This problem was present from the beginning.

Unfortunately I have not found the time to test the upstream kernel, but
I fount a workaround for now. Interestingly there is no problem when I
turn off the workspaces feature in Unity and only work on one desktop.

Nevertheless I will test the upstream kernel as soon as I find time.

Thank you for your help!

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https://bugs.launchpad.net/bugs/1645148

Title:
  Short black screens and sometimes complete crash/freeze

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  When I use Wolfram Mathematica, sometimes while typing the screen becomes 
black for a very short time. Most of the times nothing happens, but sometimes 
after the black screen the computer is completely frozen, not even the Magic 
SysRQ keys work any more.
  The error seems to be similar to this one:
  https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1550779
  but it seems that the complete crash of the system did not appear there.
  This happens on Mathematica 10 as well as 11.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.10
  Package: linux-image-4.8.0-27-generic 4.8.0-27.29
  ProcVersionSignature: Ubuntu 4.8.0-27.29-generic 4.8.1
  Uname: Linux 4.8.0-27-generic x86_64
  ApportVersion: 2.20.3-0ubuntu8
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC0:  chris      2173 F.... pulseaudio
  CurrentDesktop: Unity
  Date: Sun Nov 27 23:03:05 2016
  HibernationDevice: RESUME=UUID=36c59c75-b6bd-4c04-80b8-0d3f92e80a2b
  InstallationDate: Installed on 2016-07-29 (121 days ago)
  InstallationMedia: Ubuntu 16.04.1 LTS "Xenial Xerus" - Release amd64 
(20160719)
  Lsusb:
   Bus 002 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
   Bus 001 Device 003: ID 138a:0017 Validity Sensors, Inc. Fingerprint Reader
   Bus 001 Device 004: ID 5986:0706 Acer, Inc 
   Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
  MachineType: LENOVO 20FMS03600
  ProcFB: 0 inteldrmfb
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.8.0-27-generic 
root=UUID=2c1382ae-d83b-4b08-aa85-e6da74ec4308 ro quiet splash vt.handoff=7
  RelatedPackageVersions:
   linux-restricted-modules-4.8.0-27-generic N/A
   linux-backports-modules-4.8.0-27-generic  N/A
   linux-firmware                            1.161
  SourcePackage: linux
  UpgradeStatus: Upgraded to yakkety on 2016-10-13 (45 days ago)
  dmi.bios.date: 03/23/2016
  dmi.bios.vendor: LENOVO
  dmi.bios.version: R06ET36W (1.10 )
  dmi.board.asset.tag: Not Available
  dmi.board.name: 20FMS03600
  dmi.board.vendor: LENOVO
  dmi.board.version: Not Defined
  dmi.chassis.asset.tag: No Asset Information
  dmi.chassis.type: 10
  dmi.chassis.vendor: LENOVO
  dmi.chassis.version: None
  dmi.modalias: 
dmi:bvnLENOVO:bvrR06ET36W(1.10):bd03/23/2016:svnLENOVO:pn20FMS03600:pvrThinkPadT460:rvnLENOVO:rn20FMS03600:rvrNotDefined:cvnLENOVO:ct10:cvrNone:
  dmi.product.name: 20FMS03600
  dmi.product.version: ThinkPad T460
  dmi.sys.vendor: LENOVO

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