on what algorithms perform well on what classes of models. We take the next step forward, and present a technique to automatically select the best inference algorithm for an input GM. We validate our method experimentally on an extended version of the OpenGM2 benchmark, containing a diverse set of vision problems. On average, our method selects an inference algorithm yielding labellings with 96% of variables the same as the best available algorithm

Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity

The cystic fibrosis transmembrane conductance regulator (CFTR) is an epithelial chloride channel mutated in patients with cystic fibrosis (CF). The most prevalent CFTR mutation, ΔF508, blocks folding in the endoplasmic reticulum. Recent work has shown that some ΔF508-CFTR channel activity can be recovered by pharmaceutical modulators (“potentiators” and “correctors”), but ΔF508-CFTR can still be rapidly degraded via a lysosomal pathway involving the CFTR-associated ligand (CAL), which binds CFTR via a PDZ interaction domain. We present a study that goes from theory, to new structure-based computational design algorithms, to computational predictions, to biochemical testing and ultimately to epithelial-cell validation of novel, effective CAL PDZ inhibitors (called “stabilizers”) that rescue ΔF508-CFTR activity. To design the “stabilizers”, we extended our structural ensemble-based computational protein redesign algorithm to encompass protein-protein and protein-peptide interactions. The computational predictions achieved high accuracy: all of the top-predicted peptide inhibitors bound well to CAL. Furthermore, when compared to state-of-the-art CAL inhibitors, our design methodology achieved higher affinity and increased binding efficiency. The designed inhibitor with the highest affinity for CAL (kCAL01) binds six-fold more tightly than the previous best hexamer (iCAL35), and 170-fold more tightly than the CFTR C-terminus. We show that kCAL01 has physiological activity and can rescue chloride efflux in CF patient-derived airway epithelial cells. Since stabilizers address a different cellular CF defect from potentiators and correctors, our inhibitors provide an additional therapeutic pathway that can be used in conjunction with current methods

Home-based versus hospital-based postnatal care : a randomised trial

Objective To compare a shortened hospital stay with midwife visits at home to usual hospital care after delivery. Design Randomised controlled trial. Setting Maternity unit of a Swiss teaching hospital. Population Four hundred and fifty-nine women with a single uncomplicated pregnancy at low risk of caesarean section. Methods Women were randomised to either home-based (n= 228) or hospital-based postnatal care (n= 231). Home-based postnatal care consisted of early discharge from hospital (24 to 48 hours after delivery) and home visits by a midwife; women in the hospital-based care group were hospitalised for four to five days. Main outcome measures Breastfeeding 28 days postpartum, women's views of their care and readmission to hospital. Results Women in the home-based care group had shorter hospital stays (65 vs 106 hours, P < 0.001) and more midwife visits (4.8 vs 1.7, P < 0.001) than women in the hospital-based care group. Prevalence of breastfeeding at 28 days was similar between the groups (90%vs 87%, P= 0.30), but women in the home-based care group reported fewer problems with breastfeeding and greater satisfaction with the help received. There were no differences in satisfaction with care, women's hospital readmissions, postnatal depression scores and health status scores. A higher percentage of neonates in the home-based care group were readmitted to hospital during the first six months (12%vs 4.8%, P= 0.004). Conclusions In low risk pregnancies, early discharge from hospital and midwife visits at home after delivery is an acceptable alternative to a longer duration of care in hospital. Mothers' preferences and economic considerations should be taken into account when choosing a policy of postnatal care